Please note that more information will be announced shortly in regards to the Keynote Speakers for the HUPO 2021 World Congress.
Session Topic: New Technological Advancements in Proteomics
Presentation Title: The 3D Proteome and the Potential for Conformational Biomarkers
John R. Yates is the Ernest W. Hahn Professor in the Departments of Molecular Medicine and Neurobiology at Scripps Research. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has developed proteomic techniques to analyze protein complexes, posttranslational modifications, organelles and quantitative analysis of protein expression for the study of biology. He has received awards including the ASMS Biemann Medal, HUPO Achievement Award, Christian Anfinsen Award (Protein Society), Analytical Chemistry award (ACS), Ralph N. Adams Award, Thomson Medal (IMSF), John B. Fenn Award (ASMS), HUPO Discovery Award. He is currently the EIC at the Journal of Proteome Research.
Dr. David Fenyö received a PhD in Physics from Uppsala University in Sweden and after switching to computational biology, he did a postdoc at the Rockefeller University, co-founded a bioinformatics company and worked at GE Healthcare. He has over 30 years of experience with all aspects of biomedical data analysis in both academia and industry and his work has resulted in over 180 scientific publications. In 2010 he joined NYU School of Medicine where he is currently Professor of Biochemistry and Molecular Pharmacology, Director for the Ph.D. program in Systems and Computational Biomedicine and the Master’s program in Biomedical Informatics.. His research focuses on applying data science methods to analyze quantitative data and to model biological systems. His efforts to integrate data from multiple technologies—including mass spectrometry, sequencing, and microscopy—have provided a wide array of powerful tools to discover and verify biomarkers and therapeutic targets in cancer.
Session Topic: Spatial Proteomics
Presentation Title: To Be Announced
Session Topic: Post-Translational Modifications
Presentation Title: To Be Announced
Session Topic: To Be Announced
Kathryn Lilley received her PhD in Biochemistry from the University of Sheffield in 1990. After being a laboratory manager at the University of Leicester for eleven years, she established the Cambridge Center for Proteomics, University of Cambridge in 2000. In parallel, she developed a research programme to create technology to measure the dynamics of the proteome in high throughput in space and time during critical cellular processes. Her group has contributed many open-source informatics tools to efficiently mine and visualise complex data which is produced by spatiotemporal proteomics studies.
She became the Professor in Cellular Dynamics in Department of Biochemistry University of Cambridge in 2012. More recently she received a Wellcome Trust Investigator Award to investigate the role the site of translation plays on the protein intracellular location and how this process is controlled. She is also a partner in EPIC-XS, funded as part of the Horizon 2020 Work programme to develop and provide proteomics technologies across Europe, co-ordinated by Prof. Albert Heck.
In 2017 she was the recipient of the Juan Pablo Albar Proteome Pioneer Award from the European Proteomics Association and in 2018 received the HUPO distinguished achievements in proteomics award.
Session Topic: Immunopeptidome
Presentation Title: "Insights into the Tumour Immunopeptidome and its Role in Personalized Immunotherapy"
The use of mass spectrometry to characterise antigen presentation by cancer has undergone a revolution in recent years following the success of check point inhibition and the suggestion that post-therapy there are numerous immune targets revealed on the surface of cancers. I will discuss our approaches for the identification of different classes of antigens and how this information can be used to harness anti-tumour immune responses.
Tony Purcell is an NHMRC Principal Research Fellow and Deputy Head (Research) of the Department of Biochemistry at Monash University. In addition, he is the vice president of the Australasian Proteomics Society and a council member of the Human Proteome Organisation (HUPO). His laboratory focuses on how the diverse array of peptides presented to the immune system, coined the immunopeptidome, is influenced by infection, inflammation and the environment. He has made important contributions to understanding the role of antigen presentation, including the characterizing T cell epitopes, in several autoimmune diseases, drug hypersensitivity, cancer and infectious diseases. He is one of the most cited Australian proteomics researchers and a leader in the field of immunopeptidomics with over 230 related publications.
Session Topic: Single Cell Proteomics
Presentation Title: "Increasing the Sensitivity, Reliability, Reproducibility and Throughput of Single-Cell Proteomics"
Despite the rapid advance of mass-spectrometry methods for single-cell protein analysis, these methods have allowed quantifying mostly abundant proteins. Furthermore, not all proteins are reproducible analyzed in all single cells. I will describe methods that overcome these limitations, and the results of their large-scale application to primary cells and tissues.
