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Current and past HUPOST issues are posted here for your review. Stories, highlights, news, and announcements are gladly accepted for inclusion in the HUPOST. Please submit your information to the HUPO Office.
HUPOST November 2022
Chris Overall, University of Britich Columbia, Canada
Manuscript reviewing for the 7th Annual Special Issue of the Journal of Proteome Research on the HUPO Human Proteome Project is well under way. With 28 papers submitted, this December issue promises to be yet another success and highlight of the HPP year, albeit considerable work for the Guest Editors Young‐Ki Paik, Yonsei University, Eric Deutsch, Institute for Systems Biology, Fernando Corrales, Centro Nacional de Biotecnología (CSIC), Lydie Lane, Swiss Institute of Bioinformatics and of course the ever hard working Gilbert S. Omenn, University of Michigan. Due to the American Chemical Society publication schedule, only papers that are accepted by September 31, 2019 will be published in the December 2019 HPP Special Issue. The C-HPP, B/D-HPP and resource pillars are extremely grateful to the American Chemical Society and the Journal for their support of HUPO and the HPP.
Good luck with your papers and thank you for your support of the HPP and the Special Issue.
Chris Overall, Associate Editor, Journal of Proteome Research
Jochen Schwenk (Chair of the HUPO Plasma Proteome Project), KTH Royal Institute of Technology, Sweden
The 9th workshop on Affinity Proteomics took place in Alpbach, Austria from March 11th -13th 2019 (https://affinityproteomicsalpbach.com). What started from consortia meetings from the EU projects ProteomeBinders, Affinity Proteome and Affinomics brought together more than 140 attendees to the snowy mountains in a village where the famous Austrian scientist Erwin Schrödinger found his final rest.
The exciting agenda that Mike Taussig and his team assembled kicked off with a series of talks on applying affinity reagents to build a protein and cell atlas. These included multiplexed imaging approaches to expand the current insights into cellular structures of tissues. Following previous trends, a focus was also set on how to validate antibodies for the diverse set of downstream applications and how to liaise with other tools in proteomics. Continuing the traditions, a series of presentations covered the field of alternative binding reagents. This year’s talks provided updated insights into the advances made for generating binding molecules for research and therapeutic applications. These included the classical antibody formats and those developed from binding molecules found in other species such as camels or sharks. Besides protein-based reagents such as full-length IgG, single-chain variants such as nanobodies or ankyrin repeat proteins, talks covered the capabilities of those generated from DNA-based aptamers. A new theme included the strategies to develop binders that display bi-specific properties towards two proteins. Several presentations were given for applying affinity reagents in advanced and multiplexed analytical applications to profile human proteomes towards precise assessments of health and diseases. This theme was expanded by protein and peptide microarray systems in serology and as tools for selectivity assessment of binders.
Started during the previous event, the meeting included presentations and a panel discussion from antibody providers. They focused on the continuing task of context and application specific antibody validation and transparency of the validation information. As nowadays required by a growing number of journals, topics dealt further with the trackability of affinity reagents through standardized identifiers.
The workshop also brought some of the community’s most successful entrepreneurs to the stage. They shared their stories on building a business from generating and applying affinity tools. Another highly appreciated new feature were the flash and short talks by emerging scientists from the community as well as the lively interactions with the posters shown from nearly a third of all attendees.
The next Workshop on Affinity Proteomics is planned to be held again in Alpbach during March 2021.
Péter Horvatovich, University of Groningen, Netherlands
The C-HPP held their annual workshop in France, at the historic port town of St Malo this May. With over 45 registrants, the meeting was highly successful, due mostly to the excellent science presented by invited keynote speakers and the C-HPP teams, but also by the gastronomy selected by local convenor, Dr Charles Pineau. The central theme of the 21st C-HPP symposium was “Illuminating the Dark proteome”, which took place in May 11 – 14. The dark proteome is defined accordingly to C-HPP as “a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORFs (small potentially-translated open reading frames), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing.”
