Newsletter of the Human Proteome Organization

Current and past HUPOSTs are posted here for your review. Stories, highlights, news, and announcements are gladly accepted for inclusion in the HUPOST. Please submit your information to the HUPO Office at office@hupo.org.

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  • 26 Mar 2019 12:25 PM | Anonymous member (Administrator)

    Dr Ying Jiang, Beijing Institute of Lifeomics, Beijing, China 

    Hepatocellular carcinoma (HCC) is the third leading cause of deaths from cancer worldwide. Infection with the hepatitis B virus is one of the leading risk factors for developing HCC, particularly in East Asia. Although surgical treatment may be effective in the early stages, the five-year overall rate of survival after developing this cancer is only 50–70%. Proteomic and phospho-proteomic profiling of 110 paired tumour and non-tumour tissues of HCC stratifies HBV-related early-stage disease into 3 prognostic subtypes. The disrupted cholesterol homeostasis is characterized in the subtype associated with the lowest overall rate of survival and the greatest risk of a poor prognosis after first-line surgery. Moreover, targeting SOAT1 (either knock-down or inhibitor treatment) suggests opportunities for personalized therapies. In conclusion, CNHPP study identifies the proteomic landscape in early HCC, and the patterns of protein signatures and pathways that are altered in proteomic subtypes of HCC. The drug-targetable proteins that identified by proteomic alterations may provide a powerful tool for identifying patients with HCC subtypes associated with a poor prognosis, and who might benefit from further targeted treatment, moving us towards the era of proteomics-driven precision medicine.


    National Center for Protein Sciences (Beijing) 

  • 26 Mar 2019 10:36 AM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    The dark proteome is defined accordingly to the HPP as “a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORF (small proteins), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing.” The central theme of the 21st C-HPP symposium is “Illuminating the Dark proteome” and will take place in May 12-14, 2019 in Saint Malo (France) at the Hotel France & Chateaubriand, which is located inside the fortified city.

    The program is currently available online on the home page of the event and on the C-HPP Wiki. The program – among others – includes discussion of the version 3.0 of Human Proteome Project Data Interpretation Guidelines, updates on neXtProt, PeptideAtlas, progress on neXt-CP50 and neXt-MP50 challenges. Key-note lectures will be provided by:

    • Nuno Bandeira (University of California, San Diego) on “ProteinExplorer: integration of community-scale big data for assessment of protein existence
    • Anne-Claude Gingras (Lunenfeld-Tanenbaum Research Institute,Toronto, Canada) on “Dark proteome: shedding light on localization and interaction of uncharacterized proteins”
    • Yves Vandenbrouck (CEA Grenoble, France) on “Exploring the dark side of the Human proteome using the ProteoRE platform”
    • Marie-Christine Birling (IMPC, Strasbourg, France) on “The virtuous cycle of human genetics and mouse (and rat) models”

    Besides C-HPP, B/D HPP PIC and young investigators will contribute to the program. Places are limited, but registration for the workshop is still possible online using a registration form. The hotel block has been completely filled, but we are hoping to free some more rooms from the hotel stock available till first week of April. However, this is uncertain and in that case another hotel will have to be sought by the registrants.

    The organisers Charles Pineau, Chris Overall, Young-Ki Paik, Lydie Lane are looking forward to receive all C-HPP members and all interested participants from B/D-HPP and HUPO membership.

  • 26 Mar 2019 10:04 AM | Anonymous member (Administrator)

    Jennifer Van Eyk, Burcu Ayoglu, Ferdinando Cerciello, Justyna Fert-Bober, Ruth Hüttenhain, Mathieu Lavallée-Adam, Adriana Franco Paes Leme, Giuseppe Palmisano, Ilaria Piazza, Fábio César Sousa Nogueira)

    The ECR was launched as a new HUPO initiative at HUPO 2015 World Congress in Vancouver. The intent of the ECR is to be an open and easily reachable platform dedicated to the new generation of proteomics scientists of the HUPO community.

    The ECR aims are to (1) promote connection between generations of proteomics scientists along the visions and the ideals of HUPO; (2) promote the scientific work of the new generation of proteomics scientists and to provide training and support for their early career development; (3) promote interaction and international collaboration among early career investigators in proteomics.

