The investigators of the HUPO Human Proteome Project (HPP) will hold their annual workshops to assess and accelerate progress on the major components of the Project, including the Chromosome-centric HPP teams (C-HPP), Biology and Disease-based HPP teams (B/D-HPP) and the Resource Pillars for Antibody/Affinity Reagents Profiling, Mass Spectrometry, Knowledgebases and Pathology.
Specific focus of the program are identification of PE2-4 Missing Proteins, generation of functional annotations for uncharacterized uPE1 proteins and connecting the C-HPP and B/D-HPP teams. We aim to complete the “protein parts list” (C-HPP), to stimulate applications of targeted proteomics to organ-specific biological studies (B/D-HPP) and to address many bioinformatics and antibody profiling challenges, as well as the “uncovered proteome”. Issues around HPP Governance, HPP membership, HPP new initiative expansion are also open for discussion in this HPP Sunday program.
(Mark Baker, Macquarie University)
(10 min each)
a) Presentation of Mark Baker on "The Human Proteome Project" in df format is available. This presentation in pdf format is available here.
b) C-HPP and JPR SI, Chris Overall, University of British Columbia, Canada). This presentation in pdf format is available here.
c) B/D-HPP (Fernando Corrales, CNB-CSIC). This presentation in pdf format is available here.
d) Knowledgebase (KB) Pillar (Eric Deutsch, ISB/Lydie Lane, SIB). This presentation in pdf format is available here.
e) Mass Spectrometry (MS) Pillar update and future (Sue Weintraub, UTHSCSA). This presentation in pdf format is available here.
f) Antibody/Affinity (AB) Pillar (Jochen Schwenk, KTH Royal Institute of Technology). This presentation in pdf format is available here.
g) Pathology Pillar (Dan Chan, Johns Hopkins). This presentation in pdf format is available here.
(rooms: Hall A & Skyway 2)
(Chair, Chris Overall, University of British Columbia)
a) Data interpretation guidelines (Eric Deutsch, ISB) (20 + 10 min discussion). This presentation in pdf format is available here.
b) neXtProt, protein annotation of MPs and uPE1 proteins (Lydie Lane, SIB) (20 + 10 min discussion). This presentation in pdf format is available here.
13:30-14:30 HPP Workshop 2 (Chair Fernando Corrales, CNB-CSIC). Illuminating the dark proteome to understand human biology and disease.
3 talks (18+2 min)
a) Update on Food and Nutrition Initiative (Paola Roncada, University of Magna Graecia Catanzaro). This presentation in pdf format is available here.
b) Progress in the KUHPP initiative (John M Arthur, University of Arkansas for Medical Sciences). This presentation in pdf format is available here.
c) HPP achievements, a Pubmed analysis (Maggie Lam, University of Colorado AMC/Jenny van Eyk, Cedars Sinai)
14:30-15:15 HPP Workshop 3 (Chair, Steve Pennington, UCD School of Medicine/Mark Baker, Macquarie University): Governance, membership and expansion
- 08h30-10h00: Session #1 - Draft MassIVE input into HPP (Nuno Bandeira, UCSD)
- 10h30-11h00: Session #2a - How to contribute to the C-HPP wiki (Peter Horvatovich, Univ. of Groningen)
- 11h00-12h30: Session #2b - Stranded and Singleton Peptides (Tadashi Yamamoto, Niigata University; Gil Omenn, U Michigan)
- 14h00-15h15: Session #3 - Human Membrane Proteome Tryptic Peptide Predictor (Subash Adhikari, Macquarie University)
- 15h45-17h15: Session #4 - Current advances in DIA data analysis (Brian Searle, ISB)
- 17h15-19h15: Session #5 - HPP Data Interpretation Guidelines 3.0 (Eric Deutsch, ISB) bioRxiv
- 08h30-10h00: Session #6 - Quantifying the impact of public omics data (Henning Hermjakob, EBI, Juan Antonio Vizcaíno, EBI)
- 10h30-12h30: Session #7 - (bioinformatics parallel session)
- 14h00-15h15: Session #8 - SPARQL hands-on session (Lydie Lane, SIB)
- 15h15-16h00: Session #9a - The need for bioinformatics tools in clinical settings (Ferdinando Cerciello, University Hospital of Bern, Inselspital)
- 16h00-17h15: Session #9b - Computational predictions for uPE1 protein functional annotation with I-TASSER and COFACTOR (Gil Omenn, U Michigan; Lydie Lane, SIB; Chengxin Zhang, U Michigan; Yang Zhang, U Michigan)
- 17h15-18h30: Ask the Experts session
- 08h30-10h00: Session #10 - MS Pillar 96-phosphopeptides standard assay results (Sue Weintraub, UTHSCSA)
- 10h00-11h00: Session #11 - EuBIC (European Bioinformatics Community) Intro, discussion, developers meeting (Julian Uszkoreit, Uni. Bochum; Tim Van Den Bossche, Ghent Univ.)
