Day 2 :
Keynote Forum
Biswendu B Goswami
FDA Center for Food Safety and Applied Nutrition, USA
Keynote: Microarray based identification of viral genomes
Time : 09:30 AM
Biography:
Biswendu B Goswami received his Ph.D. in Biochemistry degree from the University of Calcutta (Kolkata) in 1975, followed by a post-doctoral fellowship from CSIR, India for two years. He came to USA on a post-doctoral fellowship in the laboratory of the Late Prof. Ernest Borek. He worked also as a Research Associate at Georgetown University Medical Center at Washington D.C. He later joined The United States Food and Drug Administration, and was in charge of the Virology laboratory at the Center for Food Safety, until he retired in 2011. He has published more than 45 research articles and book chapters.
Abstract:
Procedures for virus identification are currently going through a revolution due to two recent developments. The orthodox methods for virus identification by cell culture followed by secondary confirmation where possible, by immunological techniques have been replaced by PCR based methods. But PCR methods have the added disadvantages that they are extremely sensitive to impurities in the test material, and have very narrow specificity, requiring individual primers for each virus and strain, and therefore atleast some knowledge of the sequence of the viral genetic material. Hybridization to oligonucleotide probes on solid support was developed in the 1990s. However, the true potential for identification of viruses on a massive scale based on sequence of viral genomes did not take off until the development of in situ probe synthesis and immobilization techniques. These newer photolithographic techniques allowed for the synthesis and simultaneous immobilization of hundreds of thousands of probes in a single microarray allowing re-sequencing on a large scale by hybridization to identify virus genotypes. Since then, microarrays have been developed that can incorporate over two million probes in a single array. This development opened up the possibility of identifying multiple virus species and genotypes in a single experiment. However, to realize this potential, it is necessary to have a target synthesis method that is independent of the sequence of the viruses present in the test material. The new microarray based method developed in our laboratory at Food and Drug Administration (FDA), avoids PCR amplification with virus specific primers normally used for target synthesis in microarray experiments.
- Track 1: Types of Biomarkers
Track 7: Techniques to Maximize Biomarker Identification
Chair
Martin Weber
Austrian Institute of Technology GmbH, Austria
Co-Chair
Jan Voskuil
Everest Biotech Ltd., UK
Session Introduction
Martin Weber
Austrian Institute of Technology, GmbH, Austria
Title: DNA methylation biomarkers for Lung cancer: From tissue based discovery to cell free DNA methylation testing
Biography:
Martin Weber has completed his Ph.D. at the age of 29 at the Center for Molecular Biology (ZMBH) in Heidelberg/Germany. He then served in different positions at QIAGEN GmbH (Hilden/Germany) for more than 17 years, heading the corporate research and innovation group in his last position at the company. Since 2012 he is the Head of the Molecular Diagnostics business unit at AIT Austrian Institute of Technology, the biggest non-university research institute in Austria. He has published more than 20 papers and patent applications.
Abstract:
Disease-specific alterations of DNA methylation patterns are frequently found in cancer and are currently considered to be suitable biomarkers. These alterations are optimal biomarkers for early detection and disease monitoring when detectable in cell-free DNA. We have developed a multiplexed methyl sensitive restriction enzyme (MSRE) qPCR protocol allowing up to 96 parallel qPCR reactions out of 400µl patient’s plasma. The method was applied on 1) a panel of 35 methylation markers discovered in lung tissue by a targeted DNA methylation micro-array and 2) 63 candidate markers derived form genome wide methylation analyses using Illumina-Methylation450K-Beadchip. To test the feasibility for differential diagnosis via cell free DNA methylation testing, multivariate classification using MSREqPCR data from marker panel 1) enabled differentiation of Lung cancer (n=348; Adeno-Ca: n=100, Squamous cell-Ca: n=100, Small cell-Ca: n=100, and Large cell Ca: n=48) versus cancer-free controls (n=332) with an AUC of 0.81-0.91 depending on the lung cancer entity. Using panel 2) a total of 204 serum and plasma samples (lung cancer, n=33; fibrotic Interstitial lung disease - ILD, n=68; COPD, n=42; healthy, n=61) were tested. ROC analysis revealed an AUC of 0.91 for lung cancer, 0.815 for fibrotic ILD, 0.73 for COPD, and 0.828 for all diseases versus healthy controls. Additionally a set of independent cancer and normal samples could be classified on basis of the top 4 markers (HOXD10, PAX9, PTPRN2 and STAG3) showing an AUC 0.85. Based on 2 discovery studies Lung-cancer biomarkers suitable for minimal invasive diagnostics using multiplexed DNA methylation measurement from 10ng circulating cfDNA have been defined. Both marker-sets and the MSREqPCR approach will be the basis for further validation to improve minimal invasive diagnostics. Moreover, this study confirms that our strategy is suitable for qualifying tissue derived DNA-methylation markers for liquid biopsy testing.
Marsha A Moses
Harvard Medical School, USA
Title: Mining the human urinary proteome biomarker discovery for human cancer and its metastases
Biography:
Marsha A. Moses is the Julia Dyckman Andrus Professor at Harvard Medical School and the Director of the Vascular Biology Program at Boston Children's Hospital. She received a Ph.D. in Biochemistry from Boston University and completed a National Institutes of Health postdoctoral fellowship at Boston Children's Hospital and MIT. She is the recipient of a number of NIH and foundation grants and awards. Dr. Moses was elected to the Institute of Medicine of the National Academies of the United States in 2008 and to the National Academy of Inventors in 2013.
Abstract:
The Moses Laboratory has had a long-standing interest in identifying and characterizing the biochemical and molecular mechanisms that underlie the regulation of tumor growth and progression. Dr. Moses and her laboratory have discovered a number of inhibitors of tumor neovascularization that function at both the transcriptional and translational level, some of which are in preclinical testing. Named a pioneer in the field of Biomarker Medicine by the Journal of the National Cancer Institute, Dr. Moses established a Biomarker Discovery Initiative in her laboratory to complement these studies. This has led to the identification and validation of panels of noninvasive biomarkers that can predict disease status and stage of patients with a variety of human cancers. These cancer biomarkers have been validated using our extensive IRB-approved biorepository. They are sensitive and specific markers and have been shown to be useful in monitoring the therapeutic efficacy of cancer drugs as well. Given that Dr. Moses has focused on the urinary proteome, all of these biomarkers are noninvasive. A number of these urine tests are included in her significant patent portfolio and have been made commercially available. Dr. Moses and her group have utilized two experimental approaches to discover these biomarkers, the first being a biologically-driven (candidate biomarker) approach and the second being an unbiased global proteomics approach. Examples of each of these discovery approaches and some of the biomarkers that were discovered and validated will be presented.
Jan Voskuil
Everest Biotech Ltd., UK
Title: The road from discovery to therapy through the use of antibodies
Biography:
Jan Voskuil is a Molecular cell biologist completed his Ph.D. in Amsterdam (NL), and he had postdoc positions at Stanford (US), and at Oxford (UK). He switched from academia to industry through a leading position at the CNS drug discovery company Synaptica. He subsequently gained experience in GLP-regulatory environments at CROs in Oxfordshire and Cambridgeshire (UK). Thanks to his combined academic and commercial background together with his technical and people skills as the Chief Scientific Officer he has put Everest Biotech (UK) on the global map with the highest quality standard. Its antibodies are increasingly recognized as alternatives to unfit monoclonal antibodies.
Abstract:
Any reagent specific to a particular protein will owe its success to a series of quality assurances ranging from quality of biological samples, the reagent’s validation, validated statistic methods and analysis and clinical end point. Alternatives to antibodies, like aptamers and antibody-derived recombinant molecules, have come to light. However, together with monoclonal antibodies, the screening to find the right reagent is expensive and time consuming, and the epitope the reagent binds to needs to be identified afterwards. Problems regarding specificity are not necessarily solved by the switch from monoclonal antibody to such alternatives. Although the demand of having unlimited access to the exact same reagent will be best met once no longer dependent on hybridomas and animals, until this moment arrives, limiting access to fit-for-purpose monoclonal antibodies slows down medical progress. Then using peptide-specific polyclonal antibodies becomes a short-term option. Such reagents are being designed by the choice of the epitope as unique for the species or tissue type upfront without having to concern about cross-reactivity of the reagent. Yet, full reagent validation in the required platform remains compulsory, and depending on the type of application, the correct dilution needs to be determined for minimal non-specific background.
In the next decade, more and more aptamers and recombinant antibody derivatives will be used as an alternative to monoclonal antibodies but before then the peptide-generated polyclonal antibodies will be used more often while the troublesome other types of polyclonal antibodies are avoided.
Biography:
Scott Marshall, PhD, is Managing Director of Biomarker and IVD Analytics at Precision for Medicine. He has extensive industry experience in a leadership role, consulting in the pharmaceutical, biotechnology, and biodefense industries, specializing in the analytical component of personalized medicine, biomarker R&D, analytical methods, and strategy development, as well as medical device/diagnostic development.
Abstract:
The future of healthcare will be transformed by flexible frameworks designed to discover complex signals in rich datasets through the merger of predictive genomic analytics and systems biology. Smart machine learning algorithms designed to incorporate information about molecular and cellular systems can revolutionize our ability to discover complex hierarchical genomic effects driving disease pathogenesis or severity and treatment response patterns. To meet modern research demands, Precision for Medicine has engineered PATH™ to provide a secure, scalable, cloud-based solution for predictive genomic analytics and an intuitive graphical user interface for interactive data visualization and exploration. This case study will show the power of using a novel combination of machine learning algorithms with a systems biology based approach for identifying genes and the subsequent exonic regions driving prognosis for patients with lung squamous cell carcinoma (SQCC). PATH™ will be applied on 553 lung SQCC patients with survival outcomes and RNA-Seq exon-level mRNA expression data obtained from The Cancer Genome Atlas. This webinar will focus on two of the PATH™ Analytics Platform’s suites: • PATH™ Select: A novel predictive analytics engine, built on a combination of machine learning algorithms fused with a systems biology approach provides for high-throughput feature selection • PATH™ Explore: A secure, web based data visualization suite enables real-time, “what-if” data exploration to accelerate research and support decision making Big data has the potential to enable a precision medicine focused drug development process, resulting in increased benefit-risk profiles for patients with a particular biomarker profile and smaller, shorter clinical trials. Navigating the process from biomarker discovery to a companion or complementary diagnostic requires that researchers get the support necessary to make sense of big data being generated in NGS pipelines. Ultimately, it will be demonstrated how a cloud-based solution powered by a predictive analytics engine and an intuitive, user interface driven by interactive graphics can deliver to the needs of precision medicine programs.
Sharon Nofech Mozes
University of Toronto, Canada
Title: Prediction of local recurrence in ductal carcinoma in situ: Clinical validation of DCIS Score
Biography:
Nofech-Mozes obtained her medical degree from Tel Aviv University, Israel. She completed breast and gynecologic pathology fellowships at the University of Toronto, Canada. Dr. Nofech-Mozes is an Associate Professor in the Department of Laboratory Medicine and Pathobiology at the University of Toronto. She is the breast pathology lead in Sunnybrook. She is a member of the institutional Research Ethics Board. Her main research interest is ductal carcinoma in situ. Dr. Nofech-Mozes authored or coauthored more than 55 peer reviewed manuscripts, including provincial guidelines for hormone receptor testing in breast cancer and biomarkers synoptic report for the CAP.
Abstract:
The Ontario DCIS population-based study identified women with pure DCIS from 1994-2003. Clinical validation of DCIS Score (DS) (Rakovitch, SABCS 2014) showed prediction of risk of an ipsilateral local recurrence (LR). Centrally reviewed pathology for: focality, size, grade, subtype, comedo necrosis & clear margins, (CM=no ink on tumor) will be presented. The DS was obtained by quantitative RT-PCR. Cox modeling was used to determine the relationship between independent covariates, DS (hazard ratio (HR)/50 units) & LR. DCIS Score was evaluated in 718 women w/ DCIS tx with BCS alone (571 w/ CM). With a median follow-up of 9.4 years, 100 BCS alone w/ CM cases developed LR (44 DCIS, 57 invasive). In the primary analysis, among 571 pts treated by BCS alone with CM the continuous DS was significantly associated with LR in ER+ pts (HR 2.26; 95% CI 1.41, 3.59; P=0.001) and in all pts (HR 2.15; 95% CI 1.43, 3.22; P=<0.001). The results of univariable and multivariable analyses, hazard ratios for factors associated with in situ and distance local recurrence will be presented. DCIS Scores were widely distributed within each subgroup defined by the clinical and pathology characteristics. For DCIS pts treated with BCS alone the DCIS Score, focality, tumor size and histologic subtype provide independent LR information. Patients with low DCIS score and non-multifocal disease may be considered for BCS alone.
Biswendu B Goswami
FDA Center for Food Safety and Applied Nutrition (Retired), USA
Title: Virus identification: Development of methods in the post-PCR antiviral therapy
Biography:
Biswendu B Goswami received his PhD in Biochemistry degree from the University of Calcutta (Kolkata) in 1975, followed by a post-doctoral fellowship from CSIR, India for two years. He came to USA on a post-doctoral fellowship in the laboratory of the Late Prof. Ernest Borek. He worked also as a Research Associate at Georgetown University Medical Center at Washington D.C. He later joined The United States Food and Drug Administration, and was in charge of the Virology laboratory at the Center for Food Safety, until he retired in 2011. He has published more than 45 research articles and book chapters.
Abstract:
The necessity for rapid methods of virus identification arose from the fact that human diseases caused by viruses range from self-limiting to deadly infections. Each of these virus species have dozens of genotypes. The number of human infections reported each year has made viruses a major public health problem world-wide. Food-borne viruses in particular, are causing more and more localized epidemics that are very difficult to trace and identify, and have been associated with high morbidity and increasingly high mortality. Currently, other than common disinfection guidelines and a few synthetic antivirals, there are no effective control measures available. Development of immunologic protocols remain time consuming and expensive. Detection of viruses are mostly being done by PCR or immunological detection in blood or other body fluids. However, current available PCR methods are inadequate to identify the virus strain and emergence of new genotypes that may no longer be controlled by an established active or passive immunotherapeutic protocol agent. Here we deal with molecular techniques to circumvent these obstacles.
Biography:
N S Neki is working as Professor of Medicine, Govt. Med. College/ Guru Nanak Dev Hospital, Amritsar. He is recipient of 4 FRCP’s from Edinbourgh, Glasgow, London, and Ireland. He is Visiting Professor, Institute of Cardiovascular Sciences, University of Mannitoba St. Bonniface Hospital, Winnipeg, Canada as well as Visiting Professor, School of Medicine, Health and Pharmacy, University of Durham, UK. He has 205 publications to his credit in reputed journals. He has delivered lecture in Mannitoba Association of Asian Physicians, GIMLI, Canada, Sept7-9, 2012. He is Associate Editor, Section Editor and Editorial Board Member of various national and international journals. He was awarded Fellowship of European Society of Cardiology 2014, Barcelona, Spain and is member of American college of cardiology and American Heart Association. He has 9 oration awards to his credit.