    To achieve these aims, we explored common facilitators and challenges faced by early career researchers in proteomics during annual Mentoring Day at HUPO world congresses. The program of Mentoring Day, every year is different and has several ingredients to enhance an ECR individual’s success. Having supportive collegial relationships, institutional support, job security, and funding are critical facilitators for early career investigators. Key challenges include difficulty with time management and prioritizing, limited resources, and contacts. The talks, conversations and friendly atmosphere during Mentoring day, can potentially help transfer knowledge and expertise since it represents a variety of professional backgrounds and experience from more mature generation. This is also an exceptional opportunity to approach and interact with current and future world-renowned leaders in proteomics! For example, the focus of the mentoring day at HUPO2018 in Orlando was on “communication” and the program included various topics such as “what qualities are necessary for successful communication?”, “ten simple rules for choosing between industry and academia”, “communicating with funding agencies”, etc. Our mentors in Orlando were Beth Anderson (Arkitek Scientific), Nicolai Bache (Evosep), Sixue Chen (University of Florida, USA), Benjamin Garcia (University of Pennsylvania School of Medicine, USA), Arianna Jones (Sciex), Kathryn Lilley (Cambridge Centre for Proteomics. University of Cambridge. UK), Stephen R. Pennington (UCD Conway Institute, Dublin), Robert Rivers (NIH, USA), Jennifer Van Eyk (Cedars Sinai Medical Center).

    ECR also promotes the scientific work of the new generation by organizing manuscript competition. For the manuscript competition, early career researchers are invited to submit their scientific work in form of a manuscript, which has either been published or accepted for publication within the previous year. Three finalists are then invited to present their research at the HUPO world congress to select the proteomic highlight of the year. For our most recent manuscript competition at HUPO2018 in Orlando we had three winners, Dr. Ruth Hüttenhain (University of California, San Francisco, USA), Dr. Mathieu Lavallée-Adam (University of Ottawa, Canada) and Dr. Ilaria Piazza (Swiss Federal Institute of Technology-ETH Zurich, Switzerland)! (pictures of the winners are reported below)

    In addition to the already established activities, the ECR proudly contributed to the success of the HUPO PhD poster competition at HUPO2018 in Orlando. While the poster competition is an already established and successful tradition of HUPO, ECR started to be involved in organizing the competition as a way to highlight the work of very early career scientists! Eight finalists of the competition were selected to present their work in a three-minute power point presentation and Desmond Li (University of Sydney), Aaron Robinson (Cedars Sinai Medical Center) and Amber Weiner (University of Pennsylvania) were the winners of last year’s final! (pictures of the finalists are reported below, but CAVE: they have already been presented in a previous HUPOST)

    HUPO2018 in Orlando was not only important for the ECR for expanding their activities but also for kicking off a bigger working committee. In 2015 ECR was successfully established by Dr. Burcu Ayoglu (KTH Royal Institute of Technology), Dr. Ferdinando Cerciello (University Hospital of Bern) and Dr. Justyna Fert-Bober (Cedars Sinai Medical Center) under the mentoring of Prof. Jennifer Van Eyk (Cedars Sinai Medical Center). To expand ECR activities they are now joined by the three finalists of the 2018 ECR manuscript competition (Dr. Ruth Hüttenhain, Dr. Mathieu Lavallée-Adam and Dr. Ilaria Piazza) as well as Dr. Giuseppe Palmisano (University of San Paolo, Brazil), Dr. Fábio César Sousa Nogueira (Federal University of Rio de Janeiro, Brazil) and Dr. Adriana Franco Paes Leme (Brazilian Biosciences National Laboratory, Brazil).

    And our new members are already at hard work! Indeed, we are working on identifying new and additional opportunities to support and promote the scientific work of early career scientists, ideally in form of collaborative grants between young scientists. We are also working on defining a curriculum of “must to know” for early career scientists in proteomics. We hope that we will be able to join forces with already experienced education initiatives within HUPO and other groups of young researchers in proteomics in order to be able to establish together a series of master classes in proteomics dedicated to the early career researchers. In addition, we are reaching out to regional early career proteomics communities across the globe to connect and join forces with the intention to identify needs of early career researchers in proteomics, to further expand ECR activities and to support building up new regional communities for early career researchers!

