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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.
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 email@example.com before November 30, 2020.
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
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.
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:
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
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.
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 firstname.lastname@example.org and find his lab on Twitter @Roehrl_Lab
The 2020 Metrics of the HUPO Human Proteome Project (HPP) effort to credibly detect every protein of the human proteome has been released (see https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00485). This report now provides evidence for detected expression for >90% of the 19,773 predicted proteins coded in the human genome. The HPP annually reports on the progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. The 2020 metrics paper describes the credibly detected proteins (PE1 level) as well as the 4 other PE levels of protein evidence in a central repository for community sharing of these results. With the neXtProt release of 2020−01, 17,874 genes encoding proteins are classified as PE1 and having strong protein-level evidence. This PE1 level is up 180 proteins from 17,694 one year earlier and represent 90.4% of the 19,773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the “missing proteins” (MPs), was reduced by 230 from 2129 to 1899 since the previous year’s release neXtProt 2019−01. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry (MS) data for neXtProt, supplemented this year with extensive data from the MS repository MassIVE. The mass spectrometry data knowledge bases promoted 362 and 84 canonical proteins (PeptideAtlas and MassIVE respectively) in the last year to increase the credibly identified proteins. The Human Protein Atlas also released new protein detection repositories (based on antibody binding data to human proteins) for Blood, Brain, and Metabolic Atlases. The Biology and Disease-driven (B/D)-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions.
Of the remaining “missing proteins”, hydrophobic proteins account for about 40% of these and are compounded by protein sequence structures that are difficult to extract credible peptides for high-stringency identification. These missing proteins include large families or groups including GPCR, zinc finger, homeobox, keratin-associated, and coiled-coil domain proteins. We expect novel strategies for finding missing proteins, characterizing the functions of already-detected “dark” proteins, and utilizing proteogenomics in precision medicine to be fruitful in the coming years.
In addition, the Journal of Proteome Research will produce a year-end virtual Issue with dozens of high-impact papers from the 7 annual special issues of JPR from the Human Proteome Project.
The Human Proteome Project (HPP) releases the first Human Proteome Organization (HUPO)-endorsed, high-stringency Human Proteome Blueprint in Nature Communications (see https://www.nature.com/articles/s41467-020-19045-9). Like the draft “shotgun” Human Genome Project of the Human Genome Organization (HUGO), the HPP has now reached a significant decadal milestone of >90% completion of the Human Proteome that is referred to as the human proteome “parts-list”. This effort recognizes significant community efforts that enabled data inspection and re-analysis, culminating in a high stringency (i.e., rigorous, exacting standards for post-acquisition data processing and protein inferences made from MS spectral data) HPP knowledge base (KB). Additionally, to illustrate the many parallel historical innovations made by the scientific community that have driven proteomics advances, HUPO has created a publicly available interactive historical timeline to be released coincident with publication of this article (hupo.org/Proteomics-Timeline).
The HPP’s mission is to reanalyze and integrate community proteomics data with high-stringency processes, bringing increased granularity to our molecular understanding of the dynamic nature of the proteome, including all its modifications, and their relation to human biology and disease. This mission aligns closely with HUPO’s motto “translating the code of life”, providing crucial information that genomics per se cannot deliver. Completion of the HPP will enhance our understanding of human molecular and cellular biology, laying better foundations for diagnostic, prognostic, therapeutic and precision medicine applications.
In 2010, the Human Proteome Organization launched the Human Proteome Project (HPP), as an international endeavor to create a framework for global collaboration, data sharing and quality assurance, enhancing accurate annotation of the genome-encoded proteome. Over the last decade, the key resources of the HPP (the Human Protein Atlas, PeptideAtlas, MassIVE and neXtProt knowledge bases) have driven the development and refinement of guidelines and metrics to understand the definitive identification of any protein of the human proteome. Their high-stringency reanalysis of community data led to the current status of >90% identification completion rate of the Human Proteome. This knowledge is essential to discern the proteome’s role in health and disease. Here, on behalf of the proteomics community, we report the inaugural high-stringency human proteome project blueprint, illustrating roles in the diagnosis and treatment of cancers, cardiovascular and infectious disease pathologies.
