Time: 08:00 PDT (UTC-7), 11:00 EDT (UTC-4), 15:00 UTC, 17:00 CEST (UTC+2), 01:00 AET (UTC+10)(October 19)
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Chair: Henry Rodriguez, National Cancer Institute, National Institutes of Health, USA
Co-chair: Yu-Ju Chen, Institute of Chemistry, Academia Sinica, Taiwan
Speaker: Matthew Ellis, MB., BChir., Ph.D., FRCP, Baylor College of Medicine, USA - New Prospects for Killing ER+ Breast Cancer (Micro-scale Proteogenomics)
Speaker: Amanda Paulovich, MD, PhD, Fred Hutchinson Cancer Research Center, USA - Building New Clinical Solutions for Precision Oncology via Proteogenomics
Speaker: Albert Sickmann, PhD, Leibniz-Institut für Analytische Wissenschaften-ISAS, Germany
Ever since the announcement of the Precision Medicine Initiative, there have been increasing efforts to identify and understand the basis of cancer using high-throughput technologies and the development of specialized treatments for specific subtypes of cancer, based on molecular evidence. Clinical proteogenomics is an exciting opportunity to complement the gene testing-centric clinical community for precision medicine. However, translating proteomic measurements to real-world patient care requires synergy of multiple requirements: meaningful and actionable molecular characterization, clinical and analytical validation, defining diagnosis values, and meeting regulatory compliance.
This HUPO session showcases clinical researchers discussing their stories and strategies to move proteomics towards better patient/clinical care. During this interactive broadcast, learn about the insight of three stories:
New Prospects for Killing ER+ Breast Cancer (Micro-scale Proteogenomics)
Building New Clinical Solutions for Precision Oncology via Proteogenomics
Time: 05:00 PDT (UTC-7), 08:00 EDT (UTC-4), 12:00 UTC, 14:00 CEST (UTC+2), 22:00 AEST (UTC+10)
Co-Chair: Tim Van Den Bossche, Ghent University
Co-Chair: Jean Armengaud, University Paris-Saclay
Metaproteomics from Bench to The Clinic, Daniel Figeys, University of Ottawa
Analysis of Functions Expressed by Microbiomes Using Metaproteomics, Pratik Jagtap, University of Minnesota
Metaproteomics is a key methodology for understanding how microbiomes function. The power of metaproteomics comes from efficient connection of genomic and metabolic information. Through the large-scale characterization of the entire protein complement of microbiota and the functional dynamics of the microbiome, metaproteomics has the potential to unravel mechanistic details and identify key regulators of microbial interactions with the host/environment. Functional characterization offers numerous advantages over nucleic acid-based methods that primarily measure taxonomic composition. However, while the techniques in current use for metaproteomics are fundamentally the same as those used for single-organism proteomics, there are a number of key differences in terms of sample preparation, analysis and data processing/interpretation that require specialized expertise and tools for success in metaproteomics experiments.
Metaproteomics from Bench to The Clinic. The first speaker, Dr. Daniel Figeys, will introduce the human gut microbiome and discuss the advantages of using metaproteomics to better understand the biological processes ongoing in this dynamic microbiome environment. He will use a study of pediatric inflammatory bowel disease as an example.
Analysis of Functions Expressed by Microbiomes Using Metaproteomics. Data analysis of metaproteomics experiments presents unique challenges and requires novel software tools. The second speaker, Dr. Pratik Jagtap, will highlight efforts on the implementation of metaproteomics workflows and their use within the Galaxy bioinformatics platform (https://usegalaxy.org). These workflows analyze both the taxonomic and functional state of microbiomes and generate outputs for biological interpretation.
As Director for the Lester and Sue Smith Breast Center at Baylor College of Medicine I coordinate an interdisciplinary team of oncologists, pathologists, epidemiologists, basic scientists and statisticians focused on improving the prevention, detection and treatment of breast cancer. I bring to this position considerable experience in the oversight and execution of large projects and clinical trials of a collaborative nature on a nationwide basis. I have a strong background in molecular cell biology, molecular pharmacology, genomics and proteomics. I have been an active member of the National Clinical Trials network for over 20 years, and I am a Vice Chair for the NRG Breast Committee. I an Co-leader for The Cancer Genome Atlas (TCGA) Breast Project where I established collaborations with several Genome Centers on massive parallel sequencing of breast cancer (Nature 2010, 2012). I am a PI in the Clinical Proteomic Tumor Analysis Consortium (CPTAC) which is focused on translating proteogenomic findings into improvements in the diagnosis and treatment of breast and other cancers (Nature 2016, Nature Communications 2020, Cell 2020). I am also the principal investigator for the Baylor College of Medicine Breast Cancer SPORE, awarded in 2020. Our SPORE focuses on new treatment approaches for advanced breast cancer.
