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  • 15 Apr 2021 12:13 PM | Anonymous member (Administrator)

    Don't miss the chance to submit your candidacy to become a HUPO Council member for a three-year term (2022-2024). Complete the Nomination Form (available here) and submit it to office@hupo.org before 30 April 2021.

    The current council list can be found here: 2021 Council List

    The deadline to receive nominations is 30 April 2021.

  • 30 Mar 2021 4:01 PM | Anonymous member (Administrator)

    Chris Overall, C-HPP Chair, Canada

    Hybrid 23st C-HPP Workshop to be held July 1, 2021 in Busan (South-Korea)
    With predicted travel restrictions and vaccination progress occurring at different rates in our various team countries the form of the 23st C-HPP workshop to be held in Busan (South-Korea) on July 1, 2021 will be a hybrid meeting comprised of face-to-face with online participation of one 4-hour session occurring from 15:00-19:00 local time. Keynote speakers will be Dr Lydie Lane, Co-Chair of the C-HPP and Josh La Baer. Team presentations, next-MP50 and next-CP50 updates, new strategies and future trajectory will be discussed. On the following day, Friday July 2, the annual C-HPP PIC meeting will be held for one hour. Details will follow as the dates close in.

    We hope that vaccination program against COVID19 will progress and will allow us to meet again in person soon.

    Looking for groups hosting C-HPP Workshop in 2022 and 2023
    C-HPP is playing a central role in completing the human proteome by discovering evidence for the proteins making up the missing proteome, in identifying the function of proteins with expression evidence at the protein level (PE1), but lacking any known function (uPE1 proteins), and in identifying human protein sequence variants and post-translational modification profiles. C-HPP EC and international chromosome teams are meeting twice annually at international HUPO Congress and at bespoke C-HPP Workshop. We are looking for volunteer teams to propose and host the 2022 and 2023 C-HPP workshops, sometime in spring. Please, send your workshop organisation plan to the C-HPP EC for consideration and help in developing a fantastic proposal.

    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

  • 25 Mar 2021 4:38 PM | Anonymous member (Administrator)

    The Journal of Proteome Research will publish its ninth annual Special Issue dedicated to highlighting the progress made on the HUPO Human Proteome Project (HPP). Since 2013, these Special Issues have captured incredibly important discoveries in the field, publishing over 250 articles that have collectively received over 5,000 citations. The Special Issue considers research papers encompassing both the Chromosome-Centric Human Proteome Project (C-HPP) and the Biology and Disease Human Proteome Project (B/D-HPP), as well from the Resource Pillars (Antibody, MS, Pathology, and Knowledgebase), and short definitive reports, submitted in the Letters format, on the discovery of a Missing Protein(s). To be considered, the missing protein(s) must meet the Guidelines v 3.0 and be cast in the context of the HPP and biological setting in which they were discovered.

    Manuscripts must be submitted by 30th June, 2021 to be considered for this Special Issue. Manuscripts must be submitted electronically through the ACS Paragon Plus Environment online submission system. Specify in the authors’ cover letter that the manuscript is intended for the HPP Special Issue.

    Editorial triage will determine whether manuscripts are appropriate for the HPP Special Issue, fulfill the HPP

    Guidelines 3.0 (2019-10-15) checklist and protein evidence based on the 2021-02-18 neXtprot (https://www.nextprot.org/about/protein-existence) release to be considered for publication. The completed checklist must be included with the cover letter. The full MS data submission to ProteomeXchange must also be completed prior to initial submission, and the PXD number provided in the abstract. Nonconforming papers will be returned unreviewed. All relevant papers will go through full peer review. On acceptance papers will go online and be available in time for HUPO-2021. Due to the publication schedule, only papers that are accepted by September 31, 2021 will be published in the December 2021 HPP Special Issue. Papers requiring more time for revision or falling outside of the scope of the Special Issue will be published in regular issues of the Journal.

  • 25 Mar 2021 4:21 PM | Anonymous member (Administrator)

    By Maggie Pui Yu Lam, B/D-HPP Executive Committee, USA

    Q1: Can you please tell us about when did you first become involved in HUPO activities? I was interested in switching my research direction to biological mass spectrometry in my early career. After few years of learning basics of proteins and biology, I became really serious to devote my efforts in developing mass spectrometry-based proteomics methods and attended my first HUPO congress in Amsterdam in 2008. I was so attracted to the “race” between the proteome complexity, still mostly underexplored at that time, and the rapid advancement in mass spectrometry presented in the congress. When the Chromosome-centric Human Proteome Project (C-HPP) was launched, encouragement from Young-Ki Paik for Taiwan team to work on the Chromosome 4 made my first engagement to the HUPO initiative.

    Q2: What made you interested in becoming a HUPO member? In my term as the President of the Taiwan Proteomics Society (TPS, 2009-2011), I started to learn more about the HUPO and HPP activities and enjoyed the team work to explore the proteome research and their impact to biology and medicine. I was subsequently involved in a few activities, including Publication Committee (2012-2016), Member-at-large (2014-2016), C-HPP (chromosome 4), Council Member (2014-2016), President-elect (2020) and President (2021-2022) of HUPO. It is truly a great honor and a big responsibility to serve as the HUPO president. I always believe that joint leadership and collaborative efforts can inspire new ideas with success beyond the expectation of a single mind. I look forward to working together to create an enabling environment for exploring the utility of proteomics to impact our life in the near future.