The complete scientific program with abstract and some presentations is available on the C-HPP Wiki, along with most other past annual C-HPP workshops. The symposium included presentations on various aspects of the human dark proteome, including structural biology, a summary of the pre-symposium full-day workshop on changes to the HPP Data Interpretation Guidelines by Eric Deutsch (see more details below), updates on neXtProt by Lydie Lane, and neXt-MP50 by Chris Overall, and the neXt-CP50 by Young Ki Paik. Also featured was a fascinating talk on an approach to reveal the localisation of human proteins by Anne-Claude Gringras, and the use of ProteinExplorer for integration of community-scale big data for assessment of protein existence by Nuno Bandeira. A full summary is being prepared now for the C-HPP newsletter.
HPP Data Interpretation Guidelines: A full-day workshop, one day prior to the symposium, featured extended discussion of 25 open questions related to updates to the HPP Mass Spectrometry Data Interpretation Guidelines and to the implementation of the workflow by which the HPP confirms the translation of potential coding genes. Each of the 25 topics were debated, potential solutions were listed, and a consensus decision among the participants achieved. The result will be an update of the guidelines from version 2.1 to version 3.0, and a manuscript that describes the open questions, the potential solutions, the consusus decisions, and the logic behind those decisions will be submnitted to the Jurnal of Proteome Research Special Issue on the HPP.
neXtProt update: neXtProt release 2019-01-11 should be used for the incoming publications in the JPR C-HPP special issue 2019. This release contains 2129 missing proteins, of which 441 have associated MS data which is insufficient for protein validation according to the current HPP guidelines. According to neXtProt query NXQ_00022, 2222 entries lack functional annotation. Out of these entries, 1254 are validated at protein level (uPE1). These are the targets of the neXt-CP50 challenge.
JPR Special Issue: The deadline has been extended to June 14 for papers on the C-HPP, B/D-HPP and from the pillars.
Edouard Nice, Monash University, Australia and Mark Baker, Macquarie University, Australia
As part of the interaction between HUPO and the Royal College of Pathologists of Australasia (RCPA), especially in Education and Training, there was strong HUPO participation in the recent “Pathology Update: The Power of Personalized Pathology” conference held at the Melbourne Convention Centre from 22nd to 24th February 2019. This meeting was attended by over 1350 delegates, including medics, pathologists, scientists, trainees and healthcare workers, with strong industry support (over 30 companies at the trade exhibition).
Prof Dan Chan opened the meeting with the David Rothfield Memorial Oration with a talk entitled “The success of Precision Pathology: Multi-Omics Building Blocks”. He explained how advances in cancer pathobiology that have helped elucidate the intricate cell signalling mechanisms that trigger oncogenesis are due to the combined effect of genomic, transcriptomic, epigenetic and proteomic changes. He gave examples of how significant advances in molecular technologies, such as the multiplex-polymerase chain reaction (PCR), next generation sequencing (NGS) and mass spectrometry (MS), coupled with computational medicine, have identified new biomarkers for improving disease classification and diagnosis, including the recently reported CancerSEEK test, which uses a combination of assays for genetic alterations and protein biomarkers, and has the capacity not only to identify the presence of relatively early cancers but also to identify their localisation. Prof Chan also made other presentations at the meeting on “Tumour Markers in Practice” and Understanding immunoassay: a practical guide” as part of the Chemical Pathology agenda. In a complimentary plenary talk on the Saturday morning, Prof Eva Raik discussed ‘Precision Cancer Medicine – cup half full or cup half empty’ discussing both the advantages and hurdles that currently exist.
On Sunday 24th a whole session was devoted to “Clinical Proteomics: Development of a Pathology Partnership”. This session was organised by Profs Ed Nice, Mark Baker and Dan Chan for HUPO and Profs Peter Stewart and Andrea Horvath representing the RCPA. The session was chaired by Dan, and comprised four talks. Ed Nice led off with a talk entitled “Clinical proteomic biomarker discovery and translation for pathology”. This started with an introduction to HUPO and the new Pathology Pillar, and the requirement for a strong interaction with clinicians and pathologists as we enter the transitional phase of proteomics. He then outlined the role of faecal proteomics in GI tract pathology.