    Finally, a motivation for all early career researchers in proteomics to get ready for HUPO2019 in Adelaide:

    • Submit your manuscript for the ECR Manuscript Competition and your abstract for the ECR PhD Poster Competition
    • Sign up for participating in the ECR Mentoring Day
    • Contact us if you are interested in contributing to the work of ECR

    And finally, a warm thank you for reading about our progresses!

    The ECR working committee

    The winners of the ECR manuscript competition at HUPO2018 in Orlando (from left to right): Dr. Ruth Hüttenhain (University of California, San Franciso, USA), Dr. Mathieu Lavallée-Adam (University of Ottawa, Canada), Dr. Ilaria Piazza (Swiss Federal Institute of Technology-ETH Zürich, Switzerland).


    The finalists of the PhD poster competition: Shubham Gupta (Canada), Andreas Hober (Sweden), Desmond Li (Australia), Benjamin Pullman (USA), Aaron Robinson (USA), Tim Van Den Bossche (Belgium), Amber Weiner (USA), Juanjuan Xie (China).


  • 01 Mar 2019 12:10 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    The Journal of Proteome Research will publish its seventh annual Special Issue dedicated to highlight progress on the HUPO Human Proteome Project (HPP). The Special Issue considers papers encompassing both the Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP). In addition, we will now consider short definitive reports, submitted in the Letters format, on the discovery of a Missing Protein(s). To be considered, the missing protein(s) must meet the Guidelines v 2.1 or later when available, and be put in the context of both the HPP and biological setting in which they were discovered. We anticipate this format will encourage many teams, particularly of the B/D-HPP, to highlight such protein discoveries in a disease and biological context.

    Guest Editors

    Young‐Ki Paik, Yonsei University
    Eric Deutsch, Institute for Systems Biology
    Fernando Corrales, Centro Nacional de Biotecnología (CSIC)
    Lydie Lane, Swiss Institute of Bioinformatics
    Gilbert S. Omenn, University of Michigan

    Associate Editor

    Christopher M.Overall, The University of British Columbia

    Thematic Priorities:

    • Completing the high-resolution draft of the human proteome with new strategies and results leading to confident identifications of neXtProt missing proteins (PE2 – 4) according to the C-HPP Guidelines v 2.1 or recent updates
    • Progress on the protein list of individual chromosomes and groups of chromosomes, annotating known proteins and their isoforms/proteoforms and/or credibly identifying missing proteins (PE2 – 4)
    • Annotating proteins and their isoforms/proteoforms and/or identifying missing proteins found in rare or under explored cells and tissues, and protein lists of human cell types as a step in creating a human cell proteome atlas
    • Produce and utilize “popular proteins” lists in B/D-HPP and contribute to the identification of missing proteins
    • Proteomic studies of proteoforms produced by proteolytic processing, PTMs, alternative splicing (ASV),
    • coding non‐synonymous single nucleotide polymorphisms (cSNPs), or chromosome abnormalities
    • Use of targeted proteomics, especially SRM and MS‐SWATH, to extend chromosome‐based protein findings
    • Disease studies utilizing chromosome information, characterizing amplicons, cis‐regulated pathways or networks
    • New bioinformatic tools and approaches for annotating the human proteome
    • Biological mechanistic analyses inspired from proteomics data in diseases or biological processes
    • Biomarker discoveries based on the identification of novel ASVs, PTMs or cSNPs in proteomic studies

    Submission Procedure

    Manuscripts must be submitted by 31st May, 2019 to be considered for this Special Issue. Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system. Specify in the authors’ cover letter that the manuscript is intended for the HPP Special Issue.

    Review and Publication Process

    Initial editorial review will determine whether manuscripts are appropriate for the HPP Special Issue and fulfill the HPP checklist (http://www.thehpp.org/guidelines/HPPDataGuidelines_2.1.0.pdf) to be considered for publication. The completed checklist must be included with the cover letter. The full MS data submission to ProteomeXchange must also be completed prior to initial submission, and the PXD number provided in the abstract. Nonconforming papers will be returned unreviewed. All relevant papers will go through full peer review. As papers are accepted they will go online and be available in time for HUPO-2019. Due to the publication schedule, only papers that are accepted by September 31, 2019 will be published in the December 2019 HPP Special Issue. Papers requiring more time for revision or falling outside of the scope of the Special Issue will be published in regular issues of the Journal

    HPP Data Guidelines

    Papers must conform to both the Journal of Proteome Research mass spectrometry guidelines and the HPP guidelines v 2.1 (see Deutsch et al. http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00392) in order to be sent to review and for acceptance. Please check for any changes to the HPP guidelines available online at http://www.thehpp.org/guidelines/ before submission. All papers must analyze their data using the Human PeptideAtlas release 2019-01 and neXtProt release 2019-02. Papers not doing so will be returned without review.

