HUPO 2021 World Congress

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Date: October 18, 2021
Title: Real-World Precision Medicine: Proteogenomics to Accelerate Drug Development and Patient Care (90 Minutes)

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)

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, Proteogenomics/Proteomics: Complementing Precision Medicine with Phenotypic Data

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:

  • Microscaled proteogenomics technology for predicting response of triple negative breast cancer
  • Development of robust targeted platforms for clinical laboratory tests, drug development, and clinical trials

New Prospects for Killing ER+ Breast Cancer (Micro-scale Proteogenomics)

Building New Clinical Solutions for Precision Oncology via Proteogenomics

Proteogenomics/Proteomics: Complementing Precision Medicine with Phenotypic Data

  • Speaker: Albert Sickmann, PhD https://www.isas.de/en/institut/abteilungen/personen/albert-sickmann/
  • Overview: Dr. Sickmann will present examples for proteogenomic phenotyping of KRASwildtype and KRASG12V in CRC liver metastases. Several peptides identified in this study represent a number of predicted somatic mutations, including KRASG12V. A tailor-made multiplexed parallel reaction monitoring (PRM) assay was used for precise quantification of mutation rates on the protein level. Such PRM-based tumor-phenotyping might improve patient stratification in the future. He will discuss the impact of regulatory compliance (from a central European perspective) for the translation of proteomics-based biomarkers towards clinical use.
  • Publication: https://doi.org/10.3390/cancers11121907

Date: August 16, 2021
Title: Metaproteomics

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.

Matthew Ellis

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.

Amanda Paulovich

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 MIT.

Daniel Figeys

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.

Jean Armengaud

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 received his PhD in Biochemistry at the University of Grenoble.

Pratik Jagtap

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). His current research interests include developing workflows for the analysis of complex data.

Tim Van Den Boscche

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).

Yu-Ju Chen

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.

Albert Sickmann, PhD

Dr. Sickmann will present examples for proteogenomic phenotyping of KRASwildtype and KRASG12V in CRC liver metastases. Several peptides identified in this study represent a number of predicted somatic mutations, including KRASG12V. A tailor made multiplexed parallel reaction monitoring (PRM) assay was used for precise quantification of mutation rates on the protein level. Such PRM-based tumor-phenotyping might improve patient stratification in the future. He will discuss the impact of regulatory compliance (from a central European perspective) for the translation of proteomics based biomarkers towards clinical use. Publication: https://doi.org/10.3390/cancers11121907

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For any inquiries regarding registration for HUPO ReCONNECT 2021, please contact the Congress Secretariat at hupo2021-registration@icsevents.com

HUPO 2020, HUPO 2020 World Congress, Clinical Proteomics for the Benefit of Patients

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