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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.


  • 27 Jul 2019 10:40 AM | Anonymous member (Administrator)

    Methods are essential in all omics domains, including proteomics and metabolomics. JPR has therefore created a biannual Special Issue that will highlight novel and/or significantly updated methods for proteomics, metabolomics and omics studies in general. For readers, this Methods Special Issue will be an easily identifiable source of methods that have been specifically reviewed for their applicability and ease of adoption. For authors, the Special Issue provides visibility and wider adoption of methods in the proteomics community through dissemination and documentation. In addition, the Special Issue will become a facile platform to publish significantly updated and improved methods that may have been already published.

    The Methods Special Issue will be managed by JPR Associate Editor Josh Labear with guest editors Laurence Florens and Meng-Qiu Dong and will cover all subdisciplines within the scope of the Journal of Proteome Research.


    • Authors must present either a complete description of a relevant novel method (“Research Article” submission) or a substantial and meaningful update of a previously published method (“Technical Note” submission). The focus of the paper should be on the unique functionality of the method. It should be clear to any reader what questions the method addresses and how it is used.
    • Demonstration of at least one example of an important application of the method should be included in the paper. Data generated to illustrate a method should be supported by an appropriate number of replicates and statistical analyses. In addition, there should be sufficient detail about the method to allow easy replication.
    • Data associated with demonstrating the method must be submitted to an appropriate repository at the time of submission, along with full access information to the data provided in the manuscript (dataset identifier(s), username, and password).

    Instructions for submission

    Manuscripts must adhere to the guidelines available on the Journal of Proteome Research Information for Authors page and in Martens et al., J. Proteome Res. 2015, 14(5):2002-4; doi: 10.1021/pr501318d, and be submitted electronically through the ACS Paragon Plus portal.
    In Paragon, specify manuscript type, and activate the special issue feature to designate the paper for Methods for Omics Research. In addition, include a statement in your cover letter that the paper is being submitted for the special issue. Provide names and contact information for at least four suggested reviewers who can meaningfully comment on the described method.

    The deadline for submission of manuscripts for the 2020 Special Issue on Methods is August 7, 2019. Manuscripts will be screened for suitability for the Special Issue.

    Open Access
    There are diverse open-access options for publications in American Chemical Society journals. Please see http://acsopenaccess.org/.

  • 26 Jul 2019 3:54 PM | Anonymous member (Administrator)

    Sudhir Srivastava, US National Insititutes of Health, National Cancer Institute USA

    The Human Proteome Organization has established a HUPO External Initiative (HEDI) committee to foster interaction between the HUPO membership and international thought leaders who are responsible for developing strategy for funding proteomic-centric projects in their respective countries. HEDI will be chaired by Dr. Sudhir Srivastava, Chief, Cancer Biomarkers Research Group, National Cancer Institute, National Institutes of Health along with co-chairs Dr. Rob Moritz, HUPO Vice President and Institute for Systems Biology, Seattle WA USA and Dr. Mike Snyder (HUPO Past President and Stanford University, CA USA). The objectives of this initiative are:

    • Identifying emerging scientific opportunities, rising public health challenges, or scientific knowledge gaps that merit further research by international funding agencies, non-profit governmental organizations and foundations, hereafter called Funders.
    • Understanding scientific priorities and strategic planning of Funders globally in developing and applying resources (databases, analytic tools, and methodologies) and producing specifications for new resources in support of proteomic research
    • If requested, assisting the Funders to address areas of emerging scientific opportunities and public health challenges effectively
    • Proactively discussing and providing technical assistance to Funders in the development of proteomic-based initiatives.

    The first inaugural meeting of this committee will take place during the HUPO Annual Meeting, September 15-19, 2019 to be held in Adelaide, Australia. Planning is underway to invite thought leaders, funding officials and other policy makers to discuss their ongoing and future proteomic projects in their own countries. The format of the meeting will encourage deep interaction among the participants to learn of each other’s needs and the participatory process that culminates in development of proteomic centric projects.