This was followed by a talk from Prof Horvath on “Evidence-based evaluation of proteomic biomarkers: from unmet medical needs to clinical application” in which she described proteomics as the Knight in Shining Armour. Using a hypothetical on acceptance of biomarkers that have better performance than current tests for coronary atherosclerosis, she introduced several recent proteomics examples from the literature. She stressed the importance of unmet clinical need and validation in successful translation. Dr Steven Ramsay gave a presentation on “Challenges of developing protein biomarker assays for clinical use - method validation and quality issues” further illustrating the importance of this issue, using IGF1 as an example.
To close the session, Prof Peter Stewart, former president of the RCPA, acting as devils advocate, with a concept like the “glass half full or half empty concept introduced earlier in the meeting, discussed the “Barriers to adoption of Proteomics in clinical diagnosis”. He highlighted areas such as the complexity of the technology, measurement errors, throughput, skill base in technology and informatics and the need to up-skill pathologists (the goal of the HUPO-RACP collaboration), clinical utility and the cost and reimbursement rates.
All the slides that were presented in this session are currently available on line at https://www.rcpa.edu.au/Events/Pathology-Update/Post-Conference. Further joint HUPO/RACP sessions to further advance education and training are being planned for 2020.
Clinical Proteomics: Development of a Pathology Partnership. From left to right: Prof Peter Stewart, Prof Dan Chan Prof Rita Horvath, Dr Steven Ramsey, Prof Ed Nice
Pathology Update: The Power of Personalized PathologyFrom left to right: Prof Ed Nice, Prof Peter Stewart, Prof Dan Chan
Marta del Campo Mila, VU University, Medical Centre, Amsterdam, Charlotte Teunissen, VU University, Medical Centre, Amsterdam,
The HUPO Brain Proteome Project (HBPP) Steering Committee invites you to register for the 29th HUPO Brain Proteome Project Workshop, which will be held on 27th and 28th of May 2019 in Amsterdam.
HBPP Spring Workshops cover a wide range of topics relevant to neuroproteomics research. The program is highly dynamic and interactive, and all participants are given the opportunity to give an oral presentation on their research or updates of novel techniques and analytical approaches used in their labs. Workshops have included, for example, sessions on myelin proteomics, autoimmunity, and bioinformatics.
HBPP is committed to a strong clinical and translational focus. Hence, sessions in last meetings were dedicated to proteomics of psychiatric disorders, movement disorders, spinal cord injury & trauma, dementia, and cancers of the CNS. On top of that, there will be a very nice evening program that will allow all the delegates to have relax interactions with a unique local atmosphere.
The HBPP Steering Committee encourages every researcher interested in brain proteomics, including junior scientists to join this event. For more information about the workshop please visit https://www.hbpp2019.com/.
Don’t hesitate to extent and share this information between all your colleagues within the field.
We are looking forward to see your latest results at this inspiring meeting!
On behalf of the HBPP steering committee, thank you.
Kun-Hsing Yu (Harvard Medical School) and Maggie Lam (University of Colorado)
Among the missions of the HUPO Biology/Disease-driven Human Proteome Project (B/D-HPP) initiatives is to identify popular proteins in the human proteome associated with diseases and biological systems. Recently, there has been a number of software tools emerging that allow researchers to prioritize crucial proteins in various organ-systems and diseases from the biomedical literature. Information obtained using such tools which can be used to facilitate the development and promote the application of proteomics assays, such as multiple reaction monitoring to target disease-specific proteins. Our B/D-HPP groups have capitalized on these resources and made significant strides in assembling and sharing prioritized protein lists relevant to their biological systems and diseases of interest. Below we provide a brief overview of some of these software tools that enable the prioritization of popular proteins. These tools provide users ways to search and prioritize proteins related to their research interest and will facilitate targeted proteomics studies. Future algorithm and software development can further enable the prioritization of various proteoforms, such as phosphoproteome, glycoproteome, and alternative splicing isoforms, which will advance our understanding of the human proteome in health and disease states.
