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  • 28 Jan 2021 3:18 PM | Anonymous member (Administrator)

    Gabriel Velez1,2,3 and Vinit B. Mahajan1,2,4
    1Omics Laboratory, Stanford University, Palo Alto, CA
    2Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA
    3Medical Scientist Training Program, University of Iowa, Iowa City, IA
    4Veterans Affairs Palo Alto Health Care System, Palo Alto, CA

    Precision Medicine aims to tailor medical therapies to individual patients by taking into account their specific genetics, environments, and lifestyle choices. Recently empowered by large sets of molecular and clinical data and high-powered analytics, this concept is changing the field of medicine, such that therapies can be customized for each patient [1]. Despite these advancements, the diagnosis and treatment of organ-specific inflammatory diseases, such as intraocular inflammation (i.e., uveitis), is most often empirical, relying heavily on clinical examination.

    The inheritance and susceptibility to many inflammatory eye disorders is often polygenic and poorly understood [2]. Many rare genetic variants cannot be easily detected when screening the over 10,000 genes in the human genome. Thus, many of the recently developed genomic testing methods fail to pinpoint precise therapies for patients affected by these disorders, leaving many of them with limited treatment options. Genes are static: they do little to inform physicians when a disease will be active, when it will start, or when it will stop. For real-time analysis of a patient’s disease state, the attention should be directed towards proteins. Proteomic analysis is becoming an attractive and powerful method for characterizing the molecular profiles of diseased tissues, like the eye. Ophthalmologists have the ability to collect surgical tissue and fluid biopsies from patients and perform detailed molecular analysis.

    To streamline the personalized proteomics pipeline for eye disease, our group has designed and implemented the Stanford Biorepository for Eye and Surgical Tissue (BEST), a novel system that allows for immediate and point-of-care processing of ophthalmic surgical samples. The system has several key components: a mobile operating-room cart with a flat lab-bench surface, a computer with secure access to a sample database, a barcode scanner, and lab supplies for sample processing away from the sterile surgical field [3]. Once biopsies are collected in the operating room, they are handed to a clinical research coordinator who processes the sample and transfers it to a 2D-barcoded cryotube for immediate flash-freezing. The barcode and corresponding patient phenotypic data is entered into the electronic database, allowing for efficient sample retrieval for downstream proteomic analyses [3, 4].

    Once surgical specimens are properly collected and stored, their proteomic content can be analyzed using a variety of analytical platforms (Figure 1). Since human eye fluid (e.g., vitreous and aqueous humor) can contain several thousand unique proteins, liquid chromatography-tandem mass spectrometry (LC-MS/MS) and targeted proteomic platforms (e.g., multiplex ELISA arrays) should be used concurrently in the biomarker discovery phase to maximize the number of candidate biomarkers for prospective verification and validation studies [4, 5]. The use of these analytical platforms is exemplified in our study of the vitreous proteome from patients with Neovascular Inflammatory Vitreoretinopathy (NIV), a rare inherited inflammatory eye disease. Despite knowledge of the causative gene mutation underlying NIV (i.e., mutations in the CAPN5 gene), these patients were previously treated with non-specific immunosuppressive medications, such as oral corticosteroids and infliximab (anti-TNF-α). Characterization of the NIV vitreous proteome revealed that levels of TNF-α were indistinguishable from control vitreous, explaining the previous failure of infliximab therapy. Instead, we detected elevated levels of VEGF and IL-6. We therefore repositioned bevacizumab (anti-VEGF) and tocilizumab (anti-IL-6), which successfully halted neovascularization and cleared vitreous hemorrhages, reduced inflammatory cell infiltration, and mitigated intraocular fibrosis in these patients [6]. We have started to expand this investigative approach to include more common causes of blindness, such as retinitis pigmentosa, diabetic retinopathy, proliferative vitreoretinopathy, age-related macular degeneration, intraocular tumors, and uveitis [6-11].