    21st C-HPP symposium “Illuminating the Dark proteome” - Saint Malo, France, May 12-14, 2019

    The central theme of the 21st C-HPP symposium is to discuss approaches and topics on “Illuminating the Dark proteome”, a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORF (small proteins), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing. The symposium will also welcome speakers from the B/D-HPP to discuss the functionalization of the dark proteome.

    Saint-Malo, historical home of great discoverers and corsairs, is a fortified city located on the north coast of Brittany. The symposium will take at the Hotel France & Chateaubriand, which is located inside the “stone vessel” (the nickname of the fortified city). Registration for the symposium can be done online using a registration form that must be sent directly to the hotel. We are pleased to announce that the deadline of abstract submission has been extended up to March 11. Please visit https://c-hpp.univ-rennes1.fr/ for more details.

    For sure, the wonderful location and relaxing atmosphere of Saint-Malo will allow participants of the symposium to exchange fruitfully and informally. Yet, spring has arrived in the Corsair City…


  • 28 Feb 2019 4:44 PM | Anonymous member (Administrator)

    A message from Cabezon Group and Clarivate Analytics

    The National Cancer Institute’s (NCI) Office of Cancer Clinical Proteomics Research (OCCPR) has contracted with Cabezon Group and Clarivate Analytics to conduct a third-party, external evaluation which includes a research survey of the external perception of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program. The survey is designed to be relatively short and should only take approximately 10 to 15 minutes to complete. To complete the survey, please click on https://www.surveymonkey.com/r/CPTAC_HUPO.

    Your strictly voluntary and confidential participation in the survey is vital to our evaluation efforts. The goals of the survey are to examine the impact of CPTAC on the broader field of proteogenomics; how the proteogenomic research community perceives the CPTAC program; and to assess the impact that specific CPTAC program components and actions have had on the research community. Your feedback provides a collaborative, shared understanding of program perceptions which enables improvements intended to benefit future CPTAC activities and impact.

    The research results from the evaluation and survey will be disseminated publicly. A summary of the survey results will be placed on the Office of Cancer Clinical Proteomics public website (proteomics.cancer.gov). In addition, the survey results will be presented at the 2020 annual CPTAC meeting.

    You may forward the survey invitation/link to colleagues, but we ask that there is no addition or modification to the invitation message. If you have already completed this survey from another list serve we ask that you do not complete it again.

    Thank you for your time and participation.


  • 28 Feb 2019 9:27 AM | Anonymous member (Administrator)

    Vera Ignjatovic,University of Melbourne, Australia

    Glycoproteomics holds immense potential to advance understanding of the molecular and cellular processes underpinning human (patho)physiology, but remains an analytically challenging discipline (Thaysen-Andersen M et al., Mol Cell Proteomics. 15(6):1773. 2016). Accurate automated intact glycopeptide identification from high resolution tandem mass spectrometry data, a prerequisite for the further advancement of glycoproteomics, is still in its infancy despite many exciting glycoinformatics developments (Hu et al., Mass Spectrom Rev. 36(4):475. 2017).

    Formed in September 2016, the first community study of the B/D-HPP Human Glycoproteomics Initiative (HGI) sets out to provide a detailed comparison of the bioinformatics solutions currently in use for the site-specific determination of protein N- and O-linked glycosylation. For this purpose, two high resolution CID-, HCD- and EThcD-based LC-MS/MS glycopeptide datasets were acquired from a tryptic digest of serum glycoproteins and these two common data files were distributed to all study participants. The participating teams were asked to return lists of confidently identified N- and O-glycopeptides from the two LC-MS/MS data files using preformed reporting templates and, further, to provide information of their used method of identification. Significant efforts by the HGI study committee were invested to ensure uniformity and compliance of all teams with the study guidelines.