Nikolai Slavov’s group seeks principles in the coordination among protein synthesis, metabolism, cell growth and differentiation. The Slavov group has pioneered high-throughput mass-spectrometry methods for quantifying proteins in single cells and is developing new computational methods for analyzing and understanding single-cell proteomics and multimodal data. The group obtained direct evidence for a new regulatory mechanism of protein synthesis (ribosome specialization) and continues to drive research in this emerging field supported by the NIH Director’s New Innovator Award. Nikolai Slavov studied biology and physics at MIT before completing a dissertation at Princeton University (Botstein laboratory) with research focused on the coordination among metabolism, growth and gene expression. Dr. Slavov then returned to MIT (van Oudenaarden laboratory) for post-doctoral research that characterized trade-offs of aerobic glycolysis. Professor Slavov actively organizes community initiatives, such as the annual single-cell proteomics conference, which is a highly interactive and interdisciplinary meeting.
Session Topic: Proteomic Methods
Presentation Title: "Barcoding the Structural Proteome"
Protein structural changes induced by external perturbations or internal cues can profoundly influence protein activity and thus modulate cellular physiology. Mass spectrometry (MS)-based proteomic techniques are routinely used to measure changes in protein abundance, post-translational modification and protein interactors, but much less is known about protein structural changes. In my talk, I will present a structural proteomics method that enables analysis of protein structural changes on a proteome-wide scale and directly in complex biological extracts. The approach relies on the coupling of limited proteolysis (LiP) tools and MS. LiP-MS can detect subtle alterations in secondary structure content, larger scale movements such as domain motions, and more pronounced transitions such as the switch between folded and unfolded states. I will describe how we are applying this approach to study the molecular bases of protein aggregation diseases and to the identification of protein-small molecule interactions (e.g drug targets). I will also propose that monitoring protein structural states on a proteome-wide scale can serve as a new powerful readout to pinpoint altered protein functional states and the (de)regulation of biochemical pathways. Last, I will discuss the power and limitations of the new approach.
Paola Picotti obtained her PhD from the University of Padua, Italy, focusing on the analysis of protein misfolding using biochemical and mass spectrometry-based techniques. She then joined the group of Ruedi Aebersold at ETH Zurich (Switzerland), where she contributed to develop targeted proteomic technologies. In 2011, she was appointed Assistant Professor at the Institute of Biochemistry of ETH and in 2017, moved to the Institute of Molecular Systems Biology of ETH as a tenured professor. The Picotti group develops quantitative proteomics technologies for protein and protein structure analysis. These tools are applied to study intracellular protein aggregation and the molecular bases of aggregation diseases. Paola Picotti was awarded the EMBO Gold Medal, the Rössler prize, the US HUPO Cotter Award, the SGMS award, the EMBO Young Investigator Award, the Friedrich Miescher Award, the Juan-Pablo Albar award of the European Proteome Association, the ETH Latsis Prize and two ERC Grants.
Session Topic: Precision Medicine in Wellness and Disease
Presentation Title: "Proteomic Analysis of Cancer Internal Heterogeneity"
Cancer heterogeneity is one of the major challenges that hampers the ability to cure the disease. Tumors differ in their genetic profiles and the cellular interactions in the microenvironment, and each tumor may have multiple different clones with distinct molecular characteristics. Therefore understanding cancer heterogeneity has major translational implications. In my lab we use mass spectrometry-based proteomics to understand cancer heterogeneity in breast cancer and melanoma. We combine analysis of clinical samples with histopathological analysis and functional validations, to unravel novel regulators of cancer progression. Analysis of hundreds of breast cancer tumor regions associated between clinical parameters and the protein networks, and showed their heterogeneity within single tumors. Our research showed the importance of each clinical feature and the significance of the immune system in affecting tumor heterogeneity. \ These unsupervised proteomic networks set the basis for future improved therapy and precision oncology.
Tamar Geiger studied biology at the Hebrew University of Jerusalem, Israel, where she also completed her master’s and doctoral degrees in biochemistry. She carried out her Ph.D. research under the supervision of Prof. Alexander Levitzki, studying changes in signaling network during early stages of progression of cervical cancer. In 2008 she moved to the laboratory of Prof. Matthias Mann at the Max Planck Institute of Biochemistry to specialize in proteomics technology and to apply it to cancer research. In October 2011, Tami moved back to Israel and opened her own research laboratory at the Sackler Faculty of Medicine at the Tel Aviv University. She is proceeding with clinical proteomic research of breast cancer, melanoma, and ovarian cancer with emphasis on cancer progression, drug response, and tumor heterogeneity. Furthermore, her lab emphasizes development of technologies to advance analysis of clinical samples, including tissues and body fluids, as the basis for biomarker discovery. In addition to her research work Tami is also a member of the steering committee of the Israel Young Academy.