    Treatment of eye disease is now entering an era of Molecular Surgery [4]. In ophthalmology, routine microsurgical techniques can be used to safely extract fluid and tissue biopsies for downstream molecular analysis. Once molecular targets are identified, the same surgical techniques can be used to deliver precise molecular therapies in the operating room. Some of the most widely used drugs in ophthalmology today are biologics (e.g., anti-vascular endothelial growth factor [VEGF] antibodies) and engineered small molecules. It is common now to directly inject antibodies into the eye that bind to a specific protein target. As a result, physicians are becoming more aware of the exact molecular targets of the drugs they are giving patients. The same is true for a variety of immune diseases and cancers. Recasting eye surgery in molecular terms will allow scientists and ophthalmologists to take innovative approaches to curing blindness.

    Figure 1. Personalized proteomics pipeline for precision medicine in ophthalmology: Liquid vitreous biopsies can be obtained in the operating room using a vitreous cutter or 23-gauge needle (left). Vitreous samples can be analyzed for protein content using multiplex ELISA arrays (top row). Custom or commercial antibody arrays quantify protein levels in biological samples using fluorescence or chemiluminescence means. Alternatively, vitreous fluid can be analyzed using a mass spectrometry approach (bottom row). Protein mixtures are digested with trypsin and peptides are extracted. Chromatography is used to separate peptides prior to ionization and mass acquisition by mass spectrometry. protein levels are quantified, downstream bioinformatics analysis (right) can help put the identified proteins into the context of the disease. Figure adapted from Velez, G., et al., Personalized Proteomics for Precision Health: Identifying Biomarkers of Vitreoretinal Disease. Transl Vis Sci Technol, 2018. 7(5): p. 12.

    Dr. Gabriel Velez is a student and Alfred P. Sloan scholar in the Medical Scientist (MD/PhD) Training Program at the University of Iowa. He completed his PhD in Dr. Vinit B. Mahajan’s lab at the Byers Eye Institute at Stanford University where he used proteomic and structural biology methods to explore the mechanisms underlying inflammatory retinal diseases and identify therapeutic biomarkers. He is funded by an F30 training grant from the National Eye Institute and is currently finishing his final years of medical school at the University of Iowa. He plans to pursue residency training in ophthalmology after obtaining his MD degree.


    1. Velez, G., et al., Personalized Proteomics for Precision Health: Identifying Biomarkers of Vitreoretinal Disease. Transl Vis Sci Technol, 2018. 7(5): p. 12.

    2. Li, A.S., et al., Whole-Exome Sequencing of Patients With Posterior Segment Uveitis. Am J Ophthalmol, 2021. 221: p. 246-259.

    3. Skeie, J.M., et al., A biorepository for ophthalmic surgical specimens. Proteomics Clin Appl, 2014. 8(3-4): p. 209-17.

    4. Velez, G. and V.B. Mahajan, Molecular Surgery: Proteomics of a Rare Genetic Disease Gives Insight into Common Causes of Blindness. iScience, 2020. 23(11): p. 101667.

    5. Skeie, J.M., C.N. Roybal, and V.B. Mahajan, Proteomic insight into the molecular function of the vitreous. PLoS One, 2015. 10(5): p. e0127567.

    6. Velez, G., et al., Therapeutic drug repositioning using personalized proteomics of liquid biopsies. JCI Insight, 2017. 2(24).

    7. Roybal, C.N., et al., Personalized Proteomics in Proliferative Vitreoretinopathy Implicate Hematopoietic Cell Recruitment and mTOR as a Therapeutic Target. Am J Ophthalmol, 2018. 186: p. 152-163.

    8. Sepah, Y.J., et al., Proteomic analysis of intermediate uveitis suggests myeloid cell recruitment and implicates IL-23 as a therapeutic target. Am J Ophthalmol Case Rep, 2020. 18: p. 100646.

    9. Velez, G., et al., Precision Medicine: Personalized Proteomics for the Diagnosis and Treatment of Idiopathic Inflammatory Disease. JAMA Ophthalmol, 2016. 134(4): p. 444-8.

    10. Velez, G., et al., Proteomic insight into the pathogenesis of CAPN5-vitreoretinopathy. Sci Rep, 2019. 9(1): p. 7608.

    11. Wert, K.J., et al., Metabolite therapy guided by liquid biopsy proteomics delays retinal neurodegeneration. EBioMedicine, 2020. 52: p. 102636.