PubPular (Lau et al. J Proteome Res. 2018) PubPular is an R/Shiny web interface for querying and visualizing popular proteins for custom search terms using Gene2PubMed/PubTator data sources and semantic similarity metrics. Recent updates of PubPular also support the query of pre-compiled protein lists from Disease Ontology and Human Phenotype Ontology disease terms as well as reverse protein-to-topic searches. PubPular can be accessed via http://pubpular.net.
PURPOSE and metaPURPOSE (Yu et al. J Proteome Res. 2018) The Protein Universal Reference Publication-Originated Search Engine (PURPOSE) tool prioritizes proteins by the strength and specificity of the associations between proteins and the query terms. For each query, the number of PubMed publications are retrieved in real-time, and the results are summarized in the user-friendly web interface. PURPOSE is accessible through http://rebrand.ly/proteinpurpose.
metaPURPOSE is an extension of PURPOSE and prioritizes metabolites associated with any search terms. This tool addresses the challenges arisen from multiple synonyms associated with common metabolites and uses the PURPOSE algorithm to rank the retrieved metabolites. metaPURPOSE is hosted at http://rebrand.ly/metapurpose.
GLAD4U (Jourquin et al. BMC Genomics. 2012) Gene List Automatically Derived For You (GLAD4U) is a web-based tool that allows users to retrieve a prioritized list of Entrez-Gene IDs. The tool leverages the hypergeometric test to rank the list of biological entities associated with the query. Their user interface enables users to download the query results, conduct functional enrichment analysis using WebGestalt, and view the detailed publication list related to the retrieved genes. The GLAD4U tool is at http://glad4u.zhang-lab.org.
FACTA+ (Tsuruoka et al. Bioinformatics. 2011) Finding Associated Concepts with Text Analysis+ (FACTA+) is a text mining tool developed by the National Centre for Text Mining (NaCTeM), School of Computer Science, The University of Manchester, UK. The tool aims to assist users to identify associations among biomedical concepts, including genes, proteins, diseases, symptoms, drugs, and chemical compounds. For each query term, the associated biomedical concepts are retrieved and ranked. Users can view the snippets from the literature that describe the association. FACTA+ also allows users to find indirectly associated concepts by ranking the second-order associations between the query term and the target concepts. For access, go to http://www.nactem.ac.uk/facta/.
The dark proteome is defined accordingly to C-HPP as “a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORF (small proteins), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing.” The central theme of the 21st C-HPP symposium is “Illuminating the Dark proteome” and will take place in May 12 – 14, 2019 in Saint Malo (France) at the Hotel France & Chateaubriand, which is located inside the fortified city.
The complete scientific program and abstracts are now available online home page of the event and at C-HPP Wiki. The program – amongst others – includes discussion of the 3.0 version of Human Proteome Project Data Interpretation Guidelines, updates on neXtProt, PeptideAtlas, as well as progress on neXt-CP50 and neXt-MP50 challenges. Keynote lectures will be provided by:
In addition 23 talks were selected from the abstracts.
The organisers Charles Pineau, Chris Overall, Young-Ki Paik, Lydie Lane are looking forward to meeting with all C-HPP members and all interested participants, especially B/D-HPP members.