    An update of the study progress was presented by Dr Thaysen-Andersen at the B/D-HPP Investigator Meeting during the 17th World Congress HUPO, Orlando, FL. The study has been very well received by the community with 22 glycoproteomics laboratories encompassing 9 software developers and 13 user teams located across all major continents completing the identification task by the end of the reporting deadline (October 2018). Recent analysis of the glycopeptide data reports by the HGI study committee encouragingly shows the existing of diverse informatics tools and approaches with a great potential for (semi-)automated glycopeptide identification from complex LC-MS/MS datasets, but, at the same time, highlighted a significant variance of glycopeptide/protein identifications within and between the user and developer teams. Discordance was also observed between participants using the same software. The underlying reasons for this spread and further data comparisons to delineate the more exact overlap and differences between the glycopeptides reported by the 22 teams are currently being investigated.

    We aim to publish the 1st HGI study results in 2019 and will present the final study outcomes at the 2nd Australasian Glycoscience Symposium (2nd AGS) to be held on the 14th September in Adelaide, Australia (more information to follow) immediately prior to the 18th World Congress HUPO, Adelaide, Australia where the prospects and scope of a potential 2nd HGI study also will be discussed.

  • 01 Feb 2019 12:23 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    The dark proteome is defined accordingly to C-HPP as “a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORF (small proteins), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing.” The central theme of the 21st C-HPP symposium is to discuss approaches and topics on “Illuminating the Dark proteome” and will take place in May 12-14, 2019 in Saint Malo (France) at the Hotel France & Chateaubriand, which is located inside the fortified city. The program is currently under construction and will be placed online either on the home page of the event or at C-HPP Wiki soon. Registartion for the workshop can be performed online using a registration form. The organisers Charles Pineau, Chris Overall, Young-Ki Paik, Lydie Lane are looking forward to receive all C-HPP members and all interest participants. Please visit https://c-hpp.univ-rennes1.fr/ for more details.

  • 01 Feb 2019 11:56 AM | Anonymous member (Administrator)

    Vera Ignjatovic,University of Melbourne, Australia

    Gil Omenn is one of the founding members of the Human Proteome Organization, has led the Plasma Proteome Project from 2002 through 2010, and chaired the Human Proteome Project from 2010 through 2018. He also served as President of the U.S. HUPO. Gil is a Distinguished University Professor of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and Public Health at the University of Michigan and a member of the U.S. National Academy of Medicine.

    Human Proteome Project

    What would you like to see happen in the HPP over the next 3 years?
    Gill: I would like to see a coalescence of subsets of the C-HPP teams and subsets of the B/D-HPP teams to accelerate scientific progress on the overriding aims of the HPP: (a) completing and annotating the protein parts list and (b) making proteomics an expected part of all multi-omics studies in biomedical research. I am keen to see the four resource pillars drive collaborative studies across antibody profiling, mass spectrometry, bioinformatics, and pathology. And I would like to see significant growth in numbers of participants in the HPP and the HUPO World Congress.

    What do you see as the role of the HPP in the future progress of proteomics? Gill: The HPP has worked openly with proteomics researchers globally, with an emphasis on quality of data, sharing of complete datasets and metadata, and metrics for the annual progress on the “draft human proteome”. I hope we will see much more extensive application of quantitative proteomics and systems biology across all the fields of medical research.

    Do you see the HPP Knowledgebase as critical for the future of the HPP? Gill: Yes, indeed. The combination of neXtProt, PeptideAtlas, ProteomeXchange/PRIDE, and interchange with other resources internationally has greatly accelerated the field of proteomics. Data Quality Guidelines for Mass Spectrometry and the International Working Group on Antibody Validation are critical for credibility and progress in the field and in the HPP. Reliable, fully shared and reconfirmed data with tools like the TransProteomicPipeline, neXtProt uniqueness mapper, the Universal Spectra Identifier, and the SRM Atlas and Popular Proteins lists can accelerate biological and clinical applications from the HPP and the community at large.