- 11h00-12h00: Session #12 - Emerging PSI Standards: PEFF, USI, PROXI, SpecLib format (Eric Deutsch, ISB, Juan Antonio Vizcaíno, EBI, Nuno Bandeira, UCSD, Luis Mendoza, ISB)
See http://bit.ly/hupohub2019 for schedule.
(program coordinated by Fernando Corrales)
HPP has organized 6 thematic sessions for HUPO2019 Mon-Wed concurrent tracks. The Session Chairs chose 2 invited speakers and 4 speakers from abstracts. On each of the 3 days of the HUPO2019 Congress, there will be one morning HPP parallel session and one parallel afternoon session.
Chairs: Peipei Ping (UCLA), Ying Ge (University of Wisconsin Madison)
- REBEKAH GUNDRY (Medical College of Wisconsin) (25 mins) Chamber and cell type specific views of the human heart glycoproteome and glycome in health and disease
- MELANIE WHITE (University of Sydney) (25) Delving deeper into the cardiac proteome by analyzing the heart modificome
- STEFAN LEHR (20) Proteomic profiling of plasma lipoprotein particles as a tool to identify novel subspecies
- SANDRA GOETZE (15) Relating high density lipoprotein particle composition to clinical signaling capacity
- MARIKA MOKOU (15) Cross-species tissue proteomics analyses in cardiovascular disease: unravelling Ariadne’s thread
- LING LIN (15) An anatomically resolved human heart transcriptome and proteome landscape reveals molecular signatures and disease-relevant pathways of end-stage dilated cardiomyopathy
Chairs: Cristina Ruiz (INIBIC) and Alex J Rai (Columbia University)
- STEVEN PENNINGTON (University College Dublin) (25) Clinical evaluation of a multiplexed protein panel to discriminate patients with psoriatic arthritis from those with rheumatoid arthritis
- PETER NILSSON (KTH Royal Institute of Technology)
- RALF SCHITTENHELM (20) Allelic association with ankylosing spondylitis fails to correlate with HLA-B27 homodimer formation
- TIANFU WU (15) Development of an autoantigen microarray for the screening of novel autoantibodies in psoriatic arthritis
- TERRY C.C LIM KAM SIAN (15) HLA-B27 immunopeptidome: Understanding the connection between Salmonella typhimurium infection and ankylosing spondylitis
- YAOTING SUN (15) ThyroProt: a robust protein classification system for thyroid disease based on deep learning of proteome data.