  • 12 Jan 2021 3:46 PM | Anonymous member (Administrator)

    Chris Overall, C-HPP Chair, Canada

    The Human Proteome Project (HPP) 8th Special Issue in the Journal of Proteome Research was published on December 4, 2020, with more 15 articles and one editorial addressing different issues related to the human proteome. This is issue is celebrating progress on establishing the existence at the protein level of 90% of the human protein coding genes. The Guest Editorial team comprising Drs. Young-Ki Paik, Gil Omenn, Lydie Lane, Eric Deutsch, Fernando Corrales, and Chris Overall (Associate Editor) were responsible for this 8th Special Issue. The whole issue is available at the Journal of Proteome Research website.

    New neXtProt release with new human protein features

    The neXtProt team is happy to announce release 2020-11-26 and that features updated protein-protein interaction data from IntAct and updated expression data from Bgee. Bgee is a database to retrieve and compare gene expression patterns in multiple animal species ,which is also developed at the SIB Swiss Institute of Bioinformatics (Nucleic Acids Res. 2020 Oct 10:gkaa793. doi: 10.1093/nar/gkaa793).

    For more information, please see: https://www.nextprot.org/news/new-release-with-updated-expression-and-interaction-data.

    The next important release of neStProt with updated proteomics data is planned for February 2021 on which the C-HPP teams can measure their progress in completion of the human proteome.

    Join us! Research teams for Chromosome 21 and 22!

    C-HPP Consortium leadership is looking for partners to can join the C-HPP initiative to advance neXt-MP50 and neXt-CP50 projects by identifying missing proteins and identify function(s) to uPE1 proteins for chromosomes 21 and 22. Motivated PIs are encouraged to contact Chris Overall (Chair of C-HPP, email chris.overall@ubc.ca) or other members of the C-HPP leadership.

    We wish you and your family Happy New Year for 2021 and we hope that vaccination against SARS-CoV2 will allow our scientific community and others to meet each other again in person on international meetings, workshops and conferences.

  • 06 Jan 2021 10:56 AM | Anonymous member (Administrator)

    Cristina Ruiz-Romero, Grupo de Investigación de Reumatología (GIR), Plataforma de Proteomica-PROTEORED-ISCIII, INIBIC - Complejo Hospitalario Universitario de A Coruña and Francisco J Blanco, Grupo de Investigación de Reumatología y Salud (GIR-S), Departamento de Fisioterapia, Medicina y Ciencias Biomedicas. Universidad de A Coruña

    One of the priorities of translational proteomics is to facilitate the development of precision medicine strategies. These involve a deeper knowledge on the molecular profiles of diseases and patients, improving prediction and prevention and promoting a more personalized and participative medicine. In this field, the HPP initiative on Rheumatic and Autoimmune diseases (RAD-HPP) has focused on the application of proteomics for the development of predictive models for precision medicine. These models would enable the identification of disease phenotypes and the stratification of patients according to their future response to treatment.

    In patients with osteoarthritis (OA), the Rheumatology Research Group in A Coruña (http://girblanco.com) has recently developed a kit, named DITOBA, for its diagnosis on the basis of the measurement of four proteins in serum. These proteins were identified in previous proteomic analyses performed by the group on samples from the Prospective Cohort of OA A Coruña (PROCOAC, Spain). A first LC-MS/MS analysis identified eleven peptides associated with OA and subsequently a targeted luminex-based assay was developed to quantify the corresponding proteins in 400 samples from PROCOAC. The inclusion of these proteins into a clinical model composed of demographic and clinical data has resulted in an algorithm for the diagnosis of OA without the need of XRay. Furthermore, a clinical validation of this model has been carried out in 1200 samples from the Osteoarthritis Initiative Cohort (OAI, USA) to qualify its use to monitor disease severity in OA positive cases, and predict the incidence of the disease before 8 years in the negative ones. This kit will facilitate the personalized management of patients suffering OA.