Dr Ying Jiang, Beijing Institute of Lifeomics, Beijing, China
Hepatocellular carcinoma (HCC) is the third leading cause of deaths from cancer worldwide. Infection with the hepatitis B virus is one of the leading risk factors for developing HCC, particularly in East Asia. Although surgical treatment may be effective in the early stages, the five-year overall rate of survival after developing this cancer is only 50–70%. Proteomic and phospho-proteomic profiling of 110 paired tumour and non-tumour tissues of HCC stratifies HBV-related early-stage disease into 3 prognostic subtypes. The disrupted cholesterol homeostasis is characterized in the subtype associated with the lowest overall rate of survival and the greatest risk of a poor prognosis after first-line surgery. Moreover, targeting SOAT1 (either knock-down or inhibitor treatment) suggests opportunities for personalized therapies. In conclusion, CNHPP study identifies the proteomic landscape in early HCC, and the patterns of protein signatures and pathways that are altered in proteomic subtypes of HCC. The drug-targetable proteins that identified by proteomic alterations may provide a powerful tool for identifying patients with HCC subtypes associated with a poor prognosis, and who might benefit from further targeted treatment, moving us towards the era of proteomics-driven precision medicine.
National Center for Protein Sciences (Beijing)
The dark proteome is defined accordingly to the HPP as “a colloquial term that includes missing proteins (PE2 – PE4), uncertain/dubious predicted proteins (PE5), uPE1 proteins, smORF (small proteins), and any proteins translated by long non-coding RNAs or uncharacterized transcripts including those arising from non-coding regions of DNA and/or novel alternative splicing.” The central theme of the 21st C-HPP symposium is “Illuminating the Dark proteome” and will take place in May 12-14, 2019 in Saint Malo (France) at the Hotel France & Chateaubriand, which is located inside the fortified city.
The program is currently available online on the home page of the event and on the C-HPP Wiki. The program – among others – includes discussion of the version 3.0 of Human Proteome Project Data Interpretation Guidelines, updates on neXtProt, PeptideAtlas, progress on neXt-CP50 and neXt-MP50 challenges. Key-note lectures will be provided by:
Besides C-HPP, B/D HPP PIC and young investigators will contribute to the program. Places are limited, but registration for the workshop is still possible online using a registration form. The hotel block has been completely filled, but we are hoping to free some more rooms from the hotel stock available till first week of April. However, this is uncertain and in that case another hotel will have to be sought by the registrants.
The organisers Charles Pineau, Chris Overall, Young-Ki Paik, Lydie Lane are looking forward to receive all C-HPP members and all interested participants from B/D-HPP and HUPO membership.
Jennifer Van Eyk, Burcu Ayoglu, Ferdinando Cerciello, Justyna Fert-Bober, Ruth Hüttenhain, Mathieu Lavallée-Adam, Adriana Franco Paes Leme, Giuseppe Palmisano, Ilaria Piazza, Fábio César Sousa Nogueira)
The ECR was launched as a new HUPO initiative at HUPO 2015 World Congress in Vancouver. The intent of the ECR is to be an open and easily reachable platform dedicated to the new generation of proteomics scientists of the HUPO community.
The ECR aims are to (1) promote connection between generations of proteomics scientists along the visions and the ideals of HUPO; (2) promote the scientific work of the new generation of proteomics scientists and to provide training and support for their early career development; (3) promote interaction and international collaboration among early career investigators in proteomics.
To achieve these aims, we explored common facilitators and challenges faced by early career researchers in proteomics during annual Mentoring Day at HUPO world congresses. The program of Mentoring Day, every year is different and has several ingredients to enhance an ECR individual’s success. Having supportive collegial relationships, institutional support, job security, and funding are critical facilitators for early career investigators. Key challenges include difficulty with time management and prioritizing, limited resources, and contacts. The talks, conversations and friendly atmosphere during Mentoring day, can potentially help transfer knowledge and expertise since it represents a variety of professional backgrounds and experience from more mature generation. This is also an exceptional opportunity to approach and interact with current and future world-renowned leaders in proteomics! For example, the focus of the mentoring day at HUPO2018 in Orlando was on “communication” and the program included various topics such as “what qualities are necessary for successful communication?”, “ten simple rules for choosing between industry and academia”, “communicating with funding agencies”, etc. Our mentors in Orlando were Beth Anderson (Arkitek Scientific), Nicolai Bache (Evosep), Sixue Chen (University of Florida, USA), Benjamin Garcia (University of Pennsylvania School of Medicine, USA), Arianna Jones (Sciex), Kathryn Lilley (Cambridge Centre for Proteomics. University of Cambridge. UK), Stephen R. Pennington (UCD Conway Institute, Dublin), Robert Rivers (NIH, USA), Jennifer Van Eyk (Cedars Sinai Medical Center).