HPP Session 3. P3: Plasma, Pediatrics and Proteomics – the Basis for Early Detection, Prevention and Treatment of Disease (Tues am)
Session Chair: Jochen Schwenk (KTH Royal Institute of Technology)
- PETTER BRODIN (Karolinska Institute) Systems-level analysis of immune development early in life
- QIBING ZHANG (University of North Carolina) (25) Temporal profiles of plasma proteome during childhood development and natural progression of Type 1 Diabetes
- CRISTINA AL-KHALILI SZIGYARTO (20) Orthogonal validation of Duchenne Muscular Dystrophy biomarkers using targeted proteomics
- VALENTINA SIINO (15) Mass spectrometry workflow for characterization of plasma proteome changes related to ageing
- ESTHER WILLEMS (15) The sweet separation between bacterial and viral infections by glycopeptide profiling in pediatric infections
- SANJEEVA SRIVASTAVA (15) A comprehensive proteomic analysis of medulloblastoma subtypes reveals mechanistic insights of Group 3 tumors - Sanjeeva Srivastava
Session Chairs: Daniel Chan (Johns Hopkins University), Hui Zhang (Johns Hopkins University)
- MICHAEL ROEHRL (Memorial Sloan Kettering Cancer Center)
- DANNI LI (University of Minnesota) (25) Enabling precision medicine for Alzheimer’s Disease through biofluid-based biomarkers
- QING KAY LI (15) Heterogeneity study of pancreatic tumor tissue: Proteomic characterization of tumor cells obtained by laser micro-dissection (LMD), coring, and bulk sampling techniques
- ROSEMARY BALLEINE (15) Intra- and inter-individual variation in the proteome of high-grade serous ovarian cancer
- JACOB KAGAN (15) Proteomic Tissue Biomarkers for Early Prediction of Prostate Cancer Progression
- SOREN NAABY HANSEN (15) Oxygen-sensitive interactions between glycolytic enzymes and a cancer-testis antigen established signaling scaffold are regulated by lysine acetylation
Session Chairs: Oliver Schubert (University of Adelaide); Katrin Marcus (Ruhr University)
- MELANIE FÖCKING (Royal College of Surgeons Ireland) (25) The use of proteomics to identify blood-based protein changes in childhood that are associated with increased risk for later psychosis
- LINGJUN LI (25) Comparative glycoproteomic analyses of cerebrospinal fluids reveal novel molecular players in Alzheimer’s disease
- K. OLIVER SCHUBERT (20) Autoantibody Profiling of Schizophrenia and related Psychotic Disorders in the Australian National Survey of High Impact Psychosis (SHIP)
- SANJEEVA SRIVASTAVA (15) Human brain proteome draft atlas to understand biological function and reference for brain tumour investigations
- KELLY STAUCH (15) Proteomic and bioenergetic analyses demonstrate synaptic mitochondrial alterations due to age-related pathologic tau accumulation
- NATHAN BASISTY (15) A Proteomic Atlas of Senescence-Associated Secretomes for Aging Biomarker Development
Session Chair: Jennifer Van Eyk (Cedars-Sinai), Ferdinando Cerciello (University of Zurich)
- YING JIANG (National Center for Protein Science) (25) Proteome landscape of early stage hepatocellular carcinoma identifies proteomic subtypes and new therapeutic targets
- PAUL ALEWOOD (University of Queensland)
- WINT WINT PHOO (20) Unveiling protein targets involved in haptenation during allergic contact dermatitis via high resolution mass spectrometry
- SUNG MIN CHO (15) Reverse chemical proteomics identifies unanticipated human target of anti-malarial drug, Artesunate, for drug repositioning
- DAVID SPICIARICH (15) Proteome profiling of multiple sclerosis cerebrospinal fluid by data independent acquisition reveals changes in proteins involved in adaptive immunity
- XIAOLU ZHAO (15) Thermostable potassium channel-inhibiting neurotoxins in processed scorpion medicinal material revealed by proteomic analysis: implications of its pharmaceutical basis.
This HPP Workshop follows the HUPO2019 Congress and will focus on exciting developments in human proteomics and strategic planning for the Human Proteome Project. All are welcome to participate in building the strategic future of the HPP. The Workshop draws on insights from the Congress, Mon-Weds HPP Track and Bioinformatics Hub. This future-focussed Workshop will explore the scientific strategy and goals for components/collaborations assembled under the aegis of HUPO’s HPP. There will be feature presentations about new HPP roadmaps. The Workshop is critical for reaching community consensus about strategic planning around the HPP, including broad engagement of the mass spectrometry, antibody, knowledgebase, biology, clinical and pathology communities.
