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.

 CURRENT HUPOST ISSUES            ARCHIVE HUPOST ISSUES

FEATURED ARTICLES


  • 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.


  • 04 Jan 2019 12:38 PM | Anonymous member (Administrator)

    The 18th Human Proteome Organization World Congress - HUPO 2019 will be hosted by the Australasian Proteomics Society (APS) in the beautiful ‘City of Churches’, Adelaide. HUPO 2019 will focus on “Advancing Global Health Through Proteome Innovation” and will bring together world-leading experts and the next generation of early career scientists to promote how proteomics is advancing our knowledge of human and planetary health. HUPO 2019 will both celebrate what has been achieved and look forward to future advances and discoveries that will revolutionize global health.

    The Australasian Proteomics Society (APS) has started to design a fantastic program for HUPO 2019 in Adelaide and have confirmed the following plenary speakers:

    • Prof. Ruedi Aebersold
    • Prof. Yu-Ju Chen
    • Prof. Fuchu He
    • Prof. Albert Heck
    • Prof. Kathryn Lilley 
    • Prof. Mathias Uhlén

    With plenary lectures from outstanding speakers and over 30 parallel sessions - including 6 HPP sessions, the 2nd Australasian Glycoscience Symposium, Plant and Food Proteomics sessions - the program will offer opportunities for fruitful discussions. Other Themes include:

    • Health and Disease
    • Biological Applications of The Proteome
    • Beyond the Proteome
    • Our Human Environment
    • Enabling Technologies

    The Organizing Committee of the HUPO 2019 consists of the committee members of the Australasian Proteomics Society (APS) plus a number of prominent Australian Proteomics Scientists:

    HUPO 2019 Organizing Committee

    Prof. Stuart Cordwell (Co-Chair, APS President)
    Prof. Peter Hoffmann (Co-Chair and LOC Chair, APS Vice President))
    Prof. Anthony Purcell (APS Treasurer)
    Prof. Mark Molloy (APS Secretary)
    Prof. Marc Wilkins (APS Committee)
    Dr. Michelle Colgrave (APS Committee)
    Dr. Morten Thaysen-Andersen (APS Committee)
    Dr. Andrew Webb (APS Committee)
    Additional HUPO 2019 Organizing Committee
    Prof. Mark Baker (HPP)
    A/Prof. Michelle Hill (HUPO EC Secretary)
    A/Prof. Vera Ignjatovic (HPP)
    Prof. Ed Nice (HPP and social event committee)
    Prof. Nicolle Packer (Glycoscience)
    Prof. Paul Haynes (Plant and Food Proteome)
    Prof. Gavin Reid (Multi-omics)

    Visit the conference website www.hupo2019.org for more details.

    We look forward to welcoming you to Adelaide in 2019 for an unforgettable HUPO World Congress.

  • 04 Jan 2019 11:54 AM | Anonymous member (Administrator)

    Sanjeeva Srivastava, IIT Bombay, India

    Proteomics is the study of entire protein complement of an organism. Advancements in proteomics have been phenomenal over the last decade with several promising high-throughput technologies emerging at the forefront of various applications. Owing to the rapid advancements in state-of-the-art proteomics technologies, continuous expansion of our scientific understanding, and challenges associated with omics research, it has become essential to keep up with current trends and advances in proteomics research. In this light, we conducted three workshops at IIT Bombay, where eminent scientists and researchers from India and abroad had shared their knowledge and expertise to train the participants and familiarize them to the vast applications of proteomics.

    Basics and Advanced Proteomics Approaches (December 3 to 14, 2018)

    The DST supported programme was specially designed for Scientists/Technologists who are actively involved in research and development activities. The overall goal of the programme was to develop an educational training program on diverse proteomic technologies and offer hands-on training on the cutting edge proteomics technology to benefit the scientists in their research skill enhancement and keeping them abreast with the last technological advancements in the field of science. 25 scientists were selected for this program.