    Science 

    What is your advice to early career scientists? Gill: I am proud of the significant commitment to Early Career Scientists in the development of the HPP and especially the B/D-HPP. I urge young colleagues to ask major questions about the field of science they choose, to be alert for relevant stimulation from other fields of science, to connect research with unmet needs in clinical medicine, and to master the technical aspects of their scientific work. Always make an effort to build personal relationships and find ways to enjoy your chosen work. Make sure your potential mentors are up-to-date in the field and able to provide cogent guidance on the research you hope to undertake.

    Where do you see the gaps in technologies? Gill: One of the persistent gaps is the separate use of antibody profiling and mass spectrometry; we need studies that deploy both approaches on the same specimens. In the field of epigenetics, there is a chasm between analyses of DNA methylation and analyses of histone marks. The latter is often neglected by the genomics folks. This requires links between DNA and protein sample prep and analytical methods and the researchers. There is a similar gap between evidence of splice isoforms in the RNA-Seq transcript data and in direct studies of proteins. Alternative splicing is one of the most remarkable features of the evolution of multi-cellular organisms, with their intron/exon gene structures. It is shocking that many researchers lump together the splice isoforms from the same gene and presume that they are functionally the same; in many cases, we know that is not true. Finally, single-cell transcriptomic and CyTOF proteomic studies are proving feasible and valuable in cancer biology and developmental biology.

    What do you see would be the role of proteomics in the clinic? Are devices such as MasSpec Pen possible as future implementations in the clinical routine? Gill: We need high throughput, reasonably sensitive, moderate cost assays combined with specific biomarkers to generate actionable data for clinical decisions and for epidemiologic studies, as well. There has been progress, especially in Europe, with MS for microbial diagnoses and inherited disorders in clinical settings.

    The MasSpec Pen has generated a lot of press attention during the past 2-3 years. Articles from Hungary in 2013 and from University of Texas/Austin in 2017 in Science Translational Medicine have reported an automated, biocompatible handheld mass spectrometry device for rapid, non-destructive diagnosis of human cancer tissues. The MasSpec Pen enables controlled, automated delivery of a discrete water droplet to a tissue surface for efficient extraction of biomolecules within a few seconds, which is then delivered to the mass spectrometer for molecular analysis of proteins and metabolites. The usefulness depends on the quality of the cancer biomarkers assayed and the rapidity of analysis. The device is still in the clinical development pathway with results reported from studies on mice and on cells in vitro. I have no experience with this device, which may not yet be FDA-approved. The concept for its use in surgical removal of cancers is to sample the margin of the surgical field and rapidly analyze a few key proteins in the hand-held device.

    Personal

    What/Who was the largest influence in you moving your career into proteomics? Gill: I became interested in proteins as an undergraduate at Princeton; actually, I had problems growing and isolating sufficient protein from the acellular slime mold Physarum polycephalum, so I ended up doing electron microscopy of its previously unrecognized cytoplasmic latticework! At Harvard Medical School with a young faculty member Tom Gill III and during a summer research experience at The Weizmann Institute of Science with the inspirational Ephraim Katzir (later the President of Israel), I worked on synthetic polypeptides as models of proteins. Then, for my military duty during the Vietnam War, I had a wonderful opportunity to work at NIH with Christian B. Anfinsen on structure and function studies of staphylococcal nuclease. He received the Nobel Prize in 1972 for the concept and the compelling evidence that the amino acid sequence of proteins determines the 3-dimensional folding and function of each protein. After decades of work in human behavioral genetics and eco-genetics, and leadership roles in government, public health, and healthcare, I returned to proteins in collaboration with Sam Hanash with the founding of the Human Proteome Organization in 2002. For those interested in my personal journey, here is a link to my U of Michigan Distinguished University Professor Lecture about “Paths Less Travel’d” (a phrase from Robert Frost, who taught at the U of M), video link to my DUP lecture.

    What was the most exciting scientific finding of your career? (The eureka moment!) Gill: Clinical: As a 4th year medical student, the recognition of a syndrome of primary immune deficiency affecting 12 children in one large kindred, later named “Omenn syndrome” by McKusick of Johns Hopkins and then cured by bone marrow transplantation by a French team and linked to Rag1/Rag2 genes.

    Mechanisms: The recognition that cancers of non-endocrine organs, like lung, sometimes produced hormonal disorders not due to “disordered protein synthesis” but by activation or de-repression of the corresponding gene for the polypeptide, which is available in every cell type and would yield exactly the same sequence as the normal hormone.