    Q3: What is important for a successful collaboration with non-proteomics researchers? On the long term experiences to work with my non-proteomics colleagues, every collaboration is like a short-term intense course of a special topic. Mutual understandings on the specific biology to be studied as well as technical knowledge on the strength and limitation of the proteomics characterization are the most important criteria, which takes patience and time to align on the same page. It seems to be more challenging for non-proteomics scientist to learn the technical details of proteomics than the other way around. I found that learning to speak the same language of a biologist or physician is very helpful to jointly design the experiment and identify the novel findings. Validation of proteomic discovery also takes time, which will definitely train ourselves to be more patient to wait for fruitful results to come.

    Q4: Could you please list three practical steps that all proteomics researchers can take in improving the visibility of proteomics globally? In the real world, such as the clinical community, people tend to see what has been achieved rather than what should be established. Only when we demonstrate utility with board level visibility and critical mass, proteomics can be appreciated as a powerful tool. Everyone can contribute to enhancing its visibility by the following actions: (1) In collaboration with non-proteomics scientist, we can try to maximize the value of proteomics finding to answer the key biology or clinical question beyond the existing knowledge; (2) Outreach to expand the proteomics applications for various topics can promote it into one of the major tools for life science community; (3) The proteomics technology of its current status has achieved high degree of maturity for practical application. It is time to transform proteomics into utilizes in various aspects of life, such as clinical care, precision agriculture and food safety.

    Q5. What are the major hurdles that proteomics faces on the way to its integration into daily clinical practice? The clinical community has relatively conservative view to adapt well-established and cost-effective approach within existing clinical infrastructure. Adapting proteomics tool, a brand new concept in clinical setting, requires visible and valuable benefit to change the clinical practice. I would expect that demonstrating the clinical benefit of proteomics in large cohort beyond the publication is the most effective way. On the technical aspect, standardization (preferred to establish regulations and guidelines), highly robust sample handing pipeline with automation, rapid analysis workflows with high throughput, will facilitate acceleration of the transformation process for proteomics into clinical practice.

    Q6: What advice would you give to Early Career "proteomics practitioners" to best set up themselves for a long and prosperous career? The field of proteomics has evolved in very fast paths. Even with the availability of many tools, the ability to develop new technology or implement methodology to best address a specific question is important. In the big data era, the advanced instrumentation easily allows high quality and large-scale dataset. Thus, the expertise to develop or apply computation tools is the key to explore the gold mine of new discovery. Finally, being able to enjoy the discovery from proteomics will keep our passion to proteomics in the long run.

    Q7: Could you please list a few proactive steps that proteomics researchers can take to position proteomics in multi-omics studies (e.g., as has been done on a grand scale by CPTAC3 for proteogenomics of cancers)? As shown in the CPTAC efforts and achievements, proteomics has demonstrated complementary functionality to reflect new cancer subtypes and enhance our understanding on cancer biology. Compared to genomics, proteomics data has shown closer engagement of with clinical features. This new knowledge can be taken into action by validating biomarkers for future strategy in precision oncology. With rigorous assay optimization and validation on adequate size of cohort, the features of unprecedented accuracy on highly multiplexed analysis of mass spectrometry make them promising tools as a routine component of oncology clinic. I expect much faster path of proteomics discovery and validation in the near future.

  • 01 Mar 2021 12:31 PM | Anonymous member (Administrator)

    Chris Overall, C-HPP Chair, Canada

    Call for papers for the 9th HPP special issue in the Journal of Proteome Research 2021

    We are glad to announce that the 9th HPP Special Issue in the Journal of Proteome Research will be published in December 2021 with a submission deadline for the papers of June 30, 2021. We are looking forward to your submission on C-HPP (uPE1, missing proteins or papers on the dark proteome) or B/D-HPP topics. Please use the version on protein evidence in NextProt, published 28th February, 2021. The 8th Special issue is available @ Journal of Proteome Research website.

    New neXtProt release with new features

    The neXtProt team is happy to announce the latest release of updated neXtProt 28th February 2021, with an updated list of human proteins credibly identified along with the list peptide evidence for each protein and many more features.

    Proteins (PE1 – PE5) 20,379
    PE1 Protein Existence at protein level 18,357
    PE2 Protein Existence from transcripts 1,265
    PE3 Protein Existence from homology 147
    PE4 Protein Existence from prediction 9
    PE5 Uncertain 601
    Proteins (PE1 – PE4) 19,778
    PE2 – PE4: Missing Proteins 1,421

    Join us! Research teams for Chromosome 21 and 22!

    C-HPP Consortium leadership is seeking partners who can join the C-HPP initiative to advance MP50 and CP50 projects by identifying missing proteins and determining 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.

    Hybrid 23rd C-HPP Workshop in July 1, 2021 in Busan (South-Korea)

    In line with predicted travel restrictions and vaccination progress in different countries the form of the 23st C-HPP workshop in Busan, South-Korea, July 1, 2021 will be a limited face-to-face hybrid meeting. There will be one session of 2 hours duration commencing at 15:00 local time on July 1, 2021. The C-HPP PIC will also be scheduled for one hour during this week (TBA).

    We look forward to vaccinations and new treatments where science is recognized to play a huge part in relieving human suffering, morbidity, mortality and loss. We also look forward to meeting again in person at international meetings, workshops and conferences safely in the future

  • 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.

    Bio
    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.


    References

    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.

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