Abstract:
A biomarker is a substance used as an indicator of a biological state. With the increase in prevalence of coronary artery disease, early diagnosis and management of acute coronary syndromes and myocardial infarction (MI) as well as risk stratification and prognostication is of utmost importance. Hence there is need of cardiac biomarkers. Cardiac biomarkers are very useful in a non diagnostic ECG which is observed in 50% cases. Amongst various cardiac biomarkers, CPK-MB and Troponins (T & I) are the markers of choice for detecting myocardial dysfunction since other cardiac markers may be elevated in muscle injury, kidney and liver disease. Troponins are commonly used in the diagnosis of acute coronary events and myocardial damage because of high specificity and sensitivity, thus detecting myocardial injury in patients presenting late. They have replaced CPK-MB for diagnosis of MI. The levels of Troponin are increased within 4-8 hours after the onset of chest pain reaching peak concentration in 12-24 hours and remaining elevated for 4-10 days following acute MI. Although no ideal biomarker exists, yet Troponins fulfill most of the criteria of ideal biomarker. However false elevation of Troponins level may occur in pulmonary embolism, non-ischemic cardiac disorders, sepsis, stroke , trauma , internal bleeding, renal failure, hypovolemia, atrial fibrillation, congestive heart failure, myocarditis etc. So one should be aware of these non-ACS conditions. However abnormal values may be interpreted carefully in the proper clinical interest.
Paul Tempst
Memorial Sloan Kettering Cancer Center, USA
Title: Aminopeptidase activities as biomarkers for cancer
Biography:
Paul Tempst, PhD, has 40 years of experience in protein chemistry, biochemistry, molecular biology and mass spectrometry, including as a Postdoc at Caltech, Junior Faculty at Harvard Medical School, and Professor at Memorial Sloan Kettering Cancer Center and at the Weill Graduate School of Cornell University (New York). He leads a proteomics and biomarker discovery team and has collaborated worldwide to identify novel proteins and protein complexes: PDGF, Prions, NFkB, IkB, NF-E2, PI3K, mTOR, Raptor, p27kip, SNAREs, Mediator, Elongator, Polycomb, RSC, SWI/SNF, Exosome, and Histone deacetylases, methylases, demethylases and ubiquitinating complexes. His lab pioneered the evaluation and use of protease activities as biomarkers for cancer.
Abstract:
Human cells produce 550 proteases with widely different functions. Several have been implicated in cancer where they promote both tumor progression and suppression. Our group has discovered exopeptidase activities in previous onco-peptidomic studies that provided class discrimination between patients with different types of solid tumors. Owing to their relatively low levels in serum on an immense proteome background, exopeptidases have rarely been detected in proteomic screens and therefore not evaluated as potential biomarkers. Our cancer biomarker discovery studies have therefore focused on proteolytic activities as opposed to steady state levels. We have developed fluorescence-based, quantitative assays to selectively measure activities of 10 individual aminopeptidases (APs) in blood serum or plasma without the need for any sample pre-fractionation or pre-treatment. These tests are uniquely suited to probe altered AP activities in cancer patients and can be applied in parallel to analyze large numbers of samples, followed by multivariate statistical analysis. So far, we have discovered a 2-plex AP activity pattern that allowed prediction of breast cancer biopsy outcome (malignant or benign) with good sensitivity and specificity, as well as a 2-plex pattern that correlates well with high risk (i.e., short survival) of patients with castrate resistant metastatic prostate cancer. Future studies will focus on development and large-scale screens of aminopeptidase and other protease activity assays as markers in a variety of tumor types. If effective functional cancer biomarker panels materialize, it would have a major clinical impact for non-invasive cancer detection and prognostication.
Shrikant Mane
Yale University School of Medicine, USA
Title: Recent advancements in mendelian genomics and data management at the Yale center for genome analysis.
Biography:
Dr. Mane completed his PhD at the age of 28 years from The University of Bombay and postdoctoral studies from The Johns Hopkins University School of Medicine. He is the director of Yale Center for Genome Analysis, one of the most scientifically productive and accomplished Genome Centers in the world. He has published more than 100 papers in reputed journals and has been serving as an ad hock reviewer of several journals. He is currently one of the principle investigators of a $12 million grant from NIH/NHGRI to establish The Yale Center for Genome Analysis.
Abstract:
The Yale Center for Genome Analysis (YCGA) is a state-of-the-art DNA Sequencing Center launched in 2010 to provide an open access centralized facility for services, equipment and expertise required for carrying out large-scale sequence analysis studies (http://ycga.yale.edu/). Since its inception in 2010, YCGA has emerged as one of the leaders in the field of identification of disease associated genetic factors. Our group foresaw scientific opportunities for the development and use of exome sequencing in Mendelian genetics and was the first to develop the method for exome capture on the Nimblegen/Roche platform. We were also the first to demonstrate the biological utility of exome sequencing for clinical diagnostic applications. Currently, YCGA is a part of the NHGRI supported Yale Center for Mendelian Genomics that uses NGS and computational approaches to discover the genes and variants that underlie Mendelian conditions. In the last four years, the use of next-gen sequencing has led to the publications of >150 articles in peer reviewed journals, including >30 in high profile journals such as Science, Nature, Cell, New England Journal of Medicine and Nature Genetics reporting new variants in various disorders, including hypertension, autism, several types of cancers, Gaucher disease, skin disorders, and cortical malfunctions, all using exome analysis. The presentation will focus on recent discoveries in Mendelian disorders made at YCGA, its computer infrastructure and the current challenges and solutions developed for data analysis and management.
Wancai Yang
University of Illinois at Chicago, USA
Title: Epigenetic alterations in colitis-associated colorectal cancer
Biography:
Wancai Yang is a Professor of Pathology and Dean of the School of Basic Medical Sciences at Xinxiang Medical University, China, and an Adjunct Professor of University of Illinois at Chicago, Chicago, Illinois, USA. He was trained as a pathologist in China and received postdoctoral training in Rockefeller University and Albert Einstein Cancer Center, New York, USA. He has published more than 70 papers in high-impact journals about his research on colorectal and esophageal cancers. He has also been serving as grant reviewer, article reviewer and editorial board members of reputed journals.
Abstract:
Besides the canonical and non-canonical Wnt pathway to colorectal cancer, chronic colitis is strongly associated with colorectal cancer formation. However, the mechanisms of colitis develops and how chronic colitis progress to malignance is not clear. Using a unique mouse model, we have demonstrated that the mice with targeted disruption of the intestinal mucin gene Muc2 spontaneously develop chronic inflammation at colon and rectum at early age, whose histopathology was similar to ulcerative colitis in human. After 3 months of age, the Muc2-/- mice develop colonic and rectal adenocarcinoma accompanying severe inflammation. To determine the mechanisms of the malignant transformation, we conducted miRNA array on the colonic epithelial cells from the 3-month Muc2-/- and +/+ mice. MicroRNA profiling showed differential expression of miRNAs (i.e. lower or higher expression enrichments) in Muc2-/- mice. Based on relevance to cytokines and cancer, some miRNAs were validate and were found significantly downregulated in human colitis and colorectal cancer tissues. We further characterized one of the most changed miRNA – miR-27a. We found that miR-27a was significantly reduced in colorectal cancer tissues and colorectal cancer cell lines, and that the reduced miR-27a was associated with distant metastasis and colorectal cancer clinical pathological stages. Functional studies showed that increasing miR-27a inhibited colon cancer cell proliferation, promoted apoptosis and attenuated cell migration, which were also linked to downregulation of p-STAT3 and upregulation of cleaved caspase 3. In vivo, miR-27a inhibited colon cancer cell growth in tumor-bearing mice. Bioinformatic and systemic biological analysis predicted several targets of miR-27a, among them SGPP1 and Smad2 were significantly affected, and interestedly, miRNA-associated cytokines were also significantly increased in Muc2-/-mice. SGPP1 and Smad2 were negatively correlated with miR-27a in human colorectal cancer tissues and cancer cell lines. More studies from the Muc2-/- mice showed disorder of gut microbiota. The disorder of gut microbiota could result in genetic mutations, epigenetic alterations, and activation of oncogenic signaling, in colorectal epithelial cells, leading to colitis development, promoting malignant transformation and mediating colorectal cancer metastasis.
Lynnette R. Ferguson
University of Auckland School of Medical and Health Sciences, New Zealand
Title: Assessing the efficacy of dietary interventions in prostate cancer susceptibility and progression by the use of biomarkers
Biography:
Lynnette Ferguson completed a D. Phil at Oxford University (UK), and then returned to Auckland University for Post-Doctoral studies.She has worked as part of the Auckland Cancer Society Research Centre since it was first established, in 1979.Lynnette currently holds this as a joint appointment with the University Department of Nutrition. She has supervised more than 30PhD or MSc students published more than 350 papers in reputed journals, and serves as an editorial board member of several respected journals.
Abstract:
New Zealand has one of the world’s highest rates of prostate cancer incidence. Both the likelihood of disease occurrence and its’ rate of progression are affected by diet. The dubious ethics of dietary intervention followed by waiting for a cancer endpoint are well illustrated by the example of selenium. The SELECT (Selenium and Vitamin ECancer Prevention Trial)trial began in 2001, and recruited large numbers of men to see if one or both of these dietary supplements could help prevent prostate cancer. In 2014, analysis showed that men who started the trial with high levels of selenium, doubled their risk of developing a high-grade prostate cancer by taking the selenium supplement tested (selenomethionine). This is highly relevant to New Zealand, since our soils are low in this element. Our own studies have used various biomarker endpoints to assess the efficacy of a different form of selenium (selenised yeast), especially in men who show low blood selenium levels, to reduce the probable disease risk and rate of progression. The meaning, relevance and efficacy of these endpoints will be compared.
Rinu Sharma
Guru Gobind Singh Indraprastha University, India
Title: Diagnostic implications of altered miRNA profiles in esophageal cancer
Biography:
Dr. Rinu Sharma has obtained her master's degree in Biotechnology and Ph.D. in Biochemistry from All India Institute of Medical Sciences. She is a faculty in School of Biotechnology, Guru Gobind Singh Indraprastha University, India. She has published more than 20 papers in reputed international journals some of which are the first reports. Her current areas of interest are identification of non-invasive blood based biomarkers for early diagnosis of esophageal cancer and functional analysis of significantly altered genes using gene silencing and proteomic approaches.
Abstract:
The asymptomatic nature of esophageal cancer (EC) at early stages of the disease results in late clinical presentation leading to poor prognosis and limited success of therapeutic modalities. Despite advancement in diagnostic and therapeutic strategies, the five year survival rate of the disease still remains less than 20%. This is primarily due to lack of sensitive and specific markers for early diagnosis and monitoring response to therapy for this disease. Hence, there is a pressing need for establishment of novel non-invasive or minimally-invasive biomarkers for esophageal cancer. Growing evidence suggests importance of alteration in microRNA (miRNA) expression in development and progression of cancer. Moreover, presence of miRNAs in various body fluids such as serum, plasma, saliva, and urine, has opened a new era of disease research. . Our group is interested in deciphering the clinical and functional significance of miRNAs in esophageal cancer. We have evaluated the expression of a panel of miRNAs in tissues as well as sera of esophageal cancer patients. The analysis revealed significant dysregulation of these miRNAs in EC tissues as compared to matched distant nonmalignant tissues. Receiver operated curves generated for these miRNAs showed that they possessed significant diagnostic potential individually and as a panel. Moreover, relative levels of circulating miRNAs in serum significantly distinguished EC patients from normal controls with a high sensitivity. The present paper will discuss the individual as well as collective diagnostic potential of these miRNAs and their targets in EC.
Arjumand Warsy
King Saud University, Saudi Arabia
Title: DNA repair gene polymorphisms as genetic markers of breast cancer
Biography:
Arjumand Warsy completed her PhD at the age of 27 years from Nottingham University, and postdoctoral studies from Birmingham University, UK. She has been working at King Saud University from 1977 and is Professor of Biochemistry at College of Science, King Saud University, Riyadh, Saudi Arabia. She has published over 230 papers in reputed journals and is serving as an editorial board member of Arab Journal of Forensic Sciences & Forensic Medicine. She has presented over 280 papers at different conferences/symposia. She has received several awards and was awarded the President’s Award at King Saud University in 2008.
Abstract:
Breast cancer is the most common cancer in females both in the developed and developing countries and constitutes a major cause of cancer related morbidity and mortality. The etiology of breast cancer is multifactorial, where genetic, environmental, and lifestyle factors interact to produce the malignant transformation. Interest in single nucleotide polymorphism (SNPs) in different genes has gained considerable momentum and many genes have been investigated on the lookout for specific genetic markers of cancer. DNA repair genes constitute one such group. Defects in DNA repair pathways have been shown as predisposing factors to the development of several types of cancers. We investigated several SNPs in RAD51, XRCC2, XRCC4, XRCC3 involved in DNA double-strand break (DSB) repair mechanisms and ERCC1 and ERCC4 in involved in Nucleotide-excision repair (NER), using TaqMan genotyping assay, PCR-RFLP and sequencing. rs861539 and rs1799794 in XRCC3, rs1800067 in ERCC4, rs1801321 and rs2619681 in RAD51 were significantly associated with breast cancer in Saudi females. We compared the results in ER+/ER-, PR+/PR-, HER+/HER-, females with different stages of the disease and different age of disease development and identified several associations. When the results were compared with results reported in different populations and ethnic groups, significant differences were identified. This paper will cover a comprehensive overview of DNA repair mechanisms and the defects which have been observed linked to breast and other cancers in different populations and will also discuss the pros and cons of using SNPs as markers of breast cancer.
- Track 3 : Biomarkers in Clinical Research and Development
Track 4 : Omics Technologies in Biomarkers Discovery and Validation
Chair
Alain Moreau
Sainte-Justine University Hospital, Canada
Co-Chair
Chee Gee See
Proteome Sciences, UK
Session Introduction
Alain Moreau
Sainte-Justine University Hospital, Canada
Title: Osteoarthritis unmasked: Identification of nuclear prohibitin as a new specific OA biomarker and therapeutic target
Biography:
Alain Moreau is Full Professor in the Faculty of Dentistry and the Faculty of Medicine at the Université de Montréal. He is the Director of Research and Chief Scientific Officer of Sainte-Justine University Hospital. He received his PhD in Microbiology and Immunology from the Université de Montréal in 1993. He did a first Postdoctoral training at the Protein Engineering Center of University of Liège, Belgium (1992-1993), followed by a second Postdoctoral fellowship at the Shriners Hospital for Children in Montrealaffiliated with McGill University (1993-1997). He is an internationally recognized expert on molecular genetics of pediatric scoliosis and osteoarthritis. His discoveries led to multiple peer-reviewed papers, international conferences as guest speaker, several awards as well as 32 patents issued.
Abstract:
Osteoarthritis (OA) is one of the most common age-related chronic disorders affecting articular cartilage, joints and bone tissues. According to datamonitor, up to 81.4 million cases in adults aged 25 and older suffer from OA in seven major markets (USA, Japan, UK, Germany, Italy, France and Spain). The current drug treatment for OA is symptom-relieving, and the need for pharmacological treatments to retard, prevent or repair cartilage destruction in OA is urgent. Target selection has been problematic, which includes the identification of selective biomarkers, establishment of appropriate preclinical animal models that reflect human OA, the limitations of the current radiographic standard for structural assessment (KL score), and the lack of stratification of patients in clinical trials by phenotype or tissue involvement. Yet, the search for disease-modifying OA drugs (DMOADs) has proven to be an exceptional challenge, largely because OA usually progresses slowly, with few patients reporting worsening symptoms throughout the clinical trial, which typically lasts months, not years. In that context, we developed a new predictive diagnostic assay intended to measure a specific biomarker, Prohibitin (PHB1) through an immunoassay on blood samples. This test is sensitive enough to detect OA at its earliest stage in asymptomatic subjects and for the first time provides a therapeutic window for intervention, to stop or reverse the mechanism of cartilage matrix degradation associated with primary OA. The integration of specific biomarkers in a companion diagnostic test has the potential to accelerate drug development and thus time to market access for the pharma industry.