ECR also promotes the scientific work of the new generation by organizing manuscript competition. For the manuscript competition, early career researchers are invited to submit their scientific work in form of a manuscript, which has either been published or accepted for publication within the previous year. Three finalists are then invited to present their research at the HUPO world congress to select the proteomic highlight of the year. For our most recent manuscript competition at HUPO2018 in Orlando we had three winners, Dr. Ruth Hüttenhain (University of California, San Francisco, USA), Dr. Mathieu Lavallée-Adam (University of Ottawa, Canada) and Dr. Ilaria Piazza (Swiss Federal Institute of Technology-ETH Zurich, Switzerland)! (pictures of the winners are reported below)
In addition to the already established activities, the ECR proudly contributed to the success of the HUPO PhD poster competition at HUPO2018 in Orlando. While the poster competition is an already established and successful tradition of HUPO, ECR started to be involved in organizing the competition as a way to highlight the work of very early career scientists! Eight finalists of the competition were selected to present their work in a three-minute power point presentation and Desmond Li (University of Sydney), Aaron Robinson (Cedars Sinai Medical Center) and Amber Weiner (University of Pennsylvania) were the winners of last year’s final! (pictures of the finalists are reported below, but CAVE: they have already been presented in a previous HUPOST)
HUPO2018 in Orlando was not only important for the ECR for expanding their activities but also for kicking off a bigger working committee. In 2015 ECR was successfully established by Dr. Burcu Ayoglu (KTH Royal Institute of Technology), Dr. Ferdinando Cerciello (University Hospital of Bern) and Dr. Justyna Fert-Bober (Cedars Sinai Medical Center) under the mentoring of Prof. Jennifer Van Eyk (Cedars Sinai Medical Center). To expand ECR activities they are now joined by the three finalists of the 2018 ECR manuscript competition (Dr. Ruth Hüttenhain, Dr. Mathieu Lavallée-Adam and Dr. Ilaria Piazza) as well as Dr. Giuseppe Palmisano (University of San Paolo, Brazil), Dr. Fábio César Sousa Nogueira (Federal University of Rio de Janeiro, Brazil) and Dr. Adriana Franco Paes Leme (Brazilian Biosciences National Laboratory, Brazil).
And our new members are already at hard work! Indeed, we are working on identifying new and additional opportunities to support and promote the scientific work of early career scientists, ideally in form of collaborative grants between young scientists. We are also working on defining a curriculum of “must to know” for early career scientists in proteomics. We hope that we will be able to join forces with already experienced education initiatives within HUPO and other groups of young researchers in proteomics in order to be able to establish together a series of master classes in proteomics dedicated to the early career researchers. In addition, we are reaching out to regional early career proteomics communities across the globe to connect and join forces with the intention to identify needs of early career researchers in proteomics, to further expand ECR activities and to support building up new regional communities for early career researchers!
Finally, a motivation for all early career researchers in proteomics to get ready for HUPO2019 in Adelaide:
And finally, a warm thank you for reading about our progresses!
The ECR working committee
The winners of the ECR manuscript competition at HUPO2018 in Orlando (from left to right): Dr. Ruth Hüttenhain (University of California, San Franciso, USA), Dr. Mathieu Lavallée-Adam (University of Ottawa, Canada), Dr. Ilaria Piazza (Swiss Federal Institute of Technology-ETH Zürich, Switzerland).
The finalists of the PhD poster competition: Shubham Gupta (Canada), Andreas Hober (Sweden), Desmond Li (Australia), Benjamin Pullman (USA), Aaron Robinson (USA), Tim Van Den Bossche (Belgium), Amber Weiner (USA), Juanjuan Xie (China).
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