    Public Health: The shocking finding that the combination of beta-carotene and retinyl palmitate, hypothesized to prevent lung cancers and cardiovascular deaths, actually caused more cancers and more CVD deaths in our beta-Carotene and Retinol Efficacy Trial (CARET).

    How do you keep a work/life balance? If there is such a notion? Gill: Yes! I have always enjoyed my studies and my work, as I do currently, while pursuing a variety of interests that broadened my social interactions and made for a stimulating life. I played clarinet in the band, oboe in the orchestra, sax in the dance band, and piano lots of places (still do). I played intramural tennis at Princeton and Harvard Medical School, and remain competitive in doubles tennis. I have long been active in science policy matters and political campaigns, as well as serving in the federal government as a White House Fellow at the Atomic Energy Commission, as associate director of the White House Office of Science & Technology Policy and the Office of Management & Budget, chairing the Presidential/Congressional Commission on Risk Assessment and Risk Management, and serving on the Scientific Management Review Committee for the NIH, as well as boards of cultural organizations. My wife, Martha Darling, whom many of you have met, also has a wide range of national and international activities, which we often enjoy together.

    What do you consider the major achievements of the HUPO Human Proteome Project (HPP)?

    Gill: 1. The HPP commitment to high quality science in proteomics experiments and data analysis. This includes the development and wide utilization of the HPP Guidelines for Interpretation of Mass Spectrometry Data (v2.0, JPR 2016) and the encouragement of generations of improvements in the underlying technology platforms.

    2. The placement of neXtProt, PeptideAtlas, and Human Protein Atlas at the center of the proteomics world.

    3. The creation of ProteomeXchange in conjunction with the European Bioinformatics Institute and PRIDE to register and make widely available the primary data and meta-data from all proteomics experiments, incorporated into the HPP Guidelines.

    4. The organized effort to apply standardized reanalysis of all MS-based proteomics datasets at PeptideAtlas and curation of multiple kinds of protein studies at neXtProt to progressively complete the “protein parts list” for the human proteome. As of January 2018, 87% of predicted protein-coding genes (17,470 proteins) were rated as having protein evidence PE1 (of a total of 19,656 PE 1+2+3+4). This percentage continues to rise, with leadership from the Chromosome-centric C-HPP and the KnowledgeBase resource pillar of the HPP. Each year the HPP published the “Metrics paper” in the Journal of Proteome Research with progress from the entire community.

    5. The development of the SRM Atlas to expedite targeted proteomics for quantitative biological studies throughout the life sciences by providing spectra from synthesized, predicted proteotypic peptides of nearly every predicted protein.

    6. The use of bibliometric analyses to identify the most investigated proteins (“popular proteins”) by organ and disease category and connect those research communities to the SRM Atlas as a guide to quantitative targeted assays of those key proteins and their pathways and networks, led by the Biology and Disease-based B/D-HPP.

    7. The tissue-specific and intracellular localization of expression of proteins with immunohistochemistry/ immunofluorescence, correlation with organ-specific transcript expression, and quality assurance of antibody specificity by Human Protein Atlas (Antibody-Profiling resource pillar of the HPP).

    8. Continued effort to make proteomics an obligatory component of multi-omics research protocols, recognizing that crucial properties of proteins—dynamics of abundance, post-translational modifications, and splice isoform variants—cannot be predicted or detected at the gene or transcript levels. Complemented by the C-HPP-led initiative to find evidence of function for the 1260 PE1 proteins lacking specific functional annotation.

    9. Multiple efforts to engage, mentor, and highlight research from Early Career Researchers, the future of the field.



  • 08 Jan 2019 9:34 AM | Anonymous member (Administrator)

    Happy New Year!

    On behalf of all of the HUPO Executive Committee I’m delighted to be able to wish all HUPO members a very happy and healthy 2019. I hope your year ahead will be productive and enjoyable. Having had a successful 2018, HUPO has much to look forward to in the coming year.

    In my role as the incoming President, my main objective is to work inclusively with all the HUPO committees and members to raise awareness of the impact of proteomics. Impact that arises from the significant advances that have been made recently and from those that will undoubtedly emerge in 2019. I hope collectively we can work to ensure that the central importance of proteomics in our understanding of human biology – in health and disease - is recognized at all levels - from the public, to research funders and policy makers. I’m looking forward to working with you all to achieve this and if there is anything that I, or HUPO, can do to help you in your research endeavors and career in proteomics then please don’t hesitate to get in contact.