Alexander M Buko
Human Metabolome Technologies, USA
Title: Developing a blood metabolite HMT biomarker for Major Depression Disorder (MDD)
Biography:
Alexander M Buko received his PhD in 1980 from the University of Virginia under Professor Donald F. Hunt. He went onto work at the Bureau of Biologics and Biophysics (Today called CBER) for four years then moved to Abbott Labs for 18 years as a distinguished research fellow. From 2002 to 2012, he was Sr. Director Translational Medicine at Biogen Idec. Currently, he is the Vice President of Business and Product Development for HMT-America (Human Metabolome Technologies).
Abstract:
Depression is the leading cause of disability worldwide, affecting about 121 million people in the United States. WHO predicts that it will be the second most common global burden of disease by the year 2020. However, the diagnosis and treatment of depression can be elusive and difficult. Many depressed patients would benefit from objective biological information to determine their condition prior to referral to a therapist. PCPs are only able to recognize about half of the patients with clinical depression while 20% of non-depressed people are falsely diagnosed as depressed. There is a large unmet need for additional diagnostic tests for patient referrals and therapeutic effectiveness. To develop a blood biomarker for MDD, HMT (Human Metabolome Technologies) profiled 538 plasma metabolites from 34 clinically depressed subjects and 38 demographically matched non-depressed subjects. Results identified a potential biomarker, ethanolamine phosphate (EAP). The study was repeated on 241 patients showing patients with MDD had specifically lower plasma concentrations of EAP, as well as, showing severity-dependent behavior. The diagnostic ability of EAP was further confirmed in a single-blinded independent validation group. HMT has transferred the discovery test to a specific blood CoDx assay to measure the level of EAP and we are studying environmental and circadian influences on EAP levels as well.
Chee Gee See
Proteome Sciences, UK
Title: Proteomic strategies to overcome tumor resistance to oncology targeted medicines
Biography:
Chee Gee See is the Director of Personalised Medicine at Proteome Sciences, a company providing high end mass-spectrometry based biomarker discovery and clinical utility tools, uniquely positioned to engage with pharma partners in our quest for personalised medicines. He was previously the clinical Biomarker and Experimental Medicine Leader at Roche for 5 years. He was the BEML for the Phase III pivotal TOGA study where Herceptin was trialled for the new indication of gastric cancer. He was also a BEML for CVD, CNS and immunology so his range and awareness of disease areas and their clinical development challenges is both deep and broad. He also spent 11 years at GSK where he was a genetics expert covering 3 key therapeutic areas in preclinical research within Genetics Research Europe. Prior to industry, he spent 6 years in post-doctoral academia at the University of Birmingham and University College London, most notably in the Human Genome Mapping Project. He also has dual specialist expertise as a consultant in regulatory affairs and value-based drug pricing, reimbursement and market access. He looks forward to engaging with like-minded professionals during this conference.
Abstract:
The identification of genomic targets in cancer pathways has opened up a whole vista of personalised medicine development in recent years. The fast-tracking of such targets from discovery to drug launch has been truly astonishing, as exemplified by the 2007 initial discovery of the EML4-ALK oncogene to the 2011 FDA approval of Pfizer\'s targeted ALK+Xalkori for NSCLC. Whilst these advances are nothing short of brilliant, resistance to such targeted pathways indicate the pitfalls of single target or canonical pathway approaches. Resistance to targeted therapies has emerged as one of the greatest challenges to the personalised medicine approach. To even begin to tackle the issue of resistance, a complete picture of both the canonical and non-canonical signalling pathways in tumor biology is required. Such a complete molecular profile is now possible and this would indicate if our drug is hitting the target and also what alternative pathways the tumor might be engaging to bypass the effects of the drug. Author will present data from proteomics-based strategies to identify global signalling pathways and will demonstrate how this strategy aids decision making on the effectiveness of the targeted oncology drug and in optimizing potential combinatorial options to combat resistance. These strategies and how they are implemented clinically will be discussed. This strategy represents a very innovative and eminently actionable clinical approach to tumor resistance.
Iulia M Lazar
Virginia Tech, USA
Title: Cell cycle and the world of biomarkers: What can we learn from proteomic studies?
Biography:
Iulia M Lazar completed her PhD in Chemistry from Brigham Young University. Following two Post-Doctoral appointments at Sensar Larson-Davis and Oak Ridge National laboratory, and a Principal Research Scientist position at The Barnett Institute/Northeastern University. Presently, she is an Associate Professor with research interests focused on oncoproteomics, breast cancer cell cycle, signaling, biomarker discovery and the development of microfluidic and mass spectrometry technologies for the interrogation of biological systems. The findings of her research led to over 55 publications, book chapters, patents and numerous presentations at national and international symposia.
Abstract:
High-throughput technologies such as LC-MS/MS generate large data-sets that flood scientists with unprecedented amounts of information. The conversion of such data into knowledge has the potential to not just answer long-sought biological questions, but to also revolutionize our approach to solve complex problems that lie at the root of human disease. The goal of our research is to study the molecular mechanisms of breast cancer cell-cycle to uncover aspects that lead to uncontrolled cell proliferation and the discovery of biomarkers and drug targets. Our model system consists of ER+ (MCF7), Her2+ (SKBR3) and non-tumorigenic (MCF10A) cells. Proteomic profiling of different stages of the cell cycle resulted in the identification of ~7000 proteins, with over half of the phosphorylated proteins being involved in proliferative or apoptotic signaling processes. The data revealed protein clusters involved in various signaling pathways, providing a preliminary vista of the cause-effect relationships that confer cancer cells a proliferative advantage. In particular, the G1 stage of the cell cycle included cell cycle inhibitory and DNA damage response proteins, and, most importantly, originators of proliferation and possible drivers through the G1/S transition point. Among the differentially expressed proteins, a rich network of ~200 proteins emerged with biomarker or drug-target potential. The impact of point mutations, insertions and deletions on the functional relevance of such proteins was explored. The findings expose the inherent complexity of the biological processes that unfold within the environment of a cell, and open bold, new opportunities for addressing the problem of diseased cell states.
Maria Paola Costi
Università degli Studi di Modena e Reggio Emilia, Italia
Title: Differential mass-spectrometry proteomic and bioinformatic analysis of Leishmania donovani treated with miltefosine and analogs.
Biography:
Maria Paola Costi has completed her Ph.D Medicinal chemistry in 1989 from the University of Modena and Reggio Emilia and visiting scientist at the University of California San Francisco (UCSF). She is professor of Medicinal Chemistry at the Department of Life Science at Unimore. She has published more than 85 papers in international journals, many patents and serving as an editorial board member of a few journals in the field. Board member of translational science in oncology group of the MITO network and WG leader of drug discovery and development of EUTROC. Coordinator/scientific responsible of some FP European projects in the area of drug discovery in cancer and parasitic diseases (www.lights.eu, www.optobacteria.eu, www.nmtrypi.eu).
Abstract:
The group of infections known as neglected tropical diseases (NTDs) collectively affects one billion people worldwide and represents an enormous burden in terms of human suffering, treatment costs and loss of income. Leishmaniasis is an infection caused by obligate intracellular protozoan Leishmania parasites, which are transmitted by the bite of certain sandfly species. Multitude of Leishmania species cause disease in humans resulting in three clinical manifestations. Visceral leishmaniasis is the most severe form of leishmaniasis and it is caused by Leishmania donovani and L. infantum. Before 2002, the available agents against visceral leishmaniasis were: pentavalent antimony (SbV) compounds, liposomal amphotericin B, paromomycin, and pentamidine. All these drugs must be administered parenterally and have severe side-effects. In 2002, miltefosine, was registered as the first oral agent that does not require hospitalization and up to date is still the only oral treatment for all forms of leishmaniasis. Miltefosine belongs to the class of alkylphosphocholine drugs, which are phosphocholine esters of aliphatic long-chain alcohols. These alkylphosphocholine compounds are structurally related to the group of alkyl-lysophospholipids, which are synthetic analogues of lysophosphatidylcholines or lysolecithins, but lack their glycerol backbone. Miltefosine has demonstrated activity against Leishmania parasites and neoplastic cells. Its biological activity is exerted through (i) induction of apoptosis and (ii) disturbance of lipid-dependent cell signaling pathways; however its mechanism of action and biological target(s) are still unclear (1). The main safety concerns for miltefosine relate to its effect on the mucosa of the gastrointestinal tract and its potential teratogenicity. For these reasons many miltefosine analogues/derivatives are under study/development, to increase activity and reduce toxicity. In this work, the effects of miltefosine and a number of new miltefosine-analogues on the proteomes of L. donovani promastigote parasites have been studied. The aim is to determine molecular events triggered directly or indirectly by the agents, in order to get a better insight on the mechanism of action of this compound class and, at the same time, to identify a protein signature that may characterize their activity. The method is based on differential mass spectrometry (MS) technique of the drug treated parasite samples versus untreated controls. Preliminary studies suggest that among the different proteins affected are ribosomal proteins, heat shock proteins and translation machinery components.
S K Jain
Jamia Hamdard, India
Title: Implication of cancer proteomics in development of biomarkers for early detection of HCC
Biography:
S K Jain, PhD (1974) from AIIMS, New Delhi is Professor of Medical Biochemistry & Biotechnology, Hamdard University. He was Research Associate at Washington University Medical Centre, Tufts Medical School and Harvard Medical School (USA), senior scientist at National Institute of Immunology, New Delhi (1985-2000), visiting Professor, Catholic University, Rome; visiting scientist, Institute of Virology, Oxford; served as consultant to WHO and US-AID; has been Dean, Faculties of Science & Allied Health Sciences and officiating Vice-Chancellor of Hamdard University. He has published 175 papers in peer reviewed journals, number of book chapters and guided >50 PhD students. His current research interests are molecular biology/ immunology of typhoid and proteomics of lung and liver cancers.
Abstract:
Post-HGP era opened new vistas for understanding gene expression and initiated several specialized ‘omics’. Proteomics is analysis of total cellular proteins under different physiological and pathological conditions and is useful for discovery of novel biomarker(s) for diagnosis, and monitoring of progression of cancers by direct analysis of serum proteins. Hepatocellular carcinomas highly prevalent and leads to high morbidity and mortality. Presently serum α-fetoprotein levels form standard diagnosis of HCC, which is relatively low in sensitivity and specificity. In our efforts to develop biomarkers for early detection of HCC, a novel animal model to study ¬ chemically induced liver cancer was developed. The serum protein profiles at various stages of disease progression have been analyzed by 2D electrophoresis. Number of differentially expressed proteins have been detected, some of which bear correlation with disease progression. Histopathology and marker enzyme analyses confirmed and monitored tumor formation and disease progression. The proteins of interest have been characterized by MALDI-TOF and LC-MS/MS. We report the analysis of one of these proteins whose levels are elevated during very early stage of cancer initiation and remain elevated thereafter. The cloning and high level expression of this protein has been achieved. The sequencing of its gene revealed that specific point mutations take place in this protein during tumorogenesis and mutated protein shows immunogenicity. The diseased animals have circulating antibodies against. These findings are important in understanding the molecular mechanism of HCC development. Sera of clinically confirmed HCC patients have elevated levels of this protein that supports its potential as probable biomarker for diagnosis of HCC. The implications of these studies will be discussed.
Todd M Doran
Scripps Research Institute, USA
Title: A chemical approach to mine the immunoproteome for disease biomarkers
Biography:
Todd M Doran completed his PhD under the guidance of Bradley Nilsson at the University of Rochester in 2012 and his Postdoctoral studies at The Scripps Research Institute working with Thomas Kodadek. His work focuses on the use of organic chemistry to create combinatorial libraries that serve as surrogates for unknown, disease-linked antigens. His improvements to the synthesis and screening of combinatorial libraries against human blood samples have led to several manuscripts and pending patents.
Abstract:
The adaptive immune system reacts to foreign molecules or antigens through the amplification of antibodies. Therefore, antibodies represent easily accessed biomarkers for diseases that include cancer, autoimmune and neurodegenerative disease. Unfortunately, the most suitable capture agent for an antibody biomarker is the cognate antigen which in many diseases is not known due to the limitations of conventional antigen discovery methods. We are developing unbiased antigen discovery platforms that take a novel chemical approach to discover new biomarkers. Using combinatorial chemistry, we identify small molecules that are capable of engaging the antigen-binding site of disease-associated antibodies from patient serum. If these abiological “antigen surrogates” bind with sufficiently high affinity and specificity, they are used to detect and enrich the disease antibody population in order to identify the cognate auto-antigen. This strategy has allowed us to uncover novel auto-antigens that are involved during the progression of type 1 diabetes mellitus. These new methods for biomarker discovery will be discussed in the context of identifying new autoantibody biomarkers for type 1 diabetes and their diagnostic application.
Sid Katugampola
Centre for Drug Development at Cancer Research, UK
Title: Biomarkers in early phase oncology clinical development
Biography:
Sid Katugampola completed his PhD in Cambridge. He worked across multiple departments, spanning over 11 years at Pfizer Research UK. During his last 6 years at Pfizer he led projects in biomarkers and translational medicine across multiple therapeutic areas and targets. The past 3 years of his career he has been working at the Centre for Drug Development at Cancer Research UK, where he is responsible for delivering pharmacodynamic biomarkers, across multiple modalities and cancer types, in early phase oncology clinical trials, the majority of which are first in class agents.
Abstract:
The current process of R&D is not sustainable and there is a big drive for shorter timelines and reduced development costs. In oncology, the number of targeted anti-cancer therapies is on the rise and they are showing significant promise both in terms of efficacy and improved safety profile compared to conventional chemotherapy. In early phase oncology clinical development, biomarkers are increasingly being used to identify the right drug for the right patient, at the right dose & schedule in order to clearly demonstrate proof of mechanism and proof of principle. This is fundamentally important as often in early phase oncology trials, demonstrating proof of concept in terms of efficacy is very limited and later stage development is performed at risk. With evolving technologies, numerous methods and assays are being explored to demonstrate biological end points that enable successful go/no-go decision for further development and thereby helping to minimize phase II attrition. Surrogate end points, in addition to tumor markers, add more confidence to overall trial success. Circulating markers, in particular ctDNA has shown significant promise as a liquid biopsy. Following dose escalation, a growing number of trials now incorporate expansion arms with patient enrichment strategies.There are number of limitations and challenges in using biomarkers in early phase oncology trials, including making sense of large data sets. Despite these challenges, a positive and optimistic outlook prevails in the use of pharmacodynamic and enrichment markers in early phase trials for ultimate patient benefit.
Maria Paola Costi
University of Modena and Reggio Emilia, Italy
Title: Identification of a protein panel as pharmacodynaimic biomarker of folate directed targeted drugs in the treatment of ovarian cancer
Biography:
Maria Paola Costi has completed her Ph.D Medicinal chemistry in 1989 from the University of Modena and Reggio Emilia and visiting scientist at the University of California San Francisco (UCSF). She is professor of Medicinal Chemistry at the Department of Life Science at Unimore. She has published more than 85 papers in international journals, many patents and serving as an editorial board member of a few journals in the field. Board member of translational science in oncology group of the MITO network and WG leader of drug discovery and development of EUTROC. Coordinator/scientific responsible of some FP European projects in the area of drug discovery in cancer and parasitic diseases (www.lights.eu, www.optobacteria.eu, www.nmtrypi.eu).