    Cancer Proteogenomics Workshop (December 6 to 11, 2018)

    This training program utilized advanced genomic & proteomic technologies and their data from high-quality human biospecimens to identify potentially actionable therapeutic molecular targets. This IUSSTF funded training program was a collaborative effort by experts in the fields of proteomics and proteogenomics in cancer research from the Broad Institute of MIT and Harvard (Convener, USA: D. R. Mani) and Indian Institute of Technology Bombay (Convener, India: Sanjeeva Srivastava). The program comprised interactive lectures with case studies, hands-on sessions and demonstrations on proteogenomics aimed at accelerated understanding of cancer. 200+ participants attended this training program.


    Caner proteogenomics workshop Group 

    Cancer Moonshot India Program – December 7, 2018

    The Cancer Moonshot aims to accelerate cancer research to make effective therapies available to more patients, while also improving early and accurate detection.

    https://www.cancer.gov/research/key-initiatives/moonshot-cancer-initiative

    Similar to the Cancer Moonshot project of USA, to expedite cancer diagnosis and treatment, we have initiated the Cancer Moonshot India project. India has now become the 12th country to join the International Cancer Proteogenome Consortium (ICPC) of the National Cancer Institute (NCI), U.S. The Indian Institute of Technology Bombay (IITB) aims to study proteomics and the Tata Memorial Hospital (TMH), Mumbai, aims to study the genomics of three cancers, breast, cervix and oral. Dr. Henry Rodriguez, Director, NCI Office of Cancer Clinical Proteomics Research inaugrated this event and delivered a speech to the gathering, which included distniguished clinicians from ACTREC, TMC and KEM hospitals; key industry leaders; and scienitsists working in genomics and proteomics area.


    Enchanting dance performances by Faizal Kahan and his group

    Trans-Proteomic Pipeline (December 12 to 14, 2018)

    The TPP workshop was scheduled from 12th to 14th December 2018. This advanced mass spectrometry data analysis workshop was supported by IUSSTF joint virtual center grant and conducted by Institute for Systems Biology scientists.

    Click here for more: http://www.bio.iitb.ac.in/~sanjeeva/cpg2018/
  • 30 Nov 2018 8:02 AM | Anonymous member (Administrator)

    HUPO President (2017-2018), Mike Snyder, California, USA

    It has been a true honor to have served as HUPO President for the past two years. The field of proteomics has never been more exciting with numerous advances in technology, transformational research findings, and improved integration into systems biology and medicine. We can now profile thousands of proteins at rapid speed and with instrument sensitivities that enable single cell proteomics. Through the efforts of the Human Proteome Project (HPP) the number of uncharacterized proteins has rapidly diminished (to under 3,000) and the Human Protein Atlas has mapped the expression and subcellular localization of the majority of human proteins. Our annual HUPO meetings continue to present the very best science in proteomics and attract the very best practitioners of our field. Most importantly, we have welcomed many new scientists at our annual meeting and benefited from their outstanding contributions on numerous committees. We have undertaken many bold initiatives such as the launch of the international Human Proteomics Moonshot project. The international influence and stature of the organization is evidenced by the enthusiastic participation of former US Vice President Joseph Biden at our annual meeting. The HPP continues to make great progress as our flagship project, with Mark Baker assuming the helm after the Herculean efforts of Gil Omen to get the HPP launched and running smoothly.

    Despite our many successes, there remains much to be done and we cannot afford to be complacent—this is the same as falling behind. We still cannot profile all proteins and isoforms with low sample amounts and with high throughput. Depth and speed will be important for large studies, similar to other omics fields. Single cell proteomics is promising but still in its infancy. As leaders in the field, HUPO members need to educate our peers and funding agencies about the significant value of incorporating proteomics into all major projects going forward. Many researchers and some funding agencies are beginning to recognize that understanding biological systems requires proteomics, which is closer to phenotypes than nucleic acid assays, and this has shaped the scope of some newer initiatives, for example the MoTrPAC consortium. Finally, I believe that medicine of today using large sample volumes and visits in the clinic will be replaced by small “finger prick” sample collection and mail-in assays. HUPO and the field of proteomics needs to be at the forefront of this. I anticipate major advances in the field of proteomics in the coming years and believe HUPO will play a pivotal role in making these happen. I think we are in terrific hands under Steve Pennington’s leadership. My heartfelt thanks for everyone‘s contributions during my term.