    Regarding rheumatoid arthritis (RA), a collaboration between RAD-HPP members has identified a specific autoantibody (anti-CENPF) whose presence in serum is associated with a positive response of the patient to Infliximab (a TNF inhibitor). In this case, the screening was performed on a cohort from Santiago de Compostela (Spain) using planar antigen arrays from the Human Protein Atlas, which contain 42100 PrEST representing 19000 unique proteins. Further targeted validations were carried out on additional samples from A Coruña (Spain) and Sweden (SWEFOT cohort), in this case using in-house made suspension beads arrays. Finally, a statistical analysis was performed to assess the clinical relevance of the findings. The addition of anti-CENPF antibodies to demographic and clinical variables (age, sex and a disease activity score) resulted in the best model to predict responders to Infliximab, showing an area under the curve (AUC) of 0.756 (Lourido et al., Seminars Arthritis Rheum 2020). This study indicates the usefulness of anti-CENPF measurement to guide therapeutic interventions in RA.

    Finally, RAD-HPP members have also focused interest on the analysis of the RA citrullinome and its link to clinical phenotypes (Fert-Bober et al., Immunol Rev 2020), and others have participated through the Accelerating Medicines Partnership in RA/SLE Consortium in a ground-breaking work providing a molecular basis by which stromal cells can be therapeutically targeted in RA (Wei et al., Nature 2020). Altogether, these studies show the latest activity of RAD-HPP in the development of initiatives for the application of proteomics strategies to improve the management of patients suffering RAD.

  • 26 Nov 2020 6:11 PM | Anonymous member (Administrator)

    The Human Proteome Project (HPP) Special Issue in Journal of Proteome Research will be published on December 4, 2020, with more 15 articles and one editorial addressing different issues related to the human proteome. The Guest Editorial team comprising Drs. Young-Ki Paik, Gil Omenn, Lydie Lane, Eric Deutsch, Fernando Corrales, and Chris Overall (Associate Editor) were responsible for this 8th Special Issue.

    - The Special Issue commences with the Annual HPP Metrics paper by Omenn et al 2020 (https://doi.org/10.1021/acs.jproteome.0c00485). The HPP metrics paper provides fine grain detail of progress and challenges in credibly identifying the human proteome over the past year.

    - Two papers addressing the use of pluripotent stem cells (PSCs) to study function of uPE1 proteins, which proteins are well detected, but they have no single known molecular function by Frederik Edfors and Ghasem Salekdeh and colleagues (https://dx.doi.org/10.1021/acs.jproteome.0c00689).

    - Kotol et al (https://dx.doi.org/10.1021/acs.jproteome.0c00194) used information derived from the Human Protein Atlas to devise a series of isotopically labelled peptides with corresponding PRM assays for the detection of 21 drug targets and biomarkers in human plasma.

    - Insight into the First Phosphoproteomics challenge of the MS Resource Pillar by Rob Moritz and Sue Weintraub in Hoopmann et al (https://dx.doi.org/10.1021/acs.jproteome.0c00648). Standardised sets of 94 phosphopeptides were analysed by 22 laboratories using different approaches, MS instrumentation and bioinformatics. The data were reanalysed in a consistent manner that pointed out the challenges of correct phosphopeptide site identification.

    - Bioinformatics approaches were developed as described in this special issue to tackle the uPE1 challenge include a guilt-by-association bioinformatics approach from the Spanish team in Gonzalez-Gomariz et al 2020 (https://dx.doi.org/10.1021/acs.jproteome.0c00364). In an innovative approach, the authors employed web search tools, such as the Google page rank algorithm, to develop UPEFinder. The Korean Chromosome 11 team used the successful I-TASSER/COFACTOR approach to predict 2,413 GO terms for 22 uPE1 chromosome 11 proteins (https://dx.doi.org/10.1021/acs.jproteome.0c00482).

    - Ping Xu team used Open-pFind tool, which is an open modification search tool, which improves identification of peptide and proteins, and with this tool the authors identified peptides candidates for 103 missing proteins, from which 4 were validated in the study (https://doi.org/10.1021/acs.jproteome.0c00370) (China).

    - From the Human Protein Atlas and the Antibody Resource Pillar comes the achievement of “enhanced validation” of nearly 6,000 antibodies directed towards 3,775 proteins in many tissues detailed by Sivertsson et al (https://dx.doi.org/10.1021/acs.jproteome.0c00486) (Sweden). This led to the localization of 56 candidate MPs and 171 uncharacterised PE1 proteins (uPE1) lacking any known function.