Abstract:
Ovarian cancer (OC) is the fifth most common cause of death from cancer in women. The standard first-line treatment (platinum-derivatives and paclitaxel) suffers from rapid resistance development with still unclear mechanisms and poor prognosis. However, the resistance process includes the over-expression of Thymidylate Synthase (TS), a cell replication key enzyme involved in folate metabolism. Drugs directed to the folate metabolism are under investigation for the second line therapy of platin resistant OC (R-OC). Pemetrexed (AlimtaTM, PMX), a multitarget drug, is in clinical phase II for the treatment of R-OC. Our research group has recently developed a new class of peptide inhibitors of TS showing cytotoxic activity against OC/R-OC cell lines (in particular octapeptide LR and its analog [D-Gln]LR). The peptides suppress TS activity without causing its overexpression, overcoming the limits of well-known substrate-like inhibitors (e.g., 5-FU). The current challenge is to identify predictive and/or prognostic pool of biomarker; whose expression could be informative of the effect of candidate drugs in preclinical and clinical phases of the discovery process. In this work, the effects at the proteome level of folate pathway-directed drug candidates in the treatment of R-OC have been studied. The aim is to determine molecular events triggered directly or indirectly by folate-metabolism inhibiting agents, in order to better understand the mechanism of action of drugs and, at the same time, to identify a protein signature that could characterize their activity. The study was carried on the above mentioned investigational TS-inhibitors peptides, and PMX. The method, based on the use of mass spectrometry (MS) technique, was developed on OC/R-OC cell lines. Subsequently, the same method was applied on biopsies from R-OC patients to verify the prognostic ability of the selected proteins. In-vitro identified protein panel was tested in biopsies from patients enrolled in a phase 2 clinical trial of PMX in the treatment of R-OC. Experiments were carried out on three couple of biopsies collected before/after PMX treatment from patients who have responded differently to the administration of the drug. The evaluation of the protein signature expression was performed via western blot assay. Results showed that in biopsies before PMX treatment TS, HSP90, TRAP1, GART and DHFR are low in patient with a positive outcome (complete responder), instead, the expression is higher in not responder and partial responder patients. To reach a more informative protein profile of the clinical response to PMX treatment, the protein panel was then implemented by adding other 22 proteins. To allow the simultaneously quantification of 28 proteins in the same sample, an LC-MS/MS mass spectrometer operating in Multiple-Reaction Monitoring (MRM) mode was adopted.
Judita Kinkorova
Charles University, Czech Republic
Title: Algorithm for evaluation of the tumor markers for diagnostics and therapy monitoring in cancer diseases
Biography:
Judita Kinkorová is currently the Manager of International Research Cooperation and Affairs at Faculty Hospital in Pilsen and Medical Faculty Charles University in Pilsen. She is the Manager of European Project, Biobanking and BioMolecular Resources Research Infrastructure (BBMRI) in Pilsen. She studied Biology-Mathematics in Charles University in Prague and holds a PhD from Czech University of Life Sciences in Prague. She worked at Charles University, Faculty of Natural Sciences as a Teacher and Researcher. From 2007, she is a National Contact Point for organizations such as FP7, Priority Health, Horizon 2020 SC 1 Health, and Demographic Change and Wellbeing Academy of Sciences of the Czech Republic. She is a member of European Association for Preventive, Predictive and Personalized Medicine, and International Society of Oncology and BioMarkers and an author of 30 publications.
Abstract:
Background: Tumor markers are currently used in the daily clinical practice particularly for the recurrence detection during the follow-up period of the cancer diseases. It is very rarely used for the diagnostic purpose.
Aim: The aim was to propose algorithms for the optimization of the diagnostic approach of the cancer disease and furthermore for the optimal therapy choice and monitoring based on the serum levels of the tumor markers.
Methods & Materials/Patients: Results of the serum tumor markers from 2000 patients monitored in the Faculty Hospital in Pilsen have been retrospectively evaluated. The following markers have been evaluated: CEA, AFP, mucin, cytokeratin and proliferative tumor markers. Markers assessed during the primary diagnosis were correlated with clinical status prior to any therapy. The following cancers were evaluated: Lung, breast, colorectal and prostate cancer. All data related to the detailed clinical status and the disease course during the follow-up period were available in all the patients.
Results: The optimal diagnostic algorithms were proposed for diagnostics and therapy monitoring of the lung, breast, colorectal and prostate cancer. Selected case reports will demonstrate the use of them. Clinical and economical benefit of these proposed algorithms was evaluated.
Conclusions: Multidisciplinary approach based on these algorithms will enable to use the tumor markers for the routine clinical practice much more effectively.
Youhe Gao
Beijing Normal University, China
Title: Are urinary biomarkers from clinical studies biomarkers of disease or biomarkers of medicine?
Biography:
Youhe Gao is a Professor, Beijing Normal University. He received his MD from Peking Union Medical College, his PhD from University of Connecticut and Postdoctoral training from Beth Israel Deaconess Medical Center Harvard Medical School. He was the professor of Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/ Peking Union Medical College from 2001-2014. His research interests include biomarker discovery in urine proteome, protein interaction and related bioinformatics.
Abstract:
Urine proteome was changed by different diuretics, anticoagulants. Other medications may cause changes in urine too. When clinical biomarker studies were designed, sex, age, disease stages, complications were usually taken into consideration. But different medicines taken by the patients were usually not. If this difference can be balanced off later in the study, it may not be a problem at all. But what if the disease is strongly associated with a particular medication, and healthy control is strongly associated with no medication, the result of the study may reveal the difference of the medicine instead of the disease. And the effects of disease and medicine can never be separated in the study. Normally and ethically, we can never stop medicine for the patients; we can never give the healthy volunteers, medicines they do not need, just for the sake of biomarker study. So the patients-medicine, healthy-no medicine associations exist in all of clinical biomarker studies. It is devastating for the field. Clinical biomarker studies are not cheap. We now have to reevaluate the candidate biomarkers proposed from most of early biomarker studies. We have to rule out the effect of the medicine. This becomes so urgent; it becomes part of the foundation of urinary biomarker study. This is why the author cannot wait to propose the pharmuromics (pharm-uro-mics) which studies the effect of the medicine on urine. The other parts can probably be named physiouromics, pathouromics which are the effect of a physiological or pathological process on urine.
Mala Ranjan
Osmania University, India
Title: Immunochemical detection of glycated lens crystallins and their circulating auto-antibodies in human serum during aging
Biography:
Mala Ranjan has completed her Ph.D at the age of 46 years from Osmania University and M.phil in the School of Biological Sciences, University of Wales, Swansea, U.K. Her thrust area of research is application of advanced glycation end products (AGEs) as clinical Biomarkers. She is focus towards the Diabetic complications associated problems. Presently she is working on major project ( Biological monitoring of advanced glycated end products of protein in Diabetic Neuropathy: Prospective role of antiglycating dietary agents) funded by University Grants Commission, New Delhi, India. She has published 12 papers in reputed journals. She is the currently working as Professor of Biochemistry in the prestigious organization (St.Francis College for Women) of Hyderabad, India.
Abstract:
The aim of this investigation was to use lens specific glycated crystallins as an immunogen to detect (i) human glycated crystallins and (ii) circulating auto-antibodies to glycated crystallins in human serum during aging.Polyclonal antibodies were produced against human total lens proteins (40-80 years) in rabbits. The specificity of the antibodies produced were determined by antibody capture assay, using the purified human lens (HMW+ï¡, HMW+ï¡-glycated, ï¢-, ï¢-glycated ï§- and ï§-glycated) crystallins as antigens. The cross-reactivity of these lens specific antibodies against rat ï¢-, ï¢-glycated, ï§- and ï§-glycated lens crystallins was also analyzed. A non-competitive ELISA methodology was developed for the detection of circulating lens crystallins in human sera, using HMW+ï¡, HMW+ï¡-glycated, ï¢- and ï¢-glycated crystallins from human and rat ï§-, and ï§-glycated crystallins as immobilized antigens. Further, these polyclonal antibodies were able to detect both natural and in vitro glycated crystallins, their IC50 values were: human total lens protein (55 ng), HMW+ ï¡ (16.45 ng), HMW + ï¡-glycated (273 ng), ï¢- (37.82 ng), ï¢-glycated (260 ng), ï§- (105.34 ng) and ï§-glycated (313 ng). The immunochemical analysis of human serum indicated a significant change (p< 0.001) in the levels of circulating ï¢-glycated and ï§-glycated crystallins in the age group of 40-80 years with respect to their control groups. However, there was no consistence significant change in the levels of HMW + ï¡-glycated crystallins in the age group of 40-80 years with their respective controls. Notably, the levels of serum ï§-glycated crystallins was found to be 3 folds higher than that of HMW + ï¡-glycated and ï¢-glycated crystallins in the age group of 70-80 years. Circulating auto-antibodies to HMW + ï¡-, ï¢- and ï§-glycated crystallins were detected in the serum of both apparently normal and cataract patients in the age group of 40-80 years by antibody capture assay. The levels of these auto-antibodies were significantly higher (p< 0.05 & < 0.001) at every time point with their respective controls. Auto-antibodies to ï§-gly crystallin was found to be 2 and 3.2 fold higher as compared to the levels of auto-antibodies to ï¢-gly and HMW+ï¡-gly crystallins, respectively.During the course of aging, leakage of lens crystallins (HMW+ï¡, HMW+ ï¡-glycated, ï¢-, ï¢-glycated ï§- and ï§-glycated) elicit an immune response resulting in the formation of auto-antibodies in cataract patients (40-80 years) as compared to age matched controls. For the very first time these specifically designed polyclonal antibodies to lens specific glycated crystallins were able to detect the early leakage of glycated crystallins. This immunochemical method reported may find an application for the early detection of cataract.
Shashwati Basak
Biocon Bristol-Myers Squibb Research and Development Center, India
Title: Clinical biomarkers in drug development: Quantitative PCR-Based fit-for-purpose assay qualification
Biography:
Shashwati Basak obtained her PhD from Indian Institute of Science, Bangalore, India. She carried out postdoctoral research from The Salk Institute for Biological Sciences, San Diego and Stanford School of Medicine, Palo Alto. Research in these two places was focused on understanding the role of tumor suppressor p53 in Cancer Signaling Pathways. She worked as a Research Scientist in the Veterans Affairs Medical Center, San Francisco, before moving into the current role as a Lead Investigator in Early Clinical and Translational Research, Biocon Bristol-Myers Squibb Research and Development Center, Bangalore. Current research interests involve assay development and qualification for Clinical Biomarkers and its use in clinical sample analysis during drug development.
Abstract:
Biomarkers play a significant role during all phases of drug discovery and development. Clinical biomarker-based studies provide early information on target engagement, help guide rational selection of drug combinations, optimization of dose and schedule, serve as tools for stratifying patients and has the potential to predict clinical outcome. A “fit-for purpose” assay development and validation to meet the clinical requirements plays an important role in biomarker estimation. While a rigorous validation is usually not required for discovery-phase work, as a drug progresses into preclinical and early-phase clinical evaluation, more thorough method validation increasingly becomes valuable. The real-time quantitative polymerase chain reaction (qPCR) technology is accurate, sensitive and fast and has become the method of choice for clinical biomarker detection and quantification. Numerous quality issues may arise throughout the entire workflow influencing the accuracy of the qPCR results and the reliability of the data interpretation and conclusions. Development and use of qPCR technology for robust, accurate and reliable method is required for the emerging “fit-for-purpose” biomarker assay qualification. Key factors influencing assay performance such as sample matrix, sample preparation, experimental precision, reproducibility, sensitivity, specificity, dilution linearity and dynamic range and their impact on the assay outcome will be discussed. Based on these, we will put forth recommendations for consideration and optimization while qualifying a qPCR-assay for analysis of clinical samples. As biomarkers become integrated into drug development and clinical trials, assay qualification becomes important with an increasing emphasis on establishing standardized guidelines for analytical methods.
Manjiri Bakre
OncoStem Diagnostics Pvt. Ltd., India
Title: Development of a novel IHC based test for prediction of risk of recurrence for breast cancer patients
Biography:
Manjiri Bakre is a PhD holder in Cell Biology from the Institute of Science, Bangalore has immense work experience in cell signaling and multiple technologies in the USA, Singapore & India. She led a group iIndiann cancer drug discovery in a biotech company in India, multi-disciplinary research on ‘point-of-care’ diagnostics at Philips Research. She Young Scientist Award from International Union of Biochemists and MolecularBiologists and along with it also received Paper of the Week Award by Journal of Biological Chemists. She has published in peer reviewed journals. She has patents and given seminars in many international and national conferences. She founded Onco Stem Diagnostics Pvt. Ltd. and has been instrumental in every aspect of development of multiple prognostic Oncology tests.
Abstract:
Estimation of risk of distant recurrences in breast cancer patients based on biomarkers beyond current gold standard e.g. ER, PR, Her2, node status and Stage to influence treatment decision is of critical importance. At present there are a few molecular tests viz oncotype dx, mamma-print available for patients with ER+, node and HER2 negative, Stage 1 tumors for prediction of risk of recurrence. However use of these tests in India is very minimal as >70% of patients get diagnosed in node+, Stage 2 disease and due to cost constraints. We decided to develop an Immunohistochemistry based prognostic test to predict ‘risk of recurrence’ for ER+ patients in Stage 1-2. To this aim we carried out a retrospective, non-interventional, anonymized study on 420 left over breast FFPE tumor samples of Stage 1-3 with known outcomes about distant recurrence in first 5 years. We tested about 25 different biomarkers via immunohistochemistry belonging to multiple pathways: Proliferation, resistance, quiescence, adhesion etc. Statistical analysis finalized an algorithm with 6 biomarkers which predicts risk of recurrence as low or high for each patient. Early validation on ~200 cases shows 95% specificity and 54% sensitivity of prediction. Our biomarkers are targetable as they are membrane associated and thus in future high risk patients will be treated with new targeted drugs to reduce risk of recurrence. Thus, we believe we have developed a simple, inexpensive and highly specific test useful to majority of breast cancer patients across the globe with high specificity and sensitivity. We would like to describe the details of development of the test in my talk.
Mônica Valeria Marquezini
University of São Paulo Medical School, Brazil
Title: Sao Paulo workers exposed to air pollution: Evaluation of genotoxicity
Biography:
Mônica Valeria Marquezini is a Scientific Researcher at Pro-Blood Foundation of Blood Center of São Paulo since 1991. She is part of Experimental Air Pollution Laboratory - LPAE staff at the Department of Pathology, Medical School of University of São Paulo, Brazil, since 2010. She is a expert in Cellular and Molecular Biology with cell surface proteins studies and extracellular matrix research. She is a Teacher of Cell and Molecular Biology themes at different graduation careers, Post-graduation advisor, and Coordinator of specialization courses and National and International Projects. She holds a PhD in Science and from the Federal University of São Paulo-School of Medicine (1996) and graduated in Biological Sciences Medical Modality (1983).