  • 29 May 2018 4:29 PM | Anonymous member (Administrator)

    György Marko-Varga, Sweden

    Focusing on Patient-Relative-Friend Aspects in the 2018 Summit


    Photo by Karl Melin.

    The European Cancer Moonshot Symposium was held in Lund May 23rd. The primary goal of the meeting was to invite and discuss cancer research from the perspective of patients, relatives, and friends. Patients and relatives from the US and different parts of Europe told their stories and about their experiences from treatment of various cancer forms (https://www.facebook.com/europencancermoonshotlund/ ).

    Honest and emotional lectures were given on the factual circumstances that a patient and a close relative face when dealing with tough messages, treatments, and decisions. The mental trainer, Igor Ardoris, shared his experience of how to deal with these situations, controlling the mind and imaginational part, that can be trained to overcome and ease pain and disease pressure.

    The former athlete and world record holder in high jump Patrik Sjöberg gave a deeply touching talk about a child’s perception of having cancer. Mr Sjöberg is now working part time advocating for children with cancer, through the Tuva’s Day Foundation (Varberg för Liv/Tuvas Dag). Martin Bekken from BEWi, has been a strong support to the European Cancer Moonshot Lund Center, by getting the word out on the build of the PRF-group-that was the focus of our meeting this year.

    With the patient in focus the meeting also engaged the hospital management of the southern health care district of Sweden, experts and medical doctors from cancer treatment clinics, and prominent cancer researches in the cancer diagnostic field. The Cancer Moonshot research team in Lund hosting the Symposium also had reporting from the Cancer Moonshot Australia activities, was presented by Professor Mark Baker, where major funding and investments for future Cancer research and developments have been made recently, expanding on the US/Australia Cancer Moonshot collaboration. Dr. Henry Rodriguez, from the NIH/NCI (National Instituts of Health/National Cancer Institute), presented the overall progress and activities of the Cancer Moonshot program in the US, and Dr. Thomas Conrads, showed the latest cancer studies within the Cancer Moonshot & US/Apollo developments, which were very impressive.

    Statement from professor Johan Malm “When working with front-line clinical research at the European Cancer Moonshot Lund Center, as we are doing, it is very stimulating and inspiring to listen to all the different stories from patient and their relatives. Then you realize that what matters is not you. It is what you are working for, namely a better life for the people facing the consequences of cancer”.

    Statement from Ken Miller, Thermo Fisher Scientific “Thermo Fisher is a partner to many global Cancer Moonshot laboratories and we consider the program in Lund to be an exemplar of clinical excellence, biobanking, and analytical expertise. We are confident that this team will help the cancer research field make progress toward the dream of patient phenotyping and precision medicine.”

    The Cancer Moonshot was initiated in 2016 by the 47th vice president Joe Biden.

    The project team in Lund hosting this year’s international European Cancer Moonshot summit built the theme on Joe Biden’s vision;

    “Break down the silos and start to collaborate, involve all disciplines, with one common aim, to defeat cancer.”

    Related links:

    Watch all 5 sessions of the European Cancer Moonshot Symposium in Lund

    Session 1: https://www.youtube.com/watch?v=nsvPAvvqCLA&t=4s

    Session 2: https://www.youtube.com/watch?v=ihxSd820lNo

    Session 3: https://www.youtube.com/watch?v=Gfp6Ic8pe5U&t=3s

    Session 4: https://www.youtube.com/watch?v=vcV5rcnLT7I&t=4s

    Session 5: https://www.youtube.com/watch?v=MJe56CHUw_k

    Follow the European Cancer Moonshot Lund Center here: http://www.cancermoonshotlund.com/ 

    Hear about Eve Kelly's story here: https://www.youtube.com/watch?v=9euomHlFqnY

  • 27 Apr 2018 1:08 PM | Anonymous member (Administrator)

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

    Post-translational modifications (PTMs) on proteins can play a critical role in function by regulating protein structure, function and/or localization. Although consensus sites for some of the more well-studied PTMs have been established, PTMs are not predictable from the genetic code. Furthermore, PTMs can be either stably attached through the life of a protein, or reversibly added depending on stimulation. Hence, direct interrogation at the protein level is required to fully characterize PTM function in health and disease.