  • 26 Jun 2019 11:59 AM | Anonymous member (Administrator)

    Chris Overall, University of Britich Columbia, Canada

    Manuscript reviewing for the 7th Annual Special Issue of the Journal of Proteome Research on the HUPO Human Proteome Project is well under way. With 28 papers submitted, this December issue promises to be yet another success and highlight of the HPP year, albeit considerable work for the 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 and of course the ever hard working Gilbert S. Omenn, University of Michigan. Due to the American Chemical Society publication schedule, only papers that are accepted by September 31, 2019 will be published in the December 2019 HPP Special Issue. The C-HPP, B/D-HPP and resource pillars are extremely grateful to the American Chemical Society and the Journal for their support of HUPO and the HPP.

    Good luck with your papers and thank you for your support of the HPP and the Special Issue.

    Chris Overall, Associate Editor, Journal of Proteome Research

  • 26 Jun 2019 11:47 AM | Anonymous member (Administrator)

    Jochen Schwenk (Chair of the HUPO Plasma Proteome Project), KTH Royal Institute of Technology, Sweden

    The 9th workshop on Affinity Proteomics took place in Alpbach, Austria from March 11th -13th 2019 (https://affinityproteomicsalpbach.com). What started from consortia meetings from the EU projects ProteomeBinders, Affinity Proteome and Affinomics brought together more than 140 attendees to the snowy mountains in a village where the famous Austrian scientist Erwin Schrödinger found his final rest.

    The exciting agenda that Mike Taussig and his team assembled kicked off with a series of talks on applying affinity reagents to build a protein and cell atlas. These included multiplexed imaging approaches to expand the current insights into cellular structures of tissues. Following previous trends, a focus was also set on how to validate antibodies for the diverse set of downstream applications and how to liaise with other tools in proteomics. Continuing the traditions, a series of presentations covered the field of alternative binding reagents. This year’s talks provided updated insights into the advances made for generating binding molecules for research and therapeutic applications. These included the classical antibody formats and those developed from binding molecules found in other species such as camels or sharks. Besides protein-based reagents such as full-length IgG, single-chain variants such as nanobodies or ankyrin repeat proteins, talks covered the capabilities of those generated from DNA-based aptamers. A new theme included the strategies to develop binders that display bi-specific properties towards two proteins. Several presentations were given for applying affinity reagents in advanced and multiplexed analytical applications to profile human proteomes towards precise assessments of health and diseases. This theme was expanded by protein and peptide microarray systems in serology and as tools for selectivity assessment of binders.

    Started during the previous event, the meeting included presentations and a panel discussion from antibody providers. They focused on the continuing task of context and application specific antibody validation and transparency of the validation information. As nowadays required by a growing number of journals, topics dealt further with the trackability of affinity reagents through standardized identifiers.

    The workshop also brought some of the community’s most successful entrepreneurs to the stage. They shared their stories on building a business from generating and applying affinity tools. Another highly appreciated new feature were the flash and short talks by emerging scientists from the community as well as the lively interactions with the posters shown from nearly a third of all attendees.

    The next Workshop on Affinity Proteomics is planned to be held again in Alpbach during March 2021.

  • 31 May 2019 2:53 PM | Anonymous member (Administrator)