Abstract:
The goal of this study was to evaluate the genotoxic effects of air pollution (PM2.5) on exposed individuals, from Sao Paulo City. The study involved 58 male workers of two different exposition groups: 1) 26 taxi drivers (TD) and 17 traffic controllers (TC), high exposure and 2) 15 workers from the Forest Institute (FI), low exposure. Each voluntary used a Personal Environmental Monitoring Sampler to collect PM2.5 particles mass. The sampler were operated continuously at 4-LPM over 24-hours. Particles were collected on a polycarbonate membrane filter (37 mm diameter). The frequency of Micronuclei (MN) in buccal exfoliated cells and peripheral blood lymphocytes were determined. The average the MN in lymphocytes and buccal exfoliated cells was significantly higher on group 1 (PM2.5 p < 0.001). There is a significant correlation between MN measured in xfoliated cells and in lymphocytes (correlation coefficient of 0.80; p<0.001). So the determination of MN buccal exfoliated cells is as efficient as the determination of MN in lymphocytes, a classic biomarker for the assessment of genotoxicity. Our results have shown that individuals exposed to the highest concentrations of PM2.5 have a higher level of micronucleus. However, we found in our study some individuals that even exposed to lower concentrations of pollutants, showed higher levels of micronuclei which allowed us to identify them as individuals more susceptible to PM2.5. Thus, in order to understand this susceptibility, the methylation study of genes promoters related to inflammatory response, will be carried trough in these individuals.
Fanghua Qiu
Guangzhou Hospital of Traditional Chinese Medicine, China
Title: Dermcidin is a novel biomarker of hepatic carcinoma?
Biography:
Fanghua Qiu has completed her PhD from Guangzhou Medicine University. She has published 3 papers in reputed journals. She is currently working as an Associate Professor in Guangzhou Traditional Chinese Medicine Hospital, Guangzhou, China.
Abstract:
We previously identified a group of Nck SH2 domain-binding proteins through a combination of GST-Nck1-SH2 pull down and 2DE in hepatic carcinoma (HCC) tissues, one of the proteins is Dermcidin (DCD). Western blot demonstrated DCD is overexpressed in HCC tissues and aggressive cell. To further identify potential blood-based biomarkers for the early detection of HCC cancer, we compare DCD level from HCC and healthy people, increased DCD was also detected with ELISA methods in 100 serum samples taken from HCC cancer diagnosis (p<0.001). In conclusion, these results present novel evidence that DCD levels may increase in early carcinogenesis, particularly among more aggressive forms of HCC cancer.
Baolin Zhang
Food and Drug Administration (FDA), USA
Title: Integrating predictive biomarkers in the development of targeted cancer therapies
Biography:
Baolin Zhang is a Senior Investigator in the Office of Biotechnology Products of the Center for Drug Evaluation and Research (CDER) at the US Food and Drug Administration (FDA). Dr. Zhang has 14 years of FDA regulatory experience in product quality review (Chemistry, Manufacturing and Control) of therapeutic protein product applications under investigational new drug applications (INDs) and biologic license applications (BLAs). In addition to performing review, inspection, policy, and training activities, Dr. Zhang also leads a research team conducting FDA mission-related research aimed at improving drug safety and efficacy. Dr. Zhang’s scientific expertise lies in the areas of protein biochemistry, cell death and cell growth regulation, cancer drug resistance and biomarkers. He has published over 70 peer-reviewed articles in reputed journals, and presented at numerous scientific and regulatory conferences on the development of therapeutic proteins. Dr. Zhang earned his Ph.D. in chemistry from Peking University in China. He is a recipient of the FDA Scientific Achievement Award, the FDA/CDER Excellence in Mentoring Award, and the FDA/CDER Excellence in Leadership Award.
Abstract:
The regulatory approval of new drugs for marketing requires a demonstration that the drug is safe and effective in the intended patient population that is specified in the drug label.In evaluating potential anti-cancer agents,there is a continued interest in using predictive biomarkers to select patients likely to respond or be resistant to a particular treatment. The ability to identify the subsets of patients with molecularly defined cancers could significantly improve patient outcome. Several clinically validated biomarkers such as HER2 and K-Ras mutation status have become an essential part of the clinical use of the HER2/EGFR targeted therapies. However, the identification of clinically useful predictive biomarkers for solid tumours has proven challenging with many initially promising biomarkers failing to translate into clinically useful applications. The problem mainly lies in the inherent heterogeneity of tumor cells as being found between tumor types, individuals with the same type of tumor, and within one tumor of a patient at any given time. The complex matter also poses challenges to the regulatory review of submissions for biomarker development and drug and biomarker co-development.This presentation will introduce the recent efforts of the US Food and Drug Administration in facilitating the development of biomarkers as well as case studies to highlight the major challenges in the discovery, qualification and regulatory review of predictive cancer biomarkers.
Hem D Shukla
University of Maryland, USA
Title: The Nrf2 mediated antioxidant defense against oxidative stress in BxPC-3 cell lines and targets for therapeutic intervention
Biography:
Hem D. Shukla is Research Scientist in Department of Pharmaceutical Sciences at University of Maryland and adjunct Professor of Genomics in Notredame of Maryland University. He has also worked as Research Faculty in Department of Biology at Johns Hopkins University. Dr. Shukla has worked on proteomic analysis of oxidative stress response in BxPC-3 pancreatic cell lines and identification of biomarkers for pancreatic cancer. He has worked on “The Nrf2 mediated antioxidant defense against oxidative stress in BxPC-3 cell lines and targets for therapeutic intervention”. He has shown elevated level of Nrf2 transcriptional factor in pancreatic cancer cell lines under oxidative stress which is phosphorylated by protein kinase C and affects phosphatidylinositol 3-kinase and MAP kinase pathways. After phosphorylation, Nrf2 translocates to the nucleus, binds AREs and transactivates detoxifying enzymes and antioxidant enzymes, such as glutathione S-transferase, and superoxide dismutase. The IPA analysis has suggested a potential role of Nrf2 under oxidative stress conditions.
Abstract:
Integrins are cell surface glycoproteins that are involved in cell-cell and cell-extracellular matrix (ECM) interactions. These interactions are the basis for a number of diverse effects that include cell migration and anchorage, cell growth and invasion. In the present investigation the proteomic analysis of oxidatively stressed BxPC3 human pancreatic cancer cells have shown the elevated level of both a6b4 integrin, caveolin-1, K-RAS, EGFR, annexin a4 and annexin a11 as compared to HPDE control. We have also identified the presence of a number of gene products involved in integrin signaling pathway and MAPK pathway. The bioinformatic analysis by Protein Center and Ingenuity Pathway Analysis have shown the altered integrin signaling pathway and MAPK pathway in Pancreatic Carcinoma Cell lines. Further, the activation of NRF2 transcriptional factor in BxPC-3 treated cells shows that It may bind to the DNA at the location of the Antioxidant Response Element (ARE) or also called hARE (Human Antioxidant Response Element) which is the master regulator of the total antioxidant system. It seems likely that upon exposure of cells to oxidative stress, Nrf2 is phosphorylated in response to the protein kinase C, phosphatidylinositol 3-kinase and MAP kinase pathways. After phosphorylation, Nrf2 translocates to the nucleus, binds AREs and transactivates detoxifying enzymes and antioxidant enzymes, such as glutathione S-transferase, and superoxide dismutase. The pathway analysis has also demonstrated that at least seven signal transduction cascades were induced by ECM interaction with integrin heterodimers, which may trigger aberrant signaling and lead to pancreatic cancer adenocarcinoma. The data have clearly shown the activation of INT-ILK-PT3K-ILKAP-AKT and Caveolin-GRB2-SOS-cRas-Raf-MEK cascade. These results may have some promise in therapeutic intervention in the treatment of pancreatic cancer adenocarcinoma.
Nalinee Sripaung
Ministry of Public Health, Thailand
Title: The usage of biomarkers in terms of biological exposure indices for health surveillance in Thailand
Biography:
Dr. Nalinee Sripaung has completed her degrees of B.Sc. and M.Sc. from universities in Thailand (Mahidol University and Chulalongkorn University, in order). She has completed her Ph.D. at the age of 34 years from Tokyo Medical and Dental University (TMDU), Japan. She has ever been the editorial board member of the repute. She has published more than 10 papers in reputed journals and government reports. Presently, She is the Director of Rayong Occupational Health and Environmental Development Center. She is serving as an Department of Disease Control of Thailand Committee on Thai Biological Indices (Thai BEIs).
Abstract:
Presently, the health risk assessment becomes important for health active surveillance. The significant types of chemicals residual and/or metabolites in biological samples are selected to be the biomarkers for exposure assessment and susceptibility. The results of analytical laboratory of biomarkers concentration in biological samples are compared with the health surveillance standard values. This method are used as safety measure of exposure assessment to chemicals hazard and cancer susceptibility in occupations and environmental community. Besides, the combined effects of food, drug, and other chemicals of daily life intake accompanied with the mistaken method of collecting, transferring and preserving biolological samples act as the interference factors of laboratory analyticals results. The other important interferences are the risk behaviour and the individaul differences. Thus, Department of Disease Control of Thailand has set the pilot project focused on the concentration of biomarkers, laboratory analyticals method and interfering factors of 26 chemicals (8 heavy metals, 12 volatile organic compounds, 2 pesticides, 2 gases and 2 types of radiation) for formal workers in Thailand Kingdom. This pilot project is aimed to be the tool for setting the policy of standard measure by usage of biomarkers for exposure assessment in the program of health active surveillance. This project will be involved with active surveillance and diminishment of burden diseases caused by chemicals. This tool of safety measure should be applied to prevent and control of Chemicals Diseases in any other risk area.
Maria Paola Costi
University of Modena and Reggio Emilia, Italy
Title: Identification of a protein panelas pharmacodynaimic biomarker of foalte directed targeted drugs in the treatment of ovarian cancer
Biography:
Prof.Maria Paola Costi has completed her Ph.D Medicinal chemistry at the age of 29 years from the University of Modena and Reggio Emilia and postdoctoral studies from University of California San Francisco (UCSF). She is professor of Medicinal Chemistry at the Department of Life Science at Unimore. She has published more than 85 papers in international journals, many patents and serving as an editorial board member of a few journals. Board member of translational science in oncology group of the MITO network and WG leader of drug discovery and development of EUTROC. Coordinator of a number of FP European projects in the area of drug discovery in cancer and parasitic diseases (www.nmtrypi.eu).
Abstract:
Ovarian cancer (OC) is the fifth most common cause of death from cancer in women. The standard first-line treatment (platinum-derivatives and paclitaxel) suffers from rapid resistance development with still unclear mechanisms and poor prognosis. However, the resistance process includes the over-expression of Thymidylate Synthase (TS)1, a cell replication key enzyme involved in folate metabolism. Drugs directed to the folate metabolism are under investigation for the secondline therapy of platin resistant OC (R-OC). Pemetrexed (AlimtaTM, PMX), a multitarget drug, is in clinical phase II for the treatment of R-OC. Ourresearch group has recently developed a new class of peptide inhibitors of TS showing cytotoxic activity against OC/R-OC cell lines (in particular octapeptide LR and its analog [D-Gln4]LR)2,3. The peptides suppress TS activity without causing its overexpression, overcoming the limits of well-known substrate-like inhibitors (e.g., 5-FU). The current challenge is to identify predictive and/or prognostic pool of biomarker, whoseexpression could be informative of the effect of candidate drugs in preclinical and clinical phases of the discovery process. In this work,the effects at the proteome level offolate pathway-directed drug candidates in the treatment of R-OChave been studied. The aim is to determine molecular events triggered directly or indirectly by folate-metabolism inhibiting agents, in order to better understand the mechanism of action of drugs and, at the same time, to identify a protein signature that could characterize their activity. The study was carried on the above mentioned investigationalTS-inhibitors peptides, and PMX. The method, based on the use of mass spectrometry (MS) technique, was developed on OC/R-OC cell lines. Subsequently, the same method was applied on biopsies from R-OC patients to verify the prognostic ability of the selected proteins. In-vitro identified protein panel was tested in biopsies from patients enrolled in a phase 2 clinical trial of PMX in the treatment of R-OC. Experiments were carried out on three couple of biopsies collected before/after PMX treatment from patients whose have responded differently to the administration of the drug. The evaluation of the protein signature expression was performed via western blot assay. Results showed that in biopsies before PMX treatment TS, HSP90, TRAP1, GART and DHFR are low in patient with a positive outcome (complete responder), instead, the expression is higher in not responder and partial responder patients. To reach a more informative protein profile of the clinical response to PMX treatment, the protein panel was then implemented by adding other 22 proteins. To allow the simultaneously quantification of 28 proteins in the same sample, anLC-MS/MS mass spectrometer operating in Multiple-Reaction Monitoring (MRM) mode, was adopted. 1.Cardinale D. et al. Proc. Natl. Acad. Sci. U.S.A. 2011 , 2.F.Genovese J Proteome Res. 2014,13, 5250..3. Zhang D. et al. “Establishment of pemetrexed-resistant non-small cell lung cancer cell lines.” Cancer Lett. 2011, 309, 228. This work wassupported b.y AIRC-DROC project N.10740
- Track 2: Functional Genomics and Cytogenetic Biomarkers
Track 5: Biomarkers of Exposure Response and Susceptibility
Track 6: Biomarkers for Disorders
Track 8: Biomarkers in Nanoscience
Chair
Claude Prigent
Institute of Genetics and Development of Rennes, France
Co-Chair
Sergey Suchkov
I.M.Sechenov First Moscow State Medical University, Russia
Session Introduction
Jens Wiltfang
Georg August University Göttingen, Germany
Title: Predictive molecular diagnosis of Alzheimer’s dementia: Towards new clinical models for preventive treatment
Biography:
Jens Wiltfang is a graduate from the Faculty of Medicine of Hannover where he obtained a PhD in Psychiatry. He is the Director of the Department of Psychiatry and Psychotherapy at the University Medical Center Göttingen (UMG). He is a neurologist and psychiatrist with wide experience in the field of neurodegenerative diseases. His activity includes the clinical characterization of patients with dementia and research on the biomarker discovery and validation. In particular his main expertise is on the field of cerebrospinal fluid and blood biomarkers for early diagnosis of neurodegenerative diseases, with special interest on Alzheimer’s disease and Parkinson’s disease.
Abstract:
There is an unmet need for first preventive that is disease-modifying, treatments of Alzheimer´s dementia (AD). However, preventive treatment calls for predictive diagnosis since novel preventive treatment options can only be offered if patients are identified during preclinical stages of the incipient AD. Per definition, a preclinical stage cannot be detected by clinical tools and accordingly, patients at high risk for later AD have to be identified by biomarker guided predictive diagnostics. The presentation will demonstrate that patients with preclinical AD can meanwhile be identified within the clinically heterogenous cohort of Mild Cognitive Impairment (MCI) with positive and negative predictive values of at least 90% by a multiparameter biomarker approach relying on CSF dementia biomarkers, MRI volumetry and/or F18-Amyloid-PET. In view of a prevalence of approximately 20% of preclinical AD within the MCI risk cohort the latter predictive values are clinically significant. Moreover, it will be critically discussed in how far first blood-based assays may support the identification of preclinical AD. Finally, the presentation will exemplify that novel diagnostic targets may indicate promising novel therapeutic targets.