    Several B/D-HPP teams have been investigating the biological roles of PTMs and their disease associations, with two recent publications in leading interdisciplinary journals.

    Neil Kelleher and his team at Northwestern University used top-down proteomics to characterize proteoforms of KRAS, a gene frequently mutated in human cancer. The novel mass spectrometry-based whole protein assay enabled the team to investigate the effect of genetic mutations in KRAS on PTMs of the protein that are important for proper KRAS regulation. In collaboration with National Cancer Institute, the study, recently published in Proceedings of the National Academy of Science USA, quantified the percentage of mutant KRAS4b present in colorectal cancer tissue, and identified differences in the level of C-terminal carboxymethylation, which is critical for KRAS function. Such detailed characterization and quantification of KRAS proteoforms was only possible with the novel top down mass spectrometry-based assay. In the future, targeted assays such as this will be extended to characterize proteoforms within specific cell types to increase their sensitivity and selectivity and inform cancer prognosis and personalized therapy selection.

    A collaboration between Jenny Van Eyk’s team at Cedars-Sinai Medical Center and Shengbing Wang and David Kass at Johns Hopkins University School of Medicine, determined the functional consequences of a redox-regulated PTM on glycogen synthase kinase 3b (GSK3b). S-nitrosylation is the attachment of nitric oxide to sulfhydryl residues of proteins, and is involved in redox-based cell signaling. The study, published in Circulation Research, reported the novel finding that GSK3b can be modified by S-nitrosylation at specific sites in models of heart failure and sudden cardiac death. S-nitrosylation of GSK3b overrides the classical phospho-regulation and sends it to the nucleus, away from its usual cytoplasmic location. The result is that the S-nitrosylated GSK3b now phosphorylates a completely different repertoire of proteins in the nucleus compared to its known cytoplasmic substrates, implying that drugs meant to target cytoplasmic GSK3b may inhibit complete different nuclear pathways if the GSK3b is S-nitrosylated. “Knowing the PTM status of drug targets and the functional effect is key to next generation therapies.” Says Jenny.

    Together, these studies exemplify the work of B/D-HPP teams and clinical collaborators on apply and developing advanced proteomics methods to understanding disease. Future work of the B/D-HPP teams will be to translate the findings into the pathology or clinical chemistry laboratories, to make an impact on patients lives.


  • 27 Apr 2018 1:03 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    The Chromosome-Centric Human Proteome Project (C-HPP) plans to identify all elements of the human proteome, their proteoforms and determine their functions. C-HPP efforts are summarized as protein evidence status and functional and other annotations of human protein coding genes by neXtProt. The C-HPP is organized as an international consortium based currently on a per chromosome basis and is open to the entire scientific community for contribution. Besides individual publications, other scientific contributions are summarized in the C-HPP special issues appearing each year in the Journal of Proteome Research. On an ongoing basis, the main C-HPP achievements are highlighted in C-HPP Newsletters published every year. The C-HPP has initiated a community information sharing Wiki page, to enable sharing C-HPP–related information directly by member teams. The C-HPP Wiki includes the following sections:

    - Representation of team members information, resources, expertise, projects and results on a chromosome basis

    - Protocols, guidelines and central resources of the C-HPP project

    - The program of C-HPP workshops organized each year at HUPO congresses and at C-HPP workshops, which includes presentations with authors permission and other workshop related information

    - C-HPP news items, which includes announcement of new achievements, new guidelines and yearly appearing C-HPP Newsletters