The Human Immuno-Peptidome Project (HIPP) was launched in 2015 under the aegis of HUPO and B/D-HPP (https://hupo.org/Human-Immuno-Peptidome-Project). The vision of HIPP is to map the entire repertoire of peptides presented by HLA molecules using mass spectrometry technologies, and make its robust analysis accessible to any immunologist, clinical-investigator and other researchers around the globe. The main pillars of the HIPP program are the following: (1) method and technology development, (2) standardization, (3) effective data sharing, and (4) education . Etienne Caron and Michal Bassani-Sternberg are the current HIPP Chair and co-Chair. Under their leadership, the following short-term and middle-term goals were determined:
Since its foundation, two international HIPP workshops and one summer course have been successfully organized to move forward the field of immunopeptidomics from a community perspective.
With the expanding goals of HIPP and the increasing interest of the scientific community, we seek to engage two strong, well-organized, strategic, vibrant, enthusiastic, goal-oriented immunopeptidomics researchers who would be suitable candidates to the Chair and co-Chair positions. HIPP is keen to ensure regional, gender and early career scientist equity across its management structures.
The HIPP Chair and co-Chair position is a 2-year term (restricted to 4 consecutive years) and will commence in 2021. The responsibilities of the Chair and co-Chair can be summarised under the following areas:
1. Leadership. The overarching role of the Chair is to provide leadership, he/she must be an effective strategist and a good networker. The co-Chair will assist and support the HIPP Chair.
2. Committee. The first immediate responsibilities of the Chair/co-Chair will be to establish a HIPP Committee. The Committee will be composed of several members including a Treasurer who will manage the finances (currently in a HUPO bank account). The Committee will set short-term goals and will develop a plan to achieve those goals. The Chair/co-Chair will make the most of their committee members and will review the committee’s performance and identify and manage the process for renewal of the committee through recruitment of new members.
3. Coordination. The Chair/co-Chair will make sure that each meeting is planned effectively. They will co-ordinate the Committee to ensure that appropriate procedures are in place for the effective management of HIPP.
4. Representation. The Chair/co-Chair may from time to time be called upon to represent HIPP and sometimes be its spokesperson at, for example, HUPO meetings. The Chair/co-Chair will also be responsible for reporting HIPP’s annual progress to HPP/BD-HPP upon request by HUPO.
To apply, please submit a photo of yourself, and a brief (<1 page) vision statement outlining your background, previous activity in the HIPP initiative and why you are a suitable candidate for the HIPP leadership. Email vision statement to Michal.email@example.com before November 15, 2020.
Only HIPP members from academia can apply for the chair and co-chair positions, while members from industry can take part in the HIPP Committee. Applications will be reviewed by the Executive Committee of the B/D-HPP. In case of many applications, the current Chair and Co-Chair, together with the Executive Committee of the B/D-HPP will shortlist several most suitable candidates. The final list of candidates will be posted on the HIPP website, and the HIPP members will vote online for the suitable candidate. The applicant with the majority of votes will become the new Chair and the second place will become the co-Chair. The successful candidates will be announced shortly after the election.
1 Caron et al. (2017) A case for a human immuno-peptidome project consortium, Immunity 47, 203-208.
Dear HUPO colleagues and B/D-HPP team members:
I am happy to inform you that the B/D-HPP Executive Committee organized a 60 min BD-HPP team meeting on the last day (Thursday) of the HUPO connect.
We will use this meeting to discuss B/D-HPP goals, accomplishments, and ongoing EC efforts. These discussions will include the organization of additional annual virtual team meetings, HUPOST efforts, and modernization of the team chair election process with you.
We will also highlight four B/D-HPP teams, and short five-minute overview talks will be given by selected team members to review some of the organization and recent achievements of each initiative.
The meeting is open to all B/D-HPP investigators and other scientists interested in the B/D-HPP and free of charge.
Meeting time: Thursday, Oct 22, 3:00 - 4:00 PM UTC (i.e., 8:00 - 9:00 AM PDT; 11:00 AM - 12:00 PM EDT; 5:00 - 6:00 PM CET)
Please use the following link to find the corresponding time in other time zones: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20201022T1500
We apologize for the inconvenient time of this meeting for several geographical areas. This time was selected to avoid overlap with the first three days of HUPO Connect and the HPP Day meeting that will follow shortly after our B/D-HPP meeting. We will record this meeting and will also try to schedule future meetings at different times.
Please join us! We need your voice and feedback for an interactive B/D-HPP and an effective progress for the next year.
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Hope to see you soon!
The B/D-HPP EC Members:
Ileana Cristea (Chair)
Fernando Corrales (Past Chair)
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