Biography:
Gbandjaba Nagba Yendoubé has completed his PhD in biochemistry from Hassan IIUniversity Casablanca Morocco in 2013. As a student, he develops a good collaboration with Sherbrooke University in Canada and the International Pasteur Institute of Morocco. In 2009, he won a grant from the IRSC to accomplish his thesis in the Sherbrooke Research Centre on Ageing. Dr. Gbandjaba also called the whistle blower focuses his research on the development of oxidative stress biomarkers involved in cardiovascular diseases related to successful ageing. Dr. Gbandjaba has more than 52 publications including original research articles in reputed journals, case study, short communications, symposia and review articles.
Abstract:
Aim: The aim of the study was to investigate the Paraoxonase 1 (PON1) phenotype distribution and to measure oxidative stress markers (Vitamin E/CT, MDA) in healthy, diabetic and hemodialysis patients. Patients and Method: Three hundred subjects (healthy, diabetic and chronic renal failure patients) aged between 40 and 80 years were recruited for the study (divided in three groups of 100 subjects each). Total MDA content in plasma was measured by HPLC with thiobarbituric acid (TBA) and with fluorescence detection. Vitamin E (α-tocopherol) as the principal plasma antioxidant was also measured by HPLC with electrochemical detection. Results: Vitamin E-Tot. Cholesterol ratio increases significantly with age in diabetic patients (r= 0.30; p <0.01). Vitamin E - Total Cholesterol ratio decreases significantly with age in hemodialysis patients (r= ― 0.17; p<0.05) and in healthy subjects (r=―0.15; p=0.44). Plasma MDA concentration increases with age in diabetic patients (r= 0.09; p=0.15). The distribution of PON 1 phenotype in healthy, diabetic and hemodialysis patients was as follows: AA 79.31%, 75.00% and 69.31%; AB 14.94%, 19.04% and 20.45%; BB 5.74%, 5.95% and 10.22%. Adjusted odds ratio comparing the AA variant with the BB variant were 1.97 [95 % confidence interval (CI): 0.63-6.21] in hemodialysis patients. In diabetic patients, the adjusted odds ratio comparing the AA variant with the AB variant of PON1 were 1.37 [95% CI: 0.62-3.04]. Conclusion: Our studies show that PON1 phenotype distribution and oxidative stress markers are associated with cardiovascular diseases risk in diabetic and hemodialysis patients.
Vasile Foris
Medical University of Graz, Austria
Title: A comprehensive approach for blood-derived biomarker assessment in pulmonary hypertension
Biography:
Vasile Foris obtained his MD from University of Medicine and Pharmacy “Iuliu Hatieganu” Cluj-Napoca, Romania. He has been employed as a Junior Scientist at the Ludwig Boltzmann Institute for Lung Vascular Research in Graz, Austria, where he also joined the PhD Program “Molecular Medicine” of the Medical University of Graz. His research interests focused mainly on circulating progenitor cells as well as on clinically relevant blood-derived biomarkers for pulmonary hypertension. He is elected as a Clinical Fellow at the Department of Internal Medicine, Division of Pulmonology at the Medical University of Graz.
Abstract:
Background: Apelin, TNF-like Weak Inducer of Apoptosis (TWEAK), and Growth Differentiation Factor-15 (GDF15) may be suitable for screening and prognostic evaluation in Pulmonary Hypertension (PH).
Patients & Methods: We performed a power analysis based on a pilot study in 10 IPAH patients, 10 CTEPH and 10 controls for apelin-12, -13, -17, -36, TWEAK and GDF-15, resulting in n=31 IPAH patients and 24 CTEPH patients needed for a prospective study assessing apelin-17 and GDF-15 as compared to matched controls to provide 80% power for detection of differences.
Results: Apelin-17 was increased in IPAH and in CTEPH as compared to control (p<0.0001 CTRL vs. IPAH, p<0.001 CTRL vs. CTEPH). In addition, GDF-15 was elevated both in IPAH and in CTEPH as compared to control (p<0.0001 CTRL vs. IPAH, p<0.001 CTRL vs. CTEPH). GDF-15 was correlated with NT-proBNP in both IPAH and CTEPH. Area under the ROC curve for apelin-17 and GDF-15 were similar with an AUC of 0.86 and 0.83 respectively. A cut-off value of 1480 pg/mL for apelin-17, detected IPAH with a sensitivity of 68% and a specificity of 93%. A cut-off value of 1270 pg/ml for apelin-17, detected CTEPH with a sensitivity of 71% and a specificity of 87%.
Conclusion: Among apelin isoforms, apelin-17 may be a promising biomarker for IPAH and CTEPH and performs similar to GDF-15. Both biomarkers may be relevant for both IPAH and CTEPH.
Rinu Sharma
Guru Gobind Singh Indraprastha University, India
Title: Diagnostic implications of altered miRNA profiles in esophageal cancer
Biography:
Rinu Sharma has obtained her Master's degree in Biotechnology and PhD in Biochemistry from All India Institute of Medical Sciences. She is a Faculty in School of Biotechnology, Guru Gobind Singh Indraprastha University, India. She has published more than 20 papers in reputed international journals; some of which are the first reports. Her current areas of interest are identification of non-invasive blood based biomarkers for early diagnosis of esophageal cancer and functional analysis of significantly altered genes using gene silencing and proteomic approaches.
Abstract:
The asymptomatic nature of esophageal cancer (EC) at early stages of the disease results in late clinical presentation leads to poor prognosis and limited success of therapeutic modalities. Despite advancement in diagnostic and therapeutic strategies, the five year survival rate of the disease still remains less than 20%. This is primarily due to lack of sensitive and specific markers for early diagnosis and monitoring response to therapy for this disease. Hence, there is a pressing need for establishment of novel non-invasive or minimally-invasive biomarkers for esophageal cancer. Growing evidence suggests importance of alteration in microRNA (miRNA) expression in development and progression of cancer. Moreover, presence of miRNAs in various body fluids such as serum, plasma, saliva and urine has opened a new era of disease research. Our group is interested in deciphering the clinical and functional significance of miRNAs in esophageal cancer. We have evaluated the expression of a panel of miRNAs in tissues as well as sera of esophageal cancer patients. The analysis revealed significant dysregulation of these miRNAs in EC tissues as compared to matched distant nonmalignant tissues. Receiver operated curves generated for these miRNAs showed that they possessed significant diagnostic potential individually and as a panel. Moreover, relative levels of circulating miRNAs in serum significantly distinguished EC patients from normal controls with a high sensitivity. The present paper will discuss the individual as well as collective diagnostic potential of these miRNAs and their targets in EC.
Nalinee Sripaung
Ministry of Public Health, Thailand
Title: The usage of biomarkers in terms of biological exposure indices for health surveillance in Thailand
Biography:
Nalinee Sripaung has completed her degrees of BSc and MSc from universities in Thailand (Mahidol University and Chulalongkorn University respectively). She has completed her PhD at the age of 34 years from Tokyo Medical and Dental University (TMDU), Japan. She has ever been the Editorial Board Member of the repute. She has published more than 10 papers in reputed journals and government reports. Presently, She is the Director of Rayong Occupational Health and Environmental Development Center. She is serving as an Department of Disease Control of Thailand Committee on Thai Biological Indices (Thai BEIs).
Abstract:
Presently, the health risk assessment becomes important for health active surveillance. The significant types of chemicals residual and or metabolites in biological samples are selected to be the biomarkers for exposure assessment and susceptibility. The results of analytical laboratory of biomarkers concentration in biological samples are compared with the health surveillance standard values. This method are used as safety measure of exposure assessment to chemicals hazard and cancer susceptibility in occupations and environmental community. Besides, the combined effects of food, drug and other chemicals of daily life intake accompanied with the mistaken method of collecting, transferring and preserving biolological samples act as the interference factors of laboratory analyticals results. The other important interferences are the risk behaviour and the individaul differences. Thus, Department of Disease Control of Thailand has set the pilot project focused on the concentration of biomarkers, laboratory analyticals method and interfering factors of 26 chemicals (8 heavy metals, 12 volatile organic compounds, 2 pesticides, 2 gases and 2 types of radiation) for formal workers in Thailand Kingdom. This pilot project is aimed to be the tool for setting the policy of standard measure by usage of biomarkers for exposure assessment in the program of health active surveillance. This project will be involved with active surveillance and diminishment of burden diseases caused by chemicals. This tool of safety measure should be applied to prevent and control of Chemicals Diseases in any other risk area.
Pina J Trivedi
The Gujarat Cancer & Research Institute, India
Title: Clinical significance of cytogenetic biomarkers in acute myeloid leukemia: An Indian experience
Biography:
Pina J Trivedi has completed her PhD in March 2012 from Gujarat University. She is working in Cytogenetic department of The Gujarat Cancer & Research Institute (GCRI), Ahmedabad, Gujarat; India from last 18 years. She is also one of the Faculties in a Master degree course (MSc) Cancer Biology run by GCRI. She received a Young Scientist Award for oral presentation in Indian Society of Human Genetics conference during 2005 in cytogenetics category. She has more than 41 publications in national and international journals. She has recently visited Bremerhaven, Germany during May 6th to 8th 2014 for workshop on “Zyto vision in situ hybridization”.
Abstract:
Acute myeloid leukemia (AML) is a heterogeneous group of disorder. Recurrent translocations t (15; 17), t (8; 21) and inv (16) have good prognosis and are recognized as a biomarker for prognostication in AML, whereas loss and gain of different chromosome segments play a vital role in leukemogenesis. The aim of the present study was to appraise the clinical significance of numerical and structural chromosomal abnormalities in AML patients. Bone marrow/peripheral blood lymphocytes of 321 AML patients were carried out by cytogenetics and FISH and Multicolour FISH as and when required. Out of 321 patients, trisomy 8 showed the highest prevalence (n=14) and found as sole, complex and secondary change. Along with most commonly observed recurrent chromosomal abnormalities, there were loss and gain of different chromosomes also observed. The loss of sex chromosome was observed in the highest frequency (n=20). Gain of whole chromosomes were; 8 (X23), 10 (X5), 19 (X7), 21 (X10), 22 (X6) and loss of X (X6), Y (X17). Frequent breakpoints in structural abnormalities were gain or loss of different chromosomes i.e., 1q (X8), 5q (X5), 8q (X4), 9q (X5), 11p (X5), 11q (X8), 17q (X9) and 22q (X 6). Study revealed that the gain of chromosomal material was observed much more often than loss. Loss of tumor-suppressor genes d might be involved in mechanism of leukemogenesis. Gain as numerical abnormalities may affect gene-dosage and may play a significant role in the pathogenesis of AML. Study highlights the clinical significance of cytogenetics as an independent prognostic biomarker in AML providing the allocation for a stratified treatment approach of the disease.
Laura Gillis
BioStat Solutions, Inc., USA
Title: A Statistical Consideration on the Evaluation of Biomarkers
Biography:
Laura Gillis, Ph.D. is Associate Director of Biostatistics, at BioStat Solutions, Inc. (BSSI). She has over 20 years of consulting experience including five years in genetic data analysis. Her work at BSSI has included both GWAS and candidate gene studies focusing on both single and multi-biomarker association testing, gene level association testing and development of biomarker subgroups (i.e., patient stratification) for improved response to treatment in practical applications. Her experience also includes the analysis of biomarker discovery data in both, the vaccine development and oncology diagnostic field using epidemiological and proteomic assay data. Dr. Gillis received her Ph.D. in Statistics from Virginia Tech.
Abstract:
As the use of multiple types of biomarkers in companion diagnostics continues to grow, evaluation and validation becomes more critical and often more complicated. While DNA biomarkers are stable over time, proteomic biomarkers can change over time depending on disease progression. Epidemiological variables, such as age, often provide additional predictive capability. Combining these biomarkers can lead to better diagnostics, but statistical analysis becomes more complex. This presentation will present techniques that have proven successful in the evaluation of diverse biomarkers for disease and drug response.
Samia Perwaiz Khan
Ziauddin University, Pakistan
Title: Carotid arteries plaques regression in heterozygous familial hypercholesterolemia patients on statin therapy
Biography:
Samia Perwaiz Khan obtained her Medical Degree (MBBS) from Dow Medical College, Karachi. Her MPhil and PhD degrees were granted by Ziauddin University, Karachi where she is currently working as Professor of Pharmacology and PhD Program Coordinator. She has written 12 research articles which have been published in national and international journals with high impact factors. She has attended and presented papers at several national and international conferences where one of her papers was declared as the best oral presentation. She has been a Reviewer for national and international journals. Furthermore, she has been a member of organizing teams for national conferences, symposia and academic work shops. She also has clinical experience and in the past has worked at Sindh Institute of Urology and Transplant (SIUT), Karachi, as a Medical Officer.
Abstract:
The aim of this study is to compare carotid intima-media thickness (CIMT) variation and plaque regression in hypercholesterolemia patients on statin therapy for two years. One hundred and twenty cases of hyperlipidemia having total cholesterol more than 250 mg/dL and LDL-C levels above 160 mg/dL were selected from National Institute of Cardiovascular Diseases and Dr. Ziauddin Hospital, Karachi by performing lipid profiles after overnight fasting. Familial hypercholesterolemia was also diagnosed from premature coronary diseases, xanthomas, arcus cornealis, and family history of premature coronary diseases and by LDL-R gene mutation. B-mode ultrasound was done to show thickness of carotid intima-media on Toshiba (M # SSA-580A/E2) with linear probe. Measurement of CIMT in patients of heterozygous familial hypercholesterolemia patients was done by B-mode ultrasound of carotid arteries. Multiple soft and hard plaques were seen in heterozygous familial hypercholesterolemia (HeFH) patients in B-mode ultrasound of carotid arteries. The mean CIMT reduction in both treatment groups was significant, 0.11 mm in rosuvastatin group and 0.08 mm in atorvastatin group, regression in CIMT over a duration of two years therapy (*p<0.02). The total cholesterol reduced was 46% and reduction of LDL-C by 48% in patients on rosuvastatin as compared to total cholesterol 36% and LDL-C 37% in patients on atorvastatin for duration of 24 months (**p<0.001). Measure plaque before and after 2 years statin therapy by B-mode ultrasonography done along with measurement of thickness of carotid intima-media on Toshiba (M# SSA-580A/E2) with linear probe.
- Workshop - Biomarkers of novel generations to secure diagnostic, predictive, prognostic, therapeutic and preventive goals: A way to get the academia, faculty, biopharma and society united
Chair
Sergey Suchkov
I.M.Sechenov First Moscow State Medical University, Russia
Co-Chair
Trevor G Marshall
Autoimmunity Research Foundation, USA
Session Introduction
Sergey Suchkov
I.M.Sechenov First Moscow State Medical University, Russia
Title: PPPM as a model of healthcare services to operate biomarkers of newer generations to monitor clinical and subclinical stages of chronic inflammatory conditions of autoimmune origin
Biography:
Sergey Suchkov graduated from Astrakhan State Medical University and was awarded with MD. In 1985, Suchkov obtained his Ph.D. He is the PhD student of the I.M. Sechenov Moscow Medical Academy and Institute of Medical Enzymology, USSR Academy of Medical Sciences, Moscow, Russia. In 2001, Suchkov finished the PostDoc Research Fellowship Program and maintained his Doctor Degree at the National Institute of Immunology, Russia. From 1987 through 1989, Dr. Suchkov was a senior Researcher, Lab of Developmental Immunology, Koltzov Institute of Developmental Biology, USSR Academy of Sciences to deal to developmental immunology. From 1989 through 1995, Dr. Suchkov was being a Head of the Lab of Clinical Immunology and Immunobiotechnology, Helmholtz Eye Research Institute in Moscow. From 1995 through 2004, Dr. Suchkov was being a Chairman of the Department for Clinical Immunology, Moscow Clinical Research Institute (MONIKI) and the Immunologist-in-Chief of the Moscow Regional Ministry of Health. At present, Dr Sergey Suchkov, MD, PhD, is Professor in Immunology, Department of Pathology, School for Pharmacy, I.M. Sechenov First Moscow State Medical University, Dean of the Department (Faculty) of The PPPM Development, and the First Vice-President of the University of World Business, Politics and Law and Secretary General, United Cultural Convention (UCC), Cambridge, UK.