    C-HPP Wiki is a live non-centralized information sharing platform of C-HPP members and has as its goal to share as much information as possible for C-HPP members, for the proteomics scientific community and for interested readers. The web page for C-HPP Wiki is at https://c-hpp.webhosting.rug.nl/tiki-index.php?page=HomePage


  • 29 Mar 2018 9:54 AM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    On February 21, 2018 the new release of neXtProt was published, which serves as the definitive reference database of the human proteome and is used by the Human Proteome Project (HPP) to assess the progress of completing the map of Human Proteome. The new version of neXtProt updated the human proteome evidence using the latest data from PeptideAtlas (release Human 2018-01) and resulted in 17,470 validated human proteins (PE1), 393 more compared to the previous version of January 17, 2017, leaving 2,186 missing proteins with status PE2+PE3+PE4 and 574 uncertain proteins (PE5). In this new release a total of 51 PeptideAtlas data sets was included from cancer tissues and cell lines, with over 1.4 million peptides detected by mass spectrometry. Data from UniProtKB, Ensembl, IntAct, GOA, and GeneIDs, have been also updated. The data have been complemented with GO molecular function, biological process and cellular component annotations for most of the human protein kinases, as well as expression information, mutagenesis and variant phenotype data. The number of validated proteins with unknown function (uPE1) is now 2,271 which can be obtained with SPARQL query NXQ_00022.

    Two new rules have been implemented to reflect protein existence:

    - proteins with PE2, PE3 or PE4 status have been upgraded to evidence at protein level (PE1) status if the entry has GOLD binary interaction data from neXtProt.

    - As a consequence of UniProtKB demerging entries encoded by multiple genes, some neXtProt entries now have exactly the same protein sequence and are indistinguishable at protein level. The list can be retrieved using SPARQL query NXQ_00231. Peptides matching uniquely on such indistinguishable entries are now labeled “pseudo-unique” rather than "Found in other entries" and were used to validate protein existence if they complied with the HPP guidelines.

    The Proteomics view for entries has been revamped and now loads faster. In addition, it is now possible to search the positional annotations listed in the feature table for a specific category or for text found in the feature description. For instance, searching for "SRM" returns the number of SRM peptides mapping to the isoform and allows to the users to rapidly browse the data for all SRM peptides.

    New advanced search SPARQL queries have been added, such as to identify proteins with high proline content in the SnorQL interface (NXQ_00225), to list proteins with at least 2 uniquely mapping peptides larger than 9 amino acid lengths found in blood plasma, urine or cerebrospinal fluid to support markers research (NXQ_00226) and to identify proteins with experimentally determined lengthy alpha-helices (length larger than 75 amino acids) illustrating query of proteins with specific secondary structure (NXQ_00230).


    New letter format of Journal of Proteome Research to report missing proteins

    Discovery of a missing protein or new proteins can now be published in the Journal of Proteome Research December 2018 Special Issue as a short definitive report, submitted in the Letters format. To be considered for publication as a Letter, the missing protein(s) must meet the HUPO Data Interpretation Guidelines version 2.1 and be cast 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 and the general proteomics community, to highlight such protein discoveries when found in disease and biological sample analyses. Such side findings in a more biological focused analysis may otherwise may be lost or not further detailed as they were an incidental finding.

    Letters have a maximum length of four journal pages and should contain sufficient experiment detail for the research to be reproduced. There should be no more than 3 figures, 2 tables and 20 references. A separate Table of Contents Graphic is required, but does not count toward the 4-page or Figure limit. Reporting of missing proteins must meet both the Journal of Proteome Research technical and the HUPO Data Interpretation Guidelines (see further details in Deutsch et al. PMID 27490519) including figure(s) of the annotated spectra and the data uploaded to ProteomeXchange with a PXD number included in the abstract. To be reviewed the HPP Checklist items must be fulfilled and submitted.





Copyright 2016 - HUPO

Powered by Wild Apricot Membership Software