    Of course, I’m also looking forward to meeting as many existing and new individual HUPO members at conferences and other events throughout 2019 but especially at our flagship meeting, HUPO 2019, in Adelaide this coming September (www.hupo2019.org). I encourage you to participate in HUPO 2019 as it will undoubtedly be a superb forum for presenting and discussing your research.

    As you are hopefully aware, the Human Proteome Project (HPP) is HUPO’s flagship project. Through the quite remarkable leadership of Gil Omenn, the HPP has coordinated and been responsible for many significant achievements – far too many to document here but to be found in previous issues of HUPOST. Through Gil’s hugely impressive and dedicated efforts the HPP is now firmly established as the central hub for HUPO’s research activities and under the new leadership of former HUPO President Mark Baker is poised to develop further. 2019 is a great time to get involved in the HPP and I encourage you to find out what it is doing and get involved.

    Finally, conscious of the successes HUPO has achieved through the efforts of many individuals - too many to mention and thank – I would like to acknowledge the contribution made by our most recent past President – Mike Snyder. Of Mike’s many impressive HUPO achievements perhaps most notable and quite unique has been the hPOP initiative. Don’t know what that is? Then again I encourage you to be proactive, find out and get involved!

    I’m sure you will find much in this issue of HUPOST, please enjoy!

    My message for 2019: HUPO is an international and inclusive team that actively welcomes your participation - be proactive, get involved.

  • 04 Jan 2019 2:48 PM | Anonymous member (Administrator)

    Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

    Congratulations and thank you for accepting the role of B/D-HPP HUPOST  cordinator.

    Thank you, Michelle. It is an honour to be suggested for this position and to contribute to showcasing the excellent efforts of the BD-HPP.

    Q. Firstly, can you please teach the proper pronunciation of Ignjatovic?

    Congratulations on spelling my surname correctly! The pronunciation of my surname is problematic for many people, so they avoid trying to pronounce it at all. All I can say is that it appears harder than it is.

    My surname is Serbian. This is a country where I was born and where I spent my early childhood, until my parents decided to move across the World, to Australia, exactly 30 years ago.

    Q. Can you please explain about your research?

    My research focuses on age-specific differences, the developmental differences between neonates, children and adults. These differences are described by the concept of Developmental Haemostasis, when focusing on the blood clotting system; or a concept of Developmental Proteomics when it comes to the proteome in general. In terms of proteomics, I am using plasma as a system to study how protein expression and post translational modifications change with age, how these changes can be applied to early disease detection and their implications for therapeutic approaches in these populations.

    Q. How did you become involved in B/D-HPP?

    In 2013 I was approached to be one of the two funding members of the PediOme initiative. That was the start of an adventure that has taken me deep into the B/D-HPP and across other aspects, such as the PPP.

    Q. What was your motivation in starting the Human Pediome Initiative?

    The motivation behind the PediOme initiative was a clear lack of pediatric studies, which meant that we had a very limited knowledge of the proteome in children (including newborns and infants). What was particularly missing was the knowledge of the “healthy state”, without which early detection of disease or individuals susceptible to specific diseases simply can’t happen. There are a couple of teams internationally that are making good progress in closing these knowledge gaps, but, there is still a lot of work to do.

    I would like to take this opportunity to urge anyone who is interested in becoming a part of the PediOme initiative to contact me, as we need people who want to drive progress in pediatric proteomics.

    Q. What do you see as the next challenges for HPP and B/D-HPP?

    The HPP has made important progress since 2010 and has brought proteomics much closer to the clinic. I believe that the next challenges for the HPP and B/D-HPP will be standardization of methodological approaches, such that they can be applied to multi-site international clinical laboratories for the purpose of diagnosis, not research.

    Q. Would you like to share some of your interests outside of science?

    Science is a big part of my life, but, I ensure that I always find the time to do things that take me away from science…always good for getting a different perspective…things such as camping, spending time with family and friends, reading, cycling. I have recently crossed the finish line in my first ever marathon, the Melbourne marathon, and that is an achievement that I am extremely proud of.


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