Abstract:
A new systems approach to disease to pay its crucial attention on the trend would result in a new branch in the healthcare services, namely, predictive, preventive and personalized medicine (PPPM). To achieve the practical implementation of PPPM concept, it is necessary to create a fundamentally new strategy based upon the subclinical recognition of biopredictors of hidden abnormalities long before the disease clinically manifests itself. This strategy would give a real opportunity to secure preventive measures whose personalization could have a significant influence on demographics. The first discriminatory step illustrating the PPPM-oriented survey is estimating of the correlation strength between genetic polymorphism and risks of the disease, and subsequent construction of groups at risks. As a result, a patient or a person-at-risk would become a data carrier, and the physician can reasonably select of preventive protocol, proceeding from the assays made. Individuals, selected at the first stage, undergo the second phase of the survey, which uses a panel of phenotypic biomarkers. Etiopathogenesis of autoimmune diseases (in particular, at its subclinical stage) is still poorly known despite in-tensive research of mechanisms of autoaggression. Two examples of autoimmune conditions areT1D (type 1 diabetes) and MS (multiple sclerosis).T1D is a chronic autoimmune disease resulting in a destruction of pancreatic beta-cells capable alone of producing insulin. About half of the total risk is genetic and to be used for gene-based predictive testing and getting the proper genomic biomarkers identified. Subclinical stages are determined by identification of proteomic-related biopredictors, i.e., anti-islet auto Abs whose presence would determine risks and time points for initiating subclinical abnormalities. MS is an autoimmune disorder of the central nervous system (CNS) resulting in a destruction of neuro-myelin compartment and de-velopment of disability. Most of the studies confirmed the supreme role of the variations within HLA genes as MS gene-related risk factors and the proper genomic biomarkers identified. The crucial step in the MS evolution is a primary myelin damage which is mediated by cytotoxic anti-myelin auto Abs. A portion of those are auto Abs against myelin-basic protein/MBP en-dowing with MBP-targeted proteolytic activity (so-called, Ab-proteases). Screening for those biomarkers could become the next step to secure subclinical diagnosis of MS and to predict the clinical course. The information harvested can be used to tailor prevention. The strategy of the latter of, for chronic autoimmune diseases should contain two critical steps: (i) Arrest of auto-agression; and, (ii) restoration of structure and functions of the tissue affected. The strategy mentioned can be accomplished by: (i) gene therapy, (ii) immune-mediated therapy, and/or (iii) stem cells technologies.
Trevor G Marshall
Autoimmunity Research Foundation, USA
Title: Post-infectious autoimmune syndrome (PIFAS) as a predictive and a diagnostic factor to monitor chronic diseases of infectious and autoimmune origin (CDIO)
Biography:
Trevor G Marshall graduated from the University of Adelaide, South Australia. His Doctoral thesis has been titled with ‘Insulin metabolism in Diabetes’. Currently, he is Director of the Autoimmunity Research Foundation in California. He has won US FDA designations for Minocycline and Clindamycin in the treatment of Sarcoidosis. He is a Fellow of the European Association for Predictive, Preventive and Personalized Medicine, Brussels and a Member of the International Expert Council, Community of Practice: Preventative Medicine, Moscow.
Abstract:
Even though chronic inflammatory disease can comprise 70% of a nation's health budget, its molecular mechanisms have remained elusive. Without a clear pathogenic description, the available treatments for autoimmune, neurologic, and even psychiatric diagnoses have remained marginally effective. Preventative and predictive medicine has been stalled at the starting-gate. With meta-genomics, came the understanding that man is a super-organism, a community of thousands of species of microbes functioning in homeostasis with the human genome. Proteomics and Metabolomics have built on this foundation with the knowledge that even seemingly similar diseases result not from a single transcriptional dysfunction of DNA, but from thousands of dysfunctional interactions between the host and its micro-biome the ‘Interactome’. Antibodies are produced against components of the human micro-biome, so we all possess antibodies, even in the absence of disease. Antibody poly-specificity causes some of these to become auto-antibodies, with a definable autoimmune target. The ELI-Viscero panel, for example, measures 24 auto-antibodies which are part of a normal healthy human body, often called “natural” auto-antibodies. It appears that their proper homeostasis is essential to maintenance of a healthy body. Inflammation generated by other autoantibodies can lead, over time, to a diagnosis of chronic disease, or to an inflammatory cancer. Fortunately, the retargeting of an approved drug (Olmesartan Medoxomil) has allowed quick translation of immune-stimulative, rather than immunosuppressive therapies, resulting in a clinical paradigm shift, and improved opportunities for rapid molecular discovery.
Mandrik Mark
I.M. Sechenov First Moscow State Medical University, Russia
Title: Viral myocarditis as a model to clearly demonstrate the impact and role of the human endomicrobiota changes into the development of chronic autoimmune diseases
Biography:
Mandrik Mark is a student of I.M. Sechenov First Moscow State Medical University. He is a Member of Young Research Team under the aegis of EPMA (Brussels, EU) and ISPM (Tokyo, Japan). He is an author of serial articles about PPPM. He is also a Developer of several multimedia guides to Chemistry and Microbiology. His sphere of interests is meta-genomics, microbiology & immunology, autoimmune and chronic diseases.
Abstract:
Myocarditis is a chronic disorder with an autoimmune component which characterized by inflammation, decrease in myocardial function and damage of the heart muscle. In the case of no treatment, this process may lead to end-stage cardiac failure and death. Several thousand patients per year are diagnosed with this condition. Understanding that myocarditis is a disease of adult and pediatric patients make the situation worse. Experts believe that 5% to 20% of all cases of sudden cardiac death in children and young adults are due to myocarditis. Although inflammatory cardiomyopathy is more common among men, there is no convincing evidence of a genetic predisposition to the development of this disease. Moreover, the biomarkers, which certainly predict myocarditis development before manifestation are still unknown. Although, the exact causes of an individual case of myocarditis are not identified, it is possible to conclude that the main case of the myocarditis development is an infection while molecular mimicry is a mechanism of autoimmunity progressing and therefore development of chroniÑ disorders. Consequently, the question “Could the changes in the human endomicrobiome be an inducing factor in the myocarditis development?” is still open. The PIFAS (post-inflectional autoimmune syndrome) conception can throw light on the mechanism of viral myocarditis progressing. But only creating and clear understanding with bioinformatics instruments, full pathologic pathways maps enable to find biomarkers of novel generation, determine targets and discover high-efficient drugs based on personalized features.
Borovikov Artem
I.M. Sechenov First Moscow State Medical University, Russia
Title: Autoimmunity and autoimmune disorders-genomics and genome-based applications to set up biobanks networks and to secure genetic passportization
Biography:
Borovikov Artem is studying at I.M. Sechenov First Moscow State Medical University in the Faculty of Medicine since 2010. He is interested in human genetic and application of genomics technology in clinical use. He is also a Member of Young Professional section of EPMA and have several publications in Life Science Journals.
Abstract:
The number of people suffering from autoimmune diseases increases every year. Active growth related with two problems: Initial symptoms are often intermittent, unspecific until the condition becomes acute and a shortage of methods for the preclinical diagnostics. Discovering new biomarkers for early prediction and diagnosis is a chance for control rate and courses of autoimmune disease. The development of most autoimmune diseases includes a strong heritable component. Genetic contribution to autoimmunity is often complex interactions different genes and their products. Genomics based research can give a lot of new information about the potential risks and compounds, those can be optimal biomarkers of early prediction and indicate stage more accurately. But researchers need a lot of data to achieve real goals. Today most of the studies usually are disease-specific and limited in resources. More information-sharing and crossover among research projects on different autoimmune diseases is needed to stimulate them effectiveness. Biobanking is a primary tool for ensuring easy availability of high-quality biomaterial collections that combine essential samples and epidemiological, clinical and research data for autoimmune disease. In some cases, individual biobanks often do not have the required number of well-characterized donor materials. Possibly, the solution of this problem is networking some biobanks merging their records and evaluating them collectively. This method gives access to larger cohorts than would be possible through individual biobanks. It is opening new horizons for researchers but creating networks makes a new problem with legal, ethical and financial aspects of them work.
Irina Zhegalova
I.M. Sechenov First Moscow State Medical University, Russia
Title: Application of bioinformatics in autoimmune disorders for identifying druggable pathways and promising targets
Biography:
Irina Zhegalova is a student I.M. Sechenov First Moscow State Medical University, School of Pharmacy. She is a Member of Young Research Team under the aegis of EPMA (Brussels, EU) and ISPM (Tokyo, Japan). She is interested in bioinformatics and performs researches in application of this branch to PPPM model.
Abstract:
Targeted therapy is based on the binding of the target molecule which blocks or modifies the action of the target. The roofs of such a treatment are laid deeply in drug discovery e.g., the process by which drugs are designed or discovered. Creation of product from the original idea takes 12-15 years and costs up to $1 billion. Past records have indicated that the high failure rate (only 8% of success) of drug development can be attributed to the improper target pre-selection. So target discovery is the most crucial step in the modern drug discovery campaign. In this sense, autoimmunity is often caused by concomitant dysfunctions and imbalances at once. Due to the complicated nature of autoimmunity which is manually infeasible when examined on the proteomic level, researchers often employ machine learning methods to identify solutions. Machine learning approach allows to collect a set of samples “training data” which specify the correct output for a given input. A machine learning algorithm takes these examples and produces a program which may work with other sets perfectly. Bioinformatics provides completely new approaches which involve an artificial intelligence to target discovery process. Data mining of available biomedical data has led to a significant increase in target identification. Therefore, data mining would allow for using bioinformatics not only in identifying but also in selecting and prioritizing potential targets.
Alisa Petkevich
I.M. Sechenov First Moscow State Medical University, Russia
Title: Systemic autoimmune disorders: SLE and RA as an illustration of the clinical and predictive value of DNA-abzymes as unique biomarkers of newer generation to monitor the disorders at subclinical and clinical stages and to manage the disorders
Biography:
Alisa Petkevich has graduated from I.M. Sechenov First Moscow State Medical University and she is currently pursuing Post graduation in Experimental Oncology in N.N. Blokhin Russian Oncological Research Center; being involved into implementation of the national grants attributed to biomarkers as applicable to predictive diagnostics of the diseases.
Abstract:
Rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE) are examples of systemic autoimmune rheumatic diseases (sARDs) which are thought to develop as a result of the autoimmunity-related control mechanisms failure where the tolerance breakage would dominate. Biomarkers to suit the clinical standards and practical requirements should fit into the concept of PPPM and evidently demonstrate their high specificity, accuracy, sensitivity and reproducibility. One of the putative and unique biomarkers of the latest generations to secure the reliable monitoring of sARDs at both clinical and subclinical stages of the disorder (either SLE or RA) are appearing to be DNA-abzymes i.e., DNA-hydrolyzing auto antibodies (auto Abs) of IgG class exhibiting catalytic activity. However, most of sARDs tested in particular SLE and RA have a typical subclinical stage preceding to the canonical clinical manifestations which in turn are usually accompanied by the presence of the disease-related biomarkers to correlate with the initiation and propagation of the autoimmune condition. Among those biomarkers, catalytic auto Abs including DNA-abzymes are initially registered in sera of the persons tested at the subclinical stage (with no clinical signs) to let us speak about DNA-abzymes as subclinical and predictive biomarkers to correlate further with symptoms of the clinical illness. The presence and levels of those DNA-abzymes in sera of SLE and RA patients with different forms of the disease and in sera of the persons-at-risk illustrating the subclinical (symptom-free) stage to be transformed further into the clinical one could facilitate manipulations to secure reliable procedures of getting the right diagnosis put in time to predict the relapse or exacerbations, to control the clinical course and thus the drug dosing process and finally to monitor the subclinical and clinical courses and to manage the drug responses and the pathology development as a whole as well.
Dmitrii Cherepahin
I.M. Sechenov First Moscow State Medical University, Russia
Title: Organ-specific autoimmune disorders: Translational biomarkers to confirm the diagnosis and to predict chronification and disabling
Biography:
Dmitrii Cherepakhin is a student of I.M. Sechenov First Moscow State Medical University. He is a Member of Young professional group in structure of EPMA. He was participant and speaker of two international congress about predictive-preventive and personalized medicine (PPPM) in Bonn and in Brussels. He is the author of serial articles about PPPM in cardio-vascular pathology and nowadays his activity leads his work in genetic and in predictive and preventive medicine.
Abstract:
Autoimmune myocarditis (AIM) usually develops in genetically predisposed individuals infected with CVB3 or related viruses to represent typical manifestations of molecular mimicry. Clinical manifestations of AIM with distinct onset vary from being asymptomatic to fatal. The biomarkers to predict the course at initial presentation have not yet been established. An improved knowledge of the mechanisms of infections to proceed with the illness should help to get type of post-inflectional autoimmune syndrome (PIFAS). PIFAS defined and then be used as a combinatorial biomarker to develop preventive strategies for quenching PIFAS at the subclinical stages. The etiology of autoimmune thyroiditis (AIT) is multifactorial and is due to the development of autoimmunity against thyroid antigens. The AITs are prototypical organ-specific autoimmune disorders but the mechanisms to trigger those autoimmune responses are not clearly known. PIFAS would be a tool to secure subclinical diagnosis of AIT and it will be new paradigm of diagnosis. Simple biomarkers that are used to assess CDIO as a multifactorial disorder are effective once the disease is well established but none, thus far is reliable for the detection of the pre-early (subclinical) manifestations. The concept of combinatorial biomarkers illustrates biomarkers to unite integral components of different but logically combined functionality. Therefore, future efforts should be focused on the validation of the combinatorial biomarkers i.e., demonstration of their close correlation to the pathological process.
Sergey Suchkov
I.M.Sechenov First Moscow State Medical University, Russia
Title: Tissue-specific autoimmune disorders: Antibody-proteases as a generation of highly informative and unique biomarkers to monitor subclinical and clinical stages of demyelination in multiple sclerosis (MS)
Biography:
Sergey Suchkov graduated from Astrakhan State Medical University and was awarded with MD. In 1985, Suchkov obtained his Ph.D. He is the PhD student of the I.M. Sechenov Moscow Medical Academy and Institute of Medical Enzymology, USSR Academy of Medical Sciences, Moscow, Russia. In 2001, Suchkov finished the PostDoc Research Fellowship Program and maintained his Doctor Degree at the National Institute of Immunology, Russia. From 1987 through 1989, Dr. Suchkov was a senior Researcher, Lab of Developmental Immunology, Koltzov Institute of Developmental Biology, USSR Academy of Sciences to deal to developmental immunology. From 1989 through 1995, Dr. Suchkov was being a Head of the Lab of Clinical Immunology and Immunobiotechnology, Helmholtz Eye Research Institute in Moscow. From 1995 through 2004, Dr. Suchkov was being a Chairman of the Department for Clinical Immunology, Moscow Clinical Research Institute (MONIKI) and the Immunologist-in-Chief of the Moscow Regional Ministry of Health. At present, Dr Sergey Suchkov, MD, PhD, is Professor in Immunology, Department of Pathology, School for Pharmacy, I.M. Sechenov First Moscow State Medical University, Dean of the Department (Faculty) of The PPPM Development, and the First Vice-President of the University of World Business, Politics and Law and Secretary General, United Cultural Convention (UCC), Cambridge, UK.