    Péter Horvatovich, University of Groningen, Netherlands

    The C-HPP held their annual workshop in France, at the historic port town of St Malo this May. With over 45 registrants, the meeting was highly successful, due mostly to the excellent science presented by invited keynote speakers and the C-HPP teams, but also by the gastronomy selected by local convenor, Dr Charles Pineau. The central theme of the 21st C-HPP symposium was “Illuminating the Dark proteome”, which took place in May 11 – 14. 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, smORFs (small potentially-translated open reading frames), 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 complete scientific program with abstract and some presentations is available on the C-HPP Wiki, along with most other past annual C-HPP workshops. The symposium included presentations on various aspects of the human dark proteome, including structural biology, a summary of the pre-symposium full-day workshop on changes to the HPP Data Interpretation Guidelines by Eric Deutsch (see more details below), updates on neXtProt by Lydie Lane, and neXt-MP50 by Chris Overall, and the neXt-CP50 by Young Ki Paik. Also featured was a fascinating talk on an approach to reveal the localisation of human proteins by Anne-Claude Gringras, and the use of ProteinExplorer for integration of community-scale big data for assessment of protein existence by Nuno Bandeira. A full summary is being prepared now for the C-HPP newsletter.

    HPP Data Interpretation Guidelines: A full-day workshop, one day prior to the symposium, featured extended discussion of 25 open questions related to updates to the HPP Mass Spectrometry Data Interpretation Guidelines and to the implementation of the workflow by which the HPP confirms the translation of potential coding genes. Each of the 25 topics were debated, potential solutions were listed, and a consensus decision among the participants achieved. The result will be an update of the guidelines from version 2.1 to version 3.0, and a manuscript that describes the open questions, the potential solutions, the consusus decisions, and the logic behind those decisions will be submnitted to the Jurnal of Proteome Research Special Issue on the HPP.

    neXtProt update: neXtProt release 2019-01-11 should be used for the incoming publications in the JPR C-HPP special issue 2019. This release contains 2129 missing proteins, of which 441 have associated MS data which is insufficient for protein validation according to the current HPP guidelines. According to neXtProt query NXQ_00022, 2222 entries lack functional annotation. Out of these entries, 1254 are validated at protein level (uPE1). These are the targets of the neXt-CP50 challenge.

    JPR Special Issue: The deadline has been extended to June 14 for papers on the C-HPP, B/D-HPP and from the pillars.

  • 30 May 2019 2:59 PM | Anonymous member (Administrator)

    Edouard Nice, Monash University, Australia and Mark Baker, Macquarie University, Australia

    As part of the interaction between HUPO and the Royal College of Pathologists of Australasia (RCPA), especially in Education and Training, there was strong HUPO participation in the recent “Pathology Update: The Power of Personalized Pathology” conference held at the Melbourne Convention Centre from 22nd to 24th February 2019. This meeting was attended by over 1350 delegates, including medics, pathologists, scientists, trainees and healthcare workers, with strong industry support (over 30 companies at the trade exhibition).

    Prof Dan Chan opened the meeting with the David Rothfield Memorial Oration with a talk entitled “The success of Precision Pathology: Multi-Omics Building Blocks”. He explained how advances in cancer pathobiology that have helped elucidate the intricate cell signalling mechanisms that trigger oncogenesis are due to the combined effect of genomic, transcriptomic, epigenetic and proteomic changes. He gave examples of how significant advances in molecular technologies, such as the multiplex-polymerase chain reaction (PCR), next generation sequencing (NGS) and mass spectrometry (MS), coupled with computational medicine, have identified new biomarkers for improving disease classification and diagnosis, including the recently reported CancerSEEK test, which uses a combination of assays for genetic alterations and protein biomarkers, and has the capacity not only to identify the presence of relatively early cancers but also to identify their localisation. Prof Chan also made other presentations at the meeting on “Tumour Markers in Practice” and Understanding immunoassay: a practical guide” as part of the Chemical Pathology agenda. In a complimentary plenary talk on the Saturday morning, Prof Eva Raik discussed ‘Precision Cancer Medicine – cup half full or cup half empty’ discussing both the advantages and hurdles that currently exist.

    On Sunday 24th a whole session was devoted to “Clinical Proteomics: Development of a Pathology Partnership”. This session was organised by Profs Ed Nice, Mark Baker and Dan Chan for HUPO and Profs Peter Stewart and Andrea Horvath representing the RCPA. The session was chaired by Dan, and comprised four talks. Ed Nice led off with a talk entitled “Clinical proteomic biomarker discovery and translation for pathology”. This started with an introduction to HUPO and the new Pathology Pillar, and the requirement for a strong interaction with clinicians and pathologists as we enter the transitional phase of proteomics. He then outlined the role of faecal proteomics in GI tract pathology.