    - Vandenbrouck et al 2020 (https://dx.doi.org/10.1021/acs.jproteome.0c00516) tackled the uPE1 neXt-CP50 Challenge in a cohort of 421 uPE1 proteins found in higher abundance in the male reproductive tract by compilation of diverse evidence. To functionally annotate such proteins, contextual information from the literature, protein-protein interactions, expression levels and cellular localization were employed in a knowledge-driven approach to suggest rational, knowledge-founded hypotheses that can be experimentally tested in a targeted manner with higher probability of incise results and less false starts.

    - The Journal welcomes the new Chair of the HPP, Dr. Rob Moritz, Institute for Systems Biology, Seattle as a new Guest Editor for the 9th Annual Special Issue of the Journal of Proteome Research on the HPP in 2021.

    Join us! Research teams for Chromosome 21 and 22!

    C-HPP Consortium leadership is looking for partners, which can join C-HPP initiative to advance MP50 and CP50 projects by identifying missing proteins and identify function(s) to uPE1 proteins for chromosomes 21 and 22. Motivated PIs are encouraged to contact Chris Overall (Chair of C-HPP, email chris.overall@ubc.ca) or other members of the C-HPP leadership.

    23rd C-HPP Workshop in Busan (South-Korea), June 28-30, 2021

    Due to COVID-19 pandemic and related health risk and world-wide travel restrictions we had many meetings and workshops cancelled, amongst others the 23rd C-HPP Workshop originally planned in May 15-18, 2020 in Saint Petersburg, Russia. We hope that vaccine against SARS-CoV-2 viral infection will be available in early next year and our onsite meeting will be held in Summer 2021 as planned. Therefore, we would like to encourage you to plan on joining the 23rd C-HPP Workshop on June 28-30, 2021, in Busan, South Korea. This meeting is being organized in conjunction with Commemoration of the 20th Anniversary of AOHUPO (www.aohupo.org). The C-HPP EC will make you update on the preparation of this meeting with scientific programs through the websites of HUPO, C-HPP and C-HPP Wiki in addition to our routine email communications.

    We wish you and your family to stay safe and healthy.

  • 20 Nov 2020 1:04 PM | Anonymous member (Administrator)

    Bruno Tilocca and Paola Roncada, HUPO B/D-HPP Food and Nutrition Team, University Magna Græcia of Catanzaro, Catanzaro, Italy

    The animal gastrointestinal tract provides the perfect milieu for hosting the heterogeneous ensemble of microorganisms (bacteria, virus, fungi and protozoa) that are commonly harbored in the intestine. Here, microbiota members establish a complex and intricate network of interconnections among each other and the hosting organism. Recent investigations unveiled the importance of understanding the synergistic interactions between the host and its microbiota, enlightening how the fine orchestration of the gut microbiota composition and activity impact a variety of biochemical and physiological processes that are, in turn, responsible for both beneficial and detrimental health conditions in humans and animals. In this context, Dr. Bruno Tilocca along with the other researchers of the “Feed-gut-microbiota” group of the University of Hohenheim employed a microbial community fingerprint through 16S rRNA gene sequencing and metaproteomics to study the active bacterial fraction inhabiting the diverse sections of the chicken and pig gastrointestinal tract. Investigating the microbiota by the sole genome-targeting approaches enables a comprehensive depiction of the microbial consortia architecture and its potential functions as assessed through the functional prediction of the sequenced genetic elements. Nevertheless, structural composition assessed by microbial community fingerprint has been leveraged by Dr. Tilocca and colleagues while optimizing a metaproteomic workflow aimed at the effective functional featuring of the microbial community harbouring the diverse intestine sections. Specifically, the bacterial families identified by the 16S rRNA gene sequencing are employed for the construction of a single non-redundant in-house database. The database dependent searches performed by the custom databases resulted in a higher protein identification rate as compared with the conventional metaproteomics workflow expecting bioinformatic searches against publicly available databases. Also, the use of DNA-driven custom database enabled a statistically confident identification of the protein dataset and its successive functional classification. Through metaproteomics Dr. Tilocca and colleagues gained a fair depiction of the metabolically active bacterial fraction, allowing for the elucidation of the core microbiota composition along with the major biochemical pathways the gut microbiota members of the diverse gastrointestinal tract sections are involved in. Marked differences were observed in the microbial communities of the diverse gastrointestinal tract sections in both structural and functional terms. Both chicken and porcine animal model reported increased microbial diversity when moving toward the caudal direction. Interestingly, discrepancies were observed when comparing the microbiota architecture assessed by the DNA-based method and the metaproteomics. The higher bacteria heterogeneity highlighted by the metaproteomics has been attributed to the changing microbiota dynamics and the fact that changes in protein abundance occur earlier than changes of DNA copy numbers. This observation provides support in the identification of metaproteomics as a suitable discipline for the investigation of the microbial community composition in dynamic contexts, representing a valuable tool to highlight the microbial specimens driving the changes required to the achievement of a novel homeostatic balance. Besides, functional featuring of the microbiota in the diverse gastrointestinal sections through metaproteomics enabled deciphering biochemical involvement of the bacterial families in the diverse sections other than clarify the contribution of the microbiota in the animal physiological processes and the response to external stimuli such as the reaction to environmental stressors