Session Topic: Liver Diseases
Presentation Title: "Next Generation Proteomics to Fight Liver Diseases"
Liver has a remarkable regeneration capacity that allows an efficient repairing of the hepatic parenchyma after suffering an injury. Combined proteomic analysis of mouse models and human samples allowed identification of early drivers of liver regeneration that explain some of the of functional deficiencies associated to the severe syndrome of ABCB4 deficient patients, who require liver transplantation during the first years of life. Besides, dynamic changes of serum proteome have been monitored after liver resection in cases of living donor liver transplantation (LTDT). Mass spectrometry targeted analysis allow mapping the regulation of over 500 circulating proteins across liver regeneration phases and recapitulates the molecular and cellular events taking place during this well-orchestrated process. Integration of these results provided the basis for a precision medicine approach to manage ABCB4 patients and to improve LDTD safety.
Fernando Corrales earned his BSc degree in Biological Sciences and PhD degree in Biochemistry and Molecular Biology by the University Autónoma of Madrid. After a Postdoctoral at the University of Cambridge (UK), he joined the CIMA, University of Navarra where he was Professor of Biochemistry and head of the Proteomics, Genomics and Bioinformatics Facility. He is Senior Scientist and head of the Proteomics Laboratory at the Centro Nacional de Biotecnología. His interest are the mechanisms underlying liver function and liver diseases using proteomics. His research activity has been regularly founded and lead to the publication of 166 scientific articles. He is member of the editorial board of several proteomics and hepatology journals, General Coordinator of ProteoRed-ISCIII (Spanish Proteomics Network), Founder and Vice-President of the Spanish Proteomics Society, member of the EuPA EC, BD and C-Human Proteome Project ECs and PI of the Human Liver Proteome Project and the chromosome 16 Spanish Human Proteome Project.
Session Topic: Life Stages
Presentation Title: "The Aging Brain Proteome"
A progressive loss of protein homeostasis is characteristic of aging and a driver of neurodegeneration. To investigate this process quantitatively, we characterized proteome dynamics during brain aging in the short-lived vertebrate Nothobranchius furzeri combining transcriptomics and proteomics. We detected a progressive reduction in the correlation between protein and mRNA, mainly due to post-transcriptional mechanisms that account for over 40% of the age-regulated proteins. These changes cause a progressive loss of stoichiometry in several protein complexes, including ribosomes, which show impaired assembly and are enriched in protein aggregates in old brains. Mechanistically, we show that reduction of proteasome activity is an early event during brain aging and is sufficient to induce proteomic signatures of aging and loss of stoichiometry in vivo. Our work defines causative events in the aging process that can be targeted to prevent loss of protein homeostasis and delay the onset of age-related neurodegeneration.
Alessandro Ori holds a PhD in Biochemistry and he was a postdoctoral fellow at the European Molecular Biology Laboratory in the laboratory of Martin Beck. During his postdoc, he applied mass spectrometry-based proteomics to answer fundamental questions in the fields of structural and systems biology, and pioneered the integration of omics data to study aging. He joined the Leibniz Institute on Aging in Jena in September 2015 where he is leading a junior research group and heading the proteomic unit. His lab focuses on (i) understanding how aging predisposes to the onset of neurodegenerative disorders by impairing protein homeostasis, and (ii) how the cross-talk between adult stem cells and their niches is affected by aging leading to reduced regenerative capacity of old organs.
Concha Gil is Professor of Microbiology, Scientific Coordinator of the Proteomics Unit and Director of the Research Support Centers at the Complutense University of Madrid. Her research activity is focused on the host-pathogen interaction study and on the development of new strategies for the diagnosis of infectious diseases using invasive candidiasis as a model. Both, pathogen and host responses are evaluated at different molecular and particularly proteomic approaches such as shotgun proteomics, quantitative proteomics and targeted proteomics. Some of these investigations had unveiled the apoptosis of C. albicans inside the macrophages that was compared with other apoptotic inducers. In addition, extracellular C. albicans vesicles are being studied as vaccine candidates. Concerning the diagnosis of invasive candidiasis, her group has identified different biomarkers of diagnosis using immunoproteomics and machine learning, some of them had been validated. She participates in the Human Proteome Project, where she co-coordinates the Infectious Diseases Initiative.