    This was followed by a talk from Prof Horvath on “Evidence-based evaluation of proteomic biomarkers: from unmet medical needs to clinical application” in which she described proteomics as the Knight in Shining Armour. Using a hypothetical on acceptance of biomarkers that have better performance than current tests for coronary atherosclerosis, she introduced several recent proteomics examples from the literature. She stressed the importance of unmet clinical need and validation in successful translation. Dr Steven Ramsay gave a presentation on “Challenges of developing protein biomarker assays for clinical use - method validation and quality issues” further illustrating the importance of this issue, using IGF1 as an example.

    To close the session, Prof Peter Stewart, former president of the RCPA, acting as devils advocate, with a concept like the “glass half full or half empty concept introduced earlier in the meeting, discussed the “Barriers to adoption of Proteomics in clinical diagnosis”. He highlighted areas such as the complexity of the technology, measurement errors, throughput, skill base in technology and informatics and the need to up-skill pathologists (the goal of the HUPO-RACP collaboration), clinical utility and the cost and reimbursement rates.

    All the slides that were presented in this session are currently available on line at https://www.rcpa.edu.au/Events/Pathology-Update/Post-Conference. Further joint HUPO/RACP sessions to further advance education and training are being planned for 2020.

    Clinical Proteomics: Development of a Pathology Partnership.
    From left to right: Prof Peter Stewart, Prof Dan Chan
    Prof Rita Horvath, Dr Steven Ramsey, Prof Ed Nice

    Pathology Update: The Power of Personalized Pathology
    From left to right: Prof Ed Nice, Prof Peter Stewart, Prof Dan Chan

  • 01 May 2019 10:24 AM | Anonymous member (Administrator)

    Marta del Campo Mila, VU University, Medical Centre, Amsterdam, 
    Charlotte Teunissen, VU University, Medical Centre, Amsterdam, 

    The HUPO Brain Proteome Project (HBPP) Steering Committee invites you to register for the 29th HUPO Brain Proteome Project Workshop, which will be held on 27th and 28th of May 2019 in Amsterdam. 

    HBPP Spring Workshops cover a wide range of topics relevant to neuroproteomics research. The program is highly dynamic and interactive, and all participants are given the opportunity to give an oral presentation on their research or updates of novel techniques and analytical approaches used in their labs. Workshops have included, for example, sessions on myelin proteomics, autoimmunity, and bioinformatics.

    HBPP is committed to a strong clinical and translational focus. Hence, sessions in last meetings were dedicated to proteomics of psychiatric disorders, movement disorders, spinal cord injury & trauma, dementia, and cancers of the CNS. On top of that, there will be a very nice evening program that will allow all the delegates to have relax interactions with a unique local atmosphere.

    The HBPP Steering Committee encourages every researcher interested in brain proteomics, including junior scientists to join this event. For more information about the workshop please visit https://www.hbpp2019.com/.

    Don’t hesitate to extent and share this information between all your colleagues within the field.

    We are looking forward to see your latest results at this inspiring meeting!

    On behalf of the HBPP steering committee, thank you. 