    More recently, research interests of the Dr. Tilocca are extended to the study of the microbial communities inhabiting “abiotic” ecological niches such as the milk and its by-product. In this view, Dr. Tilocca along with the Prof. Paola Roncada, at the Department of Health Science of the University “Magna Graecia” of Catanzaro, are running an articulated research project aimed at featuring the Nicastrese raw milk, and cheese. Here, metaproteomics is the method of choice as it enables the demonstration the microbiological signature (i.e. the active bacterial fraction) of the raw milk of this typical Calabrian goat bred and describes the structural and functional shaping of the microbiota throughout the diverse cheese-making steps. Besides, metaproteomics allows for detailing the biochemical role of the microbiota in ensuring both biosafety and the development of the unique gustatory and olfactory essences of this traditional product. In this view, researchers are confident that employing such innovative approach might open new avenues for the fair valorization of this and other ancient and typical products with unevaluable benefits for the social and economic reality at a local level other than delighting the palate of the consumers, worldwide.

    Dr. Bruno Tilocca is currently Assistant Professor at the University “Magna Graecia” of Catanzaro in the field of proteomics, microbiology applied on animal infectious disease in prof. Paola Roncada’ s group. He gained a PhD at the University of Hohenheim (Germany) in animal science. His research activities concern the animal infectious disease and the study of the animal microbiota through omics sciences. His research works are summarized in over 20 peer-reviewed articles and two contributes to books.

  • 30 Oct 2020 4:18 PM | Anonymous member (Administrator)

    With the expanding goals of the HPP and aggressive timelines to drive the numerous initiatives under the HPP umbrella of activities, the HPP seek to engage a vibrant, well-organized, and goal-oriented proteomics researcher to the HPP Co-Chair position to support and assist the HPP Chair.

    The HPP Co-Chair position is a 2-year term and will commence January 2021.

    To apply, please submit a brief (<1 page) vision statement outlining why you are a suitable candidate for this position. Email vision statement to office@hupo.org before November 30, 2020.

  • 30 Oct 2020 12:03 PM | Anonymous member (Administrator)

    Since the COVID-19 pandemic and related health risk world-wide poised travel restrictions, the C-HPP 23rd C-HPP Workshop in Russia was canceled. We hope that vaccine against SARS-CoV-2 viral infection will be available, which would ease travel restrictions by summer 2021. If so we hope our PIC members and all interested C-HPP members will join the next C-HPP Workshop to be held on June 28 – 30, 2021 in Busan, South Korea. The C-HPP EC will announce in due time the program on the HUPO, C-HPP Portal and C-HPP Wiki websites.