Dr. Paulovich completed a residency in Internal Medicine at Massachusetts General Hospital and a fellowship in Oncology at Dana-Farber Cancer Institute. She completed her PhD. training in genetics with Dr. Lee Hartwell at the University of Washington and postdoctoral training in genomics at the Massachusetts Institute of Technology with Dr. Eric Lander. As an oncologist, Dr. Paulovich was struck by the paucity of quantitative assays for measuring clinically relevant phenotypes in her patients, and the limitations that this put on her ability to practice “personalized medicine.” Out of these experiences, she became passionate about developing technologies and strategies for the translation of novel diagnostics and therapeutics to enable precision medicine. Over the past 18 years, Dr. Paulovich's interdisciplinary laboratory has focused on proteogenomic approaches to understanding cancer biology and laying the groundwork for the clinical translation of novel diagnostics based on targeted, multiple reaction monitoring (MRM) mass spectrometry.
Pratik Jagtap is a Research Assistant Professor at the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota in Minneapolis, Minnesota, He received his Ph.D. degree in 2000 at the Center for Cellular and Molecular Biology, Hyderabad (India). During his post-doctoral research work at the Max-Planck Institute in Tuebingen and later at the University of Michigan in Ann Arbor, he worked on genomic and proteomic analysis of bacteria. Since 2016 - as a Galaxy-P project co-lead - he has worked with the team to utilize and publish various workflows for multi-omic data analysis. His current research interests include developing workflows for the analysis of complex data, with particular emphasis on MS-based proteomics applications in metaproteomics, proteogenomics, and data-independent acquisition (DIA) data analysis.
Daniel obtained a B.Sc. and a M.Sc. in chemistry from the Université de Montréal. He obtained a Ph.D. in chemistry from the University of Alberta. He did his postdoctoral studies at the University of Washington in Molecular Biotechnology. Daniel was previously Senior Vice-President at MDS-Proteomics and more recently co-founder of MedBiome. Daniel is a Professor and a Distinguished Research Chair in the Department of Biochemistry, Microbiology, and Immunology at the University of Ottawa. He is the co-founding director of the Shanghai Institute of Materia Medica-University of Ottawa Joint Center in Systems and Personalized Pharmacology. He was the founding director of the Ottawa Institute of Systems Biology. His research focuses on the development and applications of technologies and bioinformatic tools to study the human gut microbiome and drug-microbiome interactions. His laboratory has published over 200 papers and has been cited over 17,000 times.
Jean Armengaud is Chief Deputy of the laboratory of Innovative technologies for Detection and Diagnostics located near Avignon in France. He is also Director of the ProGénoMIX platform, specialized in proteogenomics and metaproteomics. He wishes to contribute to a better understanding of the functioning of complex biological systems and exploit this knowledge for medical and environmental purposes. He received his PhD in Biochemistry in 1994 at the University of Grenoble.
Tim Van Den Bossche is working as PhD researcher in the CompOmics lab of prof. Lennart Martens in the field of microbial community proteomics, commonly known as metaproteomics. Here, he led the first-ever, community-driven, multi-site experiment that compared the effects of different state-of-the-art metaproteomics analysis pipelines (wet-lab and computational). Next to this benchmark study, is Tim applying machine learning algorithms on metaproteomics datasets to improve peptide identifications, and downstream taxonomical and functional annotation.
Yu-Ju Chen received Ph.D. degree in physical chemistry from Iowa State University. After postdoctoral work at Ames Laboratory, USA, and National Tsing Hua University, Dr. Chen joined the Institute of Chemistry of Academia Sinica and is currently a Distinguished Research Fellow. She is also the President of Human Proteome Organization, past Vice President of Asia Oceana Human Proteome Organization, past President of Taiwan Proteomics Society and Taiwan Society for Mass Spectrometry. Dr. Chen is the Associate Editor of Analytical Chemistry and editorial board member of the Proteomics and Scientific Report. Towards comprehensive profiling of human proteome, Dr. Chen’s interests focus on integrating nanomaterials, advanced mass spectrometry, and bioinformatics to develop advanced proteomics technologies for quantitative membrane proteomics and protein post-translational modification. She also established an extensive domestic and international collaboration network to apply proteomic methodologies to delineate the disease mechanism in cancer biology.
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