HPP Future Workshop Aims:
- Build a more collegial and better unified HPP
- Generate assessment, commentary, discussion and awareness of HPP strategic directions
- Stimulate new/existing cross-HPP and strategic external HPP collaborations
- Undertake any strategic HPP scientific (re)organization
a) HUPO2019 Congress Scientific Highlights (contributors include Yu-Ju Chen, Rob Moritz, Lydie Lane, Danni Li, Elena Ponomarenko, Susan Weintraub, Hui Zhang, Fuchu He, Ferdinando Cercillo, Sudhir Srivastava, Ed Nice, Tadashi Yamamoto)
b) 2-Minute Lightning Highlights from the Floor
a) 10.00 C-HPP (Chris Overall, Lydie Lane, Young-Ki Paik)
b) 10.20 B/D-HPP (Ileana Christea). This presentation in pdf format is available here.
c) 10:40 Pathology Pillar (Dan Chan)
d) 10:55 Ab/Affinity Pillar (Cecilia Lindskog). This presentation in pdf format is available here.
a) 11:30 Current KB Pillar Plans (Lydie Lane, Eric Deutsch). This presentation in pdf format is available here and here.
b) 11:45 Futuristic HPP KB Panel (Eric Deutsch, Lydie Lane, Jochen Schwenk, Nuno Bandeira).
c) 12:15 Comments/Questions from Floor
(panel includes John Yates (HPP SAB), Ileana Cristea (B/D HPP), Mike Snyder (HPP SAB), Cecilia Lindskog (Ab Pillar), Stephen Pennington (HUPO), Ferdinando Cerciello (HUPO ECR), Maggie Lam (HPRL)
a) 1:30 C-HPP: The Dark Structural Biology Proteome (Seán O’Donoghue). This presentation in pdf format is available here.
b) 2:00 Missing Protein Search in Rare Tissues/Cells (Chris Overall). This presentation in pdf format is available here.
c) 2:20 Future Community MS Pillar Initiative Ideas (Susan Weintraub) (i.e., top-down MS, DIA, library-free DIA, XL-MS, etc)
d) 2:40 B/D-HPP: Popular/Less Popular Proteins (Fernando Corrales). This presentation in pdf format is available here.
a) 3:30 Strategic Impact of Multi-omics (Mike Snyder). This presentation in pdf format is available here.
b) 3:50 SPARQL - All that Glitters is Not Gold: (Lydie Lane). This presentation in pdf format is available here.
c) 4:10 Questions
How and When Can Proteomics Deliver? (Stephen Pennington). This presentation in pdf format is available here.
Outside the submitted abstracts stream for HUPO, again we will have a separate C-HPP poster session running the entire meeting. Please bring extra posters relevant to the C-HPP that you wish to present, especially unpublished recent data. Note, abstracts do not have to be uploaded to the HUPO-Adelaide web site, just bring your research along to present. We encourage you to bring additional extra posters for this section to translate your research, highlight your trainees, and accelerate C-HPP discussions. The C-HPP Poster Discussion, led by Gil Omenn will be at morning coffee/tea Tuesday 10:00-10:40 and possibly in the afternoon tea break also. Lightning 2-minute talks at each poster will be followed by Q & A. This will be a key part in deciding Poster Awards!
Please put up the posters Sunday afternoon or Monday morning at the latest to ensure ample viewing and discussion time. We have a great location, posters numbers 1 – 20, just as you enter the main exhibit hall on the left and en route to the Bioinformatics Hub. These posters will be displayed for the entire length of the congress. Protifi is sponsoring 3 @ USD200 C-HPP Poster Awards, which along with Certificates, will be presented at the Awards Ceremony on Wednesday at the close of the congress.