    (C-)HPP achievement on completion of 90% of the Human Proteome with high stringency

    • The “Blueprint” paper of the draft human proteome by Adhikari et al of the HPP was published announcing the completion of 90% of the human proteome in time for HUPO Connect (REF).
    • An Editorial by Chris Overall on the commemoration of the 10th anniversary of HUPO HPP. entitled "The HUPO High-Stringency Inventory of Humanity’s Shared Human Proteome Revealed", is available at the Journal of Proteome Research (JPR) website.
    • A virtual Special Issue of the JPR was published on the journal website which features a collection of 60 highly cited papers representing diverse teams, approaches, results, impact and progress on the HPP during the past 10 years.
    • The metric paper by Omenn et al. also highlights completion of >90% of the Human Proteome at the JPR website and leads the JPR virtual Issue

    C-HPP related program and highlights are available at C-HPP Wiki. The C-HPP EC wish you and for all your family to stay safe and healthy.

  • 30 Oct 2020 12:03 PM | Anonymous member (Administrator)

    The C-HPP PIC meeting at HUPO Connect 2020 was held on Monday, October 19, 17:15 – 18:10 EST time where the following topics were discussed and some important decisions were made:

    • Report and progress of chromosome teams in next-MP50 and next-CP50 projects.
    • Lydie Lane was elected unanimously as C-HPP Co- Chair for the next 3 years (2021.1 – 2023.12).
    • Discussion about stimulating our joint chromosome teams activities as well as collaboration with teams in B/D-HPP. It was also confirmed that the vacancies of PIs (Chr 21, 22) were now being sought by the B/D-HPP EC from the appropriate B/D-HPP teams.
    • A decision was made to extend by three years the neXt-CP-50 challenge due to the COVID-19 pandemic and the nature of protein characterization that takes longer times compared to MP search (new term: 2018-2024).
    • It was also recommended that all chromosome teams update their results and any changes in team members on C-HPP Wiki and the C-HPP Portal.
  • 19 Oct 2020 1:20 PM | Anonymous member (Administrator)

    In the midst of a pandemic, in the midst of the global effort to develop effective vaccines and anti-virals for SARS-CoV-2—yet, paradoxically, also in the midst of a surreal moment in history where the very science that can save millions is assailed if the facts and truth conflict with political mantra—we nonetheless can celebrate. Reminding us all of the importance and relevance of science, today, October 19, 2020, we celebrate the announcement of the draft human proteome in the opening talk at HUPO CONNECT by the First Chair of the Human Proteome Project (HPP), Dr Gil Omenn, with a virtual issue of the Journal of Proteome Research (https://pubs.acs.org/page/jprobs/vi/humanproteome). In the virtual issue the editors have compiled 60 of the most significant papers published in the Journal over the past decade on the human proteome project reflecting the diversity of the C-HPP and B/D-HPP teams, regions, approaches, impact and achievement.

    The neXtProt database posted the landmark human proteome data release covering 90% of the human proteome on 17th January, 20201, which is now reported by the HPP Consortium in Nature Communications by Adhikari et al 20202. In the companion annual human proteome metrics paper by Gil Omenn et al 20203 reporting this year’s progress of the HPP, the underlying data is presented in depth. The metrics paper will be published in the 8th Special Issue of the Journal of Proteome Research dedicated to the HPP in December 2020, with the ASAP preprint online today leading this HPP Virtual Issue and with a commentary editorial by Chris Overall4.

    The human proteome was identified by HPP global research teams and scientists from the wider scientific community and assembled by the Chromosome Centric-HPP (C-HPP) and the HPP Knowledgebase Pillar data curators from neXtProt PeptideAtlas, and MassIVE. The C-HPP was established in 2010 as the major initiative of the HPP to identify at least one protein form (proteoform) from each of the protein-encoding genes in the human genome. For the next high-fidelity compendium of the full human proteome and to develop a broader understanding of life, human conscience, and disease, proteomics needs more data, more patients, more scientists, and more doctors to understand life, individuality, personality and disease—science needs us all, but now, more than ever, humanity needs more science