Abstract:
Most autoimmune disorders including multiple sclerosis (MS) are preceded by a symptom-free subclinical stage in which the patients can be identified by specific auto Abs. Proteolytic Abs are multivalent immunoglobulins (Igs) endowed with a capacity to proteolyze the antigenic substrate. Abs against myelin basic protein/MBP endowing with proteolytic activity (Ab-proteases) are of great value to monitor demyelination to illustrate the evolution of multiple sclerosis (MS). Anti-MBP auto Abs from MS patients and mice with EAE (SJL and C57BL/6 mice as an animal model of MS) exhibited specific proteolytic cleavage of MBP The activity of the Ab-proteases markedly differs between: (i) MS patients and healthy controls; (ii) different clinical MS courses; (iii) EDSS scales of demyelination to correlate with the disability of MS patients to predict transformation prior to changes of the clinical course. The sequence-specificity of Ab-proteases demonstrates five sites of preferential proteolysis to be located within the immunodominant regions of MBP. Those sites are located within the immunodominant regions of MBP; and two of them falling inside the sequence covering a 81-103 peptide segment and its 82-98 subsegment as well, with the highest encephalitogenic properties both to act as a specific inducer of EAE and to be attacked by the MBP-targeted Ab-proteases very often in MS patients with the most severe (pro-gradient) clinical courses. Meanwhile, sites localized within the frame of 43-68 and 146-170 subsegments whilst being less immunogenic happened to be EAE inducers very rare but were shown to be attacked by Ab-proteases very often in MS patients with moderate (remission-type) clinical courses. In moderate courses, Ab-proteases focus their proteolytic effect on low-immunogenic 43-68 и 146-170 sites but in aggressive cases (progradient courses), the proteolysis was prevailed on highly-immunogenic 81-103 and 82-98 sites. The activity of Ab-proteases was first registered at the subclinical stages 1-2 years prior to the clinical illness. About 24% of the direct MS-related relatives (probands) were seropositive for low-active Ab-proteases from which 38% of the seropositive relatives established were being monitored for 2 years whilst demonstrating a stable growth of the Ab-associated proteolytic activity. Moreover, we see also low-active Ab-proteases (to target 43-68 and 146-170 sites) in persons at MS-related risks (at subclinical stages of MS), and primary clinical and MRT manifestations observed were coincided with the activity to have its mid-level reached. And registration in the evolution of highly immunogenic Ab-proteases to attack 81-103 and 82-98 sites predominantly would illustrate either risks of transformation of subclinical stages into clinical ones, or risks of exacerbations to develop. The activity of Ab-proteases in combination with the sequence-specificity would confirm a high subclinical and predictive value of the tools as applicable for personalized monitoring protocols. Moreover, Ab-proteases can be programmed and re-programmed to suit the needs of the body metabolism. Of tremendous value are Ab-proteases directly affecting the physiologic remodeling of tissues with multilevel architectonics (for instance, myelin). By changing sequence specificity of the Ab-mediated proteolysis one may reach minimizing scales of demyelination. Further studies on targeted Ab-mediated proteolysis may provide a supplementary tool for predicting demyelination and thus the disability of the MS patients.
- Workshop - Preserving urinary proteins and nucleic acids on membrane
Session Introduction
Youhe Gao
Beijing Normal University, China
Title: Saving urinary proteins and nucleic acids on a piece of membrane simply and economically
Biography:
Youhe Gao is a Professor, Beijing Normal University. He received his MD from Peking Union Medical College, his PhD from University of Connecticut and Postdoctoral training from Beth Israel Deaconess Medical Center Harvard Medical School. He was the professor of Department of Pathophysiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences/ Peking Union Medical College from 2001-2014. His research interests include biomarker discovery in urine proteome, protein interaction and related bioinformatics.
Abstract:
Urine has become more and more recognized as important biomarker source in biomarker discovery. By nature, urine accumulates all kinds of changes and changes are the most basic property of biomarker. In this sense, theoretically urine can be even better biomarker source than blood. There may be a urine biomarker era ahead of us. Even though metabolites were analyzed extensively as potential biomarker in urine, proteins and microRNAs may possess more specificity of the diseases. Saving proteins and nucleic acids were challenging because they not only took huge space but also gradually degraded even frozen in -80 degree. Here we present a simple and economical method that make storing large number of urinary proteins and nucleic acids clinical samples possible. Urine samples were filtered through the membrane, and urinary proteins were adsorbed onto the membrane. The membrane used can have high affinity to proteins or nucleic acids. Then the membrane was dried and stored in a vacuum bag, which kept the protein and microRNA faithfully preserved. The membrane may even permit storage at room temperature for weeks. This simple and inexpensive method requires minimal sample handling, uses no organic solvents, and is environmentally friendly. With this method, large number of samples will be available to biomarker discovery and validation. Biomarker research can be significantly more efficient. There has not been any new form of tissue preservation for years. This membrane, which we call urimem, may be kept with medical record of all consenting people in the future.
- Young Researchers Forum
Chair
Jens Wiltfang
Georg August University Göttingen, Germany
Session Introduction
Landoni E
University of Milan, Italy
Title: A comprehensive pipeline for biomarker discovery using circulating miRNA microarray data
Biography:
Landoni E, third-year PhD student at the University of Milan, works as biostatistician at the Fondazione IRCCS Istituto Nazionale dei Tumori in Milan. Her research project involves the application of machine learning methods for the analysis of high-dimensional ‘omics’ data. In particular, her research is focused on the discovery and development of cancer molecular biomarkers, focusing on the implementation of feature selection algorithms together with the use of original and simple graphical representations of the results. Another area of her interests is nonparametric statistics, applied in particular to the fields of molecular biology and personalized medicine.
Abstract:
Circulating miRNAs have the potential as cancer biomarkers but no consolidated guidelines are established for discovery analyses. Several issues (e.g. data normalization, expected miRNA up-regulation in one of classes, sample size limitation) can affect results making many approaches unsuitable. We developed a structured pipeline with innovative applications of existing bioinformatics methods including: 1) an assumption-independent normalization method based on miRNA ratios in data pre-processing; 2) the combination of the results of two statistical tests (t- and Anderson Darling) to detect miRNAs with significant fold change or general distributional differences in class comparison; 3) the application of a bootstrap selection procedure together with machine learning techniques to guarantee result generalizability and study the inter connections among the selected miRNAs in class prediction. We applied the pipeline to compare hemolized and non-hemolized plasma samples, identifying four miRNAs known to be hemolysis-related (miR-486-5p, miR-92a, miR-451, miR-16) together with a new one, miR-22.
Jing Zhang
Royal Military College of Canada, Canada
Title: Mammalian hair follicles: Insights into microRNAs as a Traumatic Brain Injury (TBI) biomarker
Biography:
Jing Zhang is a recent PhD graduate from Carleton University under Dr.Kenneth Storey’s supervision and joined Dr.Valerie Langlois’ group as a Postdoctoral fellow in the fall of 2013. His field is molecular physiology and previous work includes investigating molecular mechanisms behind survival adaptions under extreme environmental conditions in various stress tolerant animal models. Currently, he is focusing on exploring the potential of hair follicle as a diagnostic tool for military activity-related medical conditions including traumatic brain injury (TBI) and operational stress disorders using transcriptomic approaches.
Abstract:
With the wide adoption of explosive-dependent weaponry, blast-induced traumatic brain injury (TBI) has become a significant medical issue for military personnel. Recently, the implementation of microRNAs (miRNA) as a clinical biomarker has proposed for diseases including several types of cancer. The interaction between miRNAs and their corresponding mRNA targets usually leads to translational silencing or mRNA degradation. This work investigates the involvement of miRNAs in primary shockwave-induced TBI responses in rat whisker follicles. With an advanced blast simulator, we assess the molecular responses in the whisker follicles in the rat model that was expose under a series of single blast intensities (15, 20, 25 and 30 psi). Gene networks for miRNA-dependent gene expression were constructed using sub-network enrichment analysis (SNEA) with respect to shared and shockwave intensity-specific microarray transcription profiling. Based on the SNEA analysis, core miRNAs (miR-26a, -27b, -29a, -34a, -181c and -183), were measured using quantitative RT-PCR. All the miRNA levels tested decreased in abundance in the whisker follicles following shockwave exposures. The results suggest shared responses across multiple intensity exposures, example miR-183 in all intensities, whereas exposures at 15 and 20 psi triggered specific miRNA expressions, i.e., miR-29a and -34a respectively. Multiple pathways and biological processes (example DNA repair and mRNA processing), were enriched following a gene set enrichment analysis (GSEA). Our study provides the first evidence that miRNAs are responsive to shockwave exposures in mammalian hair follicles and these molecules may be useful biomarkers for primary blast-induced TBI.
Surasawadee Ausavarat
Mahidol University, Thailand
Title: Efficacy of TSHR mRNA as a tumor marker in the follow-up of differentiated thyroid cancer
Biography:
Surasawadee Ausavarat has completed her Ph.D in Human Molecular Genetics from Chulalongkorn University, Thailand. Her research interests are human disease gene identification and characterization. Currently, she is a lecturer of Nuclear Chemistry Laboratory, Division of Nuclear Medicine and her current research is directed toward determining a molecular marker for thyroid cancer. She has published more than 7 papers in international peer journals.
Abstract:
Objectives: Measurement of serum thyroglobulin (sTg) by immunoassay is used as a tumor marker for differentiated thyroid cancer (DTC); however, the possible interference of endogenous anti-thyroglobulin antibodies (TgAb) and low sensitivity during thyroid hormone suppression may limit its clinical usefulness. Therefore, many researchers have evaluated the efficacy of thyroid-transcripts by molecular assay instead. Here we investigated the efficacy of thyroid-stimulating hormone receptor (TSHR) mRNA during thyroid hormone suppression especially in TgAb-positive patients.
Methods: We studied 160 patients with differentiated thyroid cancer and 27 normal subjects without history of thyroid disease. All patients had undergone near-total thyroidectomy and radioactive iodine ablation. Of the 160 patients, 49 (30.6%) were classified as in-remission, 111 patients (69.4%) were disease-persistence, of which, 27 patients (24.3%) were TgAb-positive. Quantification of TSHR mRNA was performed using real-time PCR.
Results: Median TSHR mRNA level of in-remission group was significantly different from disease-persistence in TgAb-positive patients, particularly in distant metastasis patients. Analysis of TSHR mRNA at 2.00 pgEq/µg total RNA enabled us to discriminate between remission and disease-persistence at sensitivity of 88.9% and specificity of 42.9%. However, there is no correlation between level of TSHR mRNA and sTg or TSHR mRNA and TSH in all groups.
Conclusion: We demonstrated that TSHR mRNA has greater sensitivity in prediction of disease-persistence in TgAb-positive patients than sTg during thyroid hormone suppression. Further study should emphasize the cost-effectiveness of routine usage of the assay in clinical practice.
Biography:
Mahjoubeh Jalali Sefid Dashti has completed her PhD in the field of Bioinformatics at the South African National Bioinformatics Institute, University of Western Cape and is currently continuing with her Post-doctoral studies at the same Institute. Her research interest lies in biomarker discovery through the application of clinical next generation sequencing in identifying the genetic cause of multifactorial and rare disorders. She is involved in a number of groundbreaking research projects including distal muscular dystrophy, ALS-motor neuron disease, Myasthenia Gravis, post-traumatic stress disorder, maturity onset diabetes of the young and atypical breast cancer in Africans.
Abstract:
Distal muscular dystrophy (DD) is a group of genetic muscle-wasting disorders resulting in distal muscle weakness. Candidate gene and region approaches have identified several different causative mutations in a number of families with different recent ancestry. Here, we report on novel functional variants that are strong candidates as the genetic cause of a unique form of autosomal dominant DD in a South African family of admixed ancestry. We performed whole exome sequencing in five affected family members and two (one related and one unrelated) controls which identified ~80000 exonic and splicing variants in each targeted exome. As the disease displays an autosomal dominant pattern of inheritance in the family, we hypothesized that the causative mutation was likely to be a novel heterozygous variant. Therefore, in addition to identifying variants shared by the affected members yet absent in the controls, we also filtered out variants seen in the public SNP databases. This resulted in 124 variants that were further filtered based on their potential deleterious impact on the encoded protein or were at a conserved site to arrive at nine functional nsSNPs and four INDELs. As it did not link any of the mutations to known muscular dystrophy genes, our in-house BioOntological Relationship Graph (BORG) semantic database was used to assess their potential indirect links to the disease based on their documented roles in gene functions, pathways and clinical/knockout phenotypes relevant to DD. This variant prioritization strategy resulted in the identification of two novel mutations that are strong candidates for being the cause of the novel autosomal dominant form of DD.
Sewa Rijal
Monash University, Australia
Title: Inositol polyphosphate 4-phosphatase II (INPP4B) is associated with chemo-resistance and poor outcome in AML
Biography:
Sewa Rijal has completed her PhD from Monash University. She recently published her work in the prestigious journal, blood of identifying a novel prognostic biomarker protein known as INPP4B in acute myeloid leukemia. Her work was part of an inside blood commentary and also highlighted in the Australian media by ABC news as a major breakthrough. Her finding has important implications in defining prognosis and treatment options for AML patients. She is currently undertaking Post-doctoral studies to understand the mechanism of INPP4B-mediated chemo-resistance in AML so that novel therapeutics may be designed for patients who fail chemotherapy.
Abstract:
Acute Myeloid Leukemia (AML) is an aggressive blood cancer that is usually fatal within weeks without effective therapy. Current treatment with standard chemotherapy agents fail to elicit complete clinical responses in 20-30% of cases. An understanding of the mechanisms that mediate resistance to chemotherapy in AML may uncover new onco-proteins amenable to medicinal targeting. Activation of the phosphoinositide 3-kinase (PI3-K)/AKT pathway is prevalent in AML and linked to chemotherapy failure and poor outcomes. Homeostatic regulation of PI3K activity is orchestrated by a triad of lipid phosphatases, categorized functionally as 3-, 4-, or 5-phosphoinositide phosphatases. The biological relevance of most of these phosphoinositide phosphatases in acute myeloid leukemia (AML) remains poorly understood. Mass-spectrometry based gene expression profiling of 3-, 4- and 5-phosphatases in human AML revealed significant overexpression of INPP4B. Analysis of an expanded panel of 205 AML cases at diagnosis revealed INPP4B overexpression in association with reduced responses to chemotherapy, early relapse and poor overall survival independent of other risk factors. Ectopic overexpression of INPP4B conferred leukemic resistance to cytosine arabinoside (ara-C), daunorubicin and etoposide. Expression of a phosphatase inert variant (INPP4B C842A) failed to abrogate resistance of AML cells to chemotherapy in vitro or in vivo. In contrast, targeted suppression of endogenously overexpressed INPP4B by RNAi sensitized AML cell lines and primary AML to chemotherapy. These findings demonstrate a previously unsuspected and clinically relevant role for INPP4B gain-of-function as a mediator of chemo-resistance and poor survival outcome in AML independent of its phosphoinositide phosphatase function.