Session Topic: Chemical Proteomics
Presentation Title: "Exploring Drug-Target Interaction and its Translational"
Exploring protein targets of drugs and deciphering the specific mechanisms-of-action at the molecular level of these interactions are crucial steps in the development of drugs to treat human diseases. We have developed target protein identification methods including conventional affinity chromatography using labeled small molecules as well as recent method using label-free small molecules such as Drug Affinity Responsive Target Stability (DARTS) in combination with LC-MS/MS analysis to identify the direct binding proteins of drugs. The direct interaction between drug and the target protein is validated via bio-physical, and bio-informatics methods. Moreover, biological relevancy of this “drug-target” interaction is verified through genetic modulation that facilitates structure based better drug development. In this presentation, our studies on target identification of drug-target interaction for exploring new mechanism studies and translational applications will be presented by introducing our case studies of protein target identification and validation of clinical drugs and natural products perturbing autophagy.
Ho Jeong Kwon graduated from Seoul National University (BSc, Korea) and did MS and PhD from University of Tokyo (Japan) and postdoctoral training at Harvard (USA). He returned to Korea in 1999 and promoted to full professor in 2008 at Yonsei University. He has been director of GRL and serving as an adjunct professor, College of Medicine, Yonsei University and Lund University (Sweden) and SAC member of Institut Pasteur Korea. His research interests focus on discovery of bioactive small molecules, target identification and validation, integration of omics technologies toward innovations in drug translational research. He has published over 210 papers in reputed journals (google scholar citation; 16503, H-index: 49, as of 2020.10) and been serving as editor-in-chief of Proteome Science and editor of many repute journals. He was awarded ‘DongHeon Biochemistry Award’ (Korean Society of Biochemistry and Molecular Biology), ‘Sura Academy Award’ (Korean Society of Microbiology and Biotechnology), ‘Outstanding Research Professor Award’ (Yonsei University).
Presentation Title: "Multi-Regional Micro-sampling Reveals Extensive Intratumor Proteomic Heterogeneity - Scientific & Clinical Implications"
This lecture will highlight cutting edge applications in applying laser microdissection and microscaled quantitative proteomics and phosphoproteomics to uncover exquisite intra- and inter-tumor heterogeneity. The paradigm-shifting results offer unprecedented opportunities to speed progress in identifying novel molecular sub-types of cancer, therapeutic targets, prognostic signatures, and companion diagnostics.
Thomas P. Conrads, PhD is the Director of Women’s Health Research in the Inova Health System and the affiliated Women’s Health Integrated Research Center in Northern Virginia. He is also the Chief Scientific Officer of the Department of Defense Gynecologic Cancer Center of Excellence. His efforts are focused on developing and applying cutting-edge applications and workflows in proteomics for cohort-scale analysis of clinically derived specimens. The overarching goals of these efforts are toward identifying and validating protein biomarkers and surrogates for enhanced cancer patient management through improved early detection, patient stratification, and monitoring for therapeutic efficacy, outcome and recurrence.
Anne-Claude Gingras is the Canada Research Chair in Functional Proteomics, the Lea Reichmann Chair in Cancer Proteomics and a Senior Investigator at the Lunenfeld-Tanenbaum Research Institute, Sinai Health System. A Full Professor in the department of Molecular Genetics at the University of Toronto, she also serves as deputy editor of Molecular and Cellular Proteomics and as a co-director of the Network Biology Collaborative Centre (a Genome Canada technology platform). Her lab focuses on the study of signalling pathways using systematic approaches and the development of quantitative proteomics technologies. She has developed computational tools that enable better analysis and visualization of proteomics results, and contribute to training the next generation of proteomics researchers. Using the tools that she developed, her group has identified new protein complexes and signaling components that provide a better understanding of perturbations associated with cancer and rare diseases. Dr. Gingras has published >230 research articles and review articles that have already been cited 38,800 times. She is a Fellow of the Royal Society of Canada, an elected member of the European Molecular Biology Organization (EMBO), and was recently awarded the CSMB Jeanne Manery Fisher Memorial Lecture (2019), the HUPO Discovery Award (2019), and the CNPN Tony Pawson Award (2020).
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