    1. https://www.nextprot.org/about/statistics

    2. Subash Adhikari, Edouard Nice, Eric Deutsch, Lydie Lane, Gilbert Omenn, Steve Pennington, Young-ki Paik, Christopher Overall, Fernando Corrales, Ileana Cristea, Jennifer Van Eyk, Mathias Uhlen, Cecilia Lindskog, Daniel Chan, Amos Bairoch, James Waddington, Joshua Justice, Joshua LaBaer, Henry Rodriguez, Fuchu He, Markus Kostrzewa, Peipei Ping, Rebekah Gundry, Peter Stewart, Sanjeeva Srivastava, Sudhir Srivastava, Fabio Nogueira, Gilberto Domont, Yves Vandenbrouck, Maggie Lam, Sara Wennersten, Juan Antonio Vizcaino, Marc Wilkins, Jochen Schwenk, Emma Lundberg, Nuno Bandeira, György Marko-Varga, Susan Weintraub, Charles Pineau, Ulrike Kusebauch, Robert Moritz, Seong Beom Ahn, Magnas Palmblad, Michael Snyder, Ruedi Aebersold, and Mark Baker. A High-Stringency Blueprint of the Human Proteome, Nat. Communications, 2020, doi.org/10.1038/s41467-020-19045-9.

    3. Omenn G. S.; Lane L.; Overall C. M.; Cristea I. M.; Corrales F. J.; Lindskog C.; Paik Y-K.; Van Eyk J. E.; Liu S.; Pennington S.; Snyder M.P.; Baker M.; Bandeira N.; Aebersold, R.; Moritz, R.L.; Deutsch EW. Research on The Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res. 2020, Sep 15. doi: 10.1021/acs.jproteome.0c00485.

    4. Overall, C.M. J Proteome Res. 2020, October 19. The HUPO High-Stringency Inventory of Humanity’s Shared Human Proteome Revealed. https://pubs.acs.org/doi/full/10.1021/acs.jproteome.0c00794.

  • 19 Oct 2020 12:16 PM | Anonymous member (Administrator)

    In June 2020, the inaugural Chair of the HUPO Pathology Pillar, Prof. Dan Chan (Johns Hopkins University) decided to step down because of his large additional workload due to the Covid-19 pandemic. A new appointment protocol was established in order to find a suitable replacement. Applications were sought by advertising through HUPO and reaching out to possible candidates. Applicants were required to apply in writing addressing the following key points:

    i) Proteomics track record

    ii) HUPO/HPP track record

    iii) Evidence of national and International visibility

    iv) Vision for the future development of the Pathology Platform

    v) A one page CV

    vi) The names of high-profile scientific/clinical referees

    A committee consisting of 5 senior HUPO scientists was established to review the applications and a recommendation made to the chair of the HPP to take to the HUPO EC and Council for endorsement.

    We are pleased to announce Prof. Michael Roehrl (Memorial Sloan Kettering Cancer Center, New York (MSKCC)) as the new Chair of the HUPO Pathology Pillar. Michael is a practicing physician-scientist who holds an MD from Munich, Germany, and a PhD from Harvard in Biological Chemistry. He trained at Harvard Medical School and Massachusetts General Hospital and is US board-certified in both Anatomic Pathology and Laboratory Medicine. He directs the Center for Precision Pathology at MSKCC, and his clinical practice is focused on gastrointestinal oncologic pathology. Michael runs a research lab that studies the biology of solid tumors, and his group uses proteomics and protein-based biomarkers extensively with the goal of creating next generation diagnostics and theranostics for the benefit of cancer patients.

    The Pathology Pillar was launched at the 17th HUPO World Congress in Orlando in 2018 based on the realization that pathology (and clinical patient-focused applications) will play a key role in the clinical translation of proteomics methods and data and its use in precision medicine. The goals of the Pathology Pillar are to coordinate the identification of key unmet needs in clinical medicine, stimulate guidelines and standards for the development of fit-for-purpose validated clinical assays, promote awareness of best practice and coordinate access to high quality clinical samples and their associated data. The Pillar also aims to promote partnerships with key international pathology organizations, diagnostic industries, and regulatory agencies, develop educational programs and support early career researchers.

    With Michael at the helm, the HPP Pathology Pillar has a bright future and is requesting members to get involved and help drive this initiative. The integration of the other HPP Pillars to provide information and resources to the pathology Pillar will ultimately propel proteomics efforts further into the clinic and benefit health and wellbeing of all.

    Michael is honored to have been elected new Chair and, together with Co-Chair Ed Nice, is very much looking forward to engaging the entire HUPO community!

    Please contact Michael at roehrlm@mskcc.org and find his lab on Twitter @Roehrl_Lab

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