  • 01 May 2019 9:50 AM | Anonymous member (Administrator)

    Kun-Hsing Yu (Harvard Medical School) and Maggie Lam (University of Colorado)

    Among the missions of the HUPO Biology/Disease-driven Human Proteome Project (B/D-HPP) initiatives is to identify popular proteins in the human proteome associated with diseases and biological systems. Recently, there has been a number of software tools emerging that allow researchers to prioritize crucial proteins in various organ-systems and diseases from the biomedical literature. Information obtained using such tools which can be used to facilitate the development and promote the application of proteomics assays, such as multiple reaction monitoring to target disease-specific proteins. Our B/D-HPP groups have capitalized on these resources and made significant strides in assembling and sharing prioritized protein lists relevant to their biological systems and diseases of interest. Below we provide a brief overview of some of these software tools that enable the prioritization of popular proteins. These tools provide users ways to search and prioritize proteins related to their research interest and will facilitate targeted proteomics studies. Future algorithm and software development can further enable the prioritization of various proteoforms, such as phosphoproteome, glycoproteome, and alternative splicing isoforms, which will advance our understanding of the human proteome in health and disease states.

    PubPular (Lau et al. J Proteome Res. 2018)
    PubPular is an R/Shiny web interface for querying and visualizing popular proteins for custom search terms using Gene2PubMed/PubTator data sources and semantic similarity metrics. Recent updates of PubPular also support the query of pre-compiled protein lists from Disease Ontology and Human Phenotype Ontology disease terms as well as reverse protein-to-topic searches. PubPular can be accessed via http://pubpular.net.

    PURPOSE and metaPURPOSE (Yu et al. J Proteome Res. 2018)
    The Protein Universal Reference Publication-Originated Search Engine (PURPOSE) tool prioritizes proteins by the strength and specificity of the associations between proteins and the query terms. For each query, the number of PubMed publications are retrieved in real-time, and the results are summarized in the user-friendly web interface. PURPOSE is accessible through http://rebrand.ly/proteinpurpose.

    metaPURPOSE is an extension of PURPOSE and prioritizes metabolites associated with any search terms. This tool addresses the challenges arisen from multiple synonyms associated with common metabolites and uses the PURPOSE algorithm to rank the retrieved metabolites. metaPURPOSE is hosted at http://rebrand.ly/metapurpose.

    GLAD4U (Jourquin et al. BMC Genomics. 2012)
    Gene List Automatically Derived For You (GLAD4U) is a web-based tool that allows users to retrieve a prioritized list of Entrez-Gene IDs. The tool leverages the hypergeometric test to rank the list of biological entities associated with the query. Their user interface enables users to download the query results, conduct functional enrichment analysis using WebGestalt, and view the detailed publication list related to the retrieved genes. The GLAD4U tool is at http://glad4u.zhang-lab.org.

    FACTA+ (Tsuruoka et al. Bioinformatics. 2011)
    Finding Associated Concepts with Text Analysis+ (FACTA+) is a text mining tool developed by the National Centre for Text Mining (NaCTeM), School of Computer Science, The University of Manchester, UK. The tool aims to assist users to identify associations among biomedical concepts, including genes, proteins, diseases, symptoms, drugs, and chemical compounds. For each query term, the associated biomedical concepts are retrieved and ranked. Users can view the snippets from the literature that describe the association. FACTA+ also allows users to find indirectly associated concepts by ranking the second-order associations between the query term and the target concepts. For access, go to http://www.nactem.ac.uk/facta/.

  • 01 May 2019 9:37 AM | 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 “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 complete scientific program and abstracts are now available online home page of the event and at C-HPP Wiki. The program – amongst others – includes discussion of the 3.0 version of Human Proteome Project Data Interpretation Guidelines, updates on neXtProt, PeptideAtlas, as well as progress on neXt-CP50 and neXt-MP50 challenges. Keynote 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”.
    • Mirjam Czjzek (Roscoff Marine Station, Roscoff, France) on “How structural biology contributes to uncover biochemical functions of putative proteins”.
    • Fernando Corrales (Centro Nacional de Biotecnología , Madrid, Spain) on “Bridging C and B/D HPP to define the biological context of human proteins PTM” (Abstract 12).
    • Marie-Christine Birling (IMPC, Strasbourg, France) on “The virtuous cycle of human genetics and mouse (and rat) models”.

    In addition 23 talks were selected from the abstracts.

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

  • 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) 

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