The 18th Human Proteome Organization World Congress - HUPO 2019 will be hosted by the Australasian Proteomics Society (APS) in the beautiful ‘City of Churches’, Adelaide. HUPO 2019 will focus on “Advancing Global Health Through Proteome Innovation” and will bring together world-leading experts and the next generation of early career scientists to promote how proteomics is advancing our knowledge of human and planetary health. HUPO 2019 will both celebrate what has been achieved and look forward to future advances and discoveries that will revolutionize global health.

The Australasian Proteomics Society (APS) has started to design a fantastic program for HUPO 2019 in Adelaide and have confirmed the following plenary speakers:

• Prof. Ruedi Aebersold
• Prof. Yu-Ju Chen
• Prof. Fuchu He
• Prof. Albert Heck
• Prof. Kathryn Lilley 
• Prof. Mathias Uhlén

With plenary lectures from outstanding speakers and over 30 parallel sessions - including 6 HPP sessions, the 2nd Australasian Glycoscience Symposium, Plant and Food Proteomics sessions - the program will offer opportunities for fruitful discussions. Other Themes include:

• Health and Disease
• Biological Applications of The Proteome
• Beyond the Proteome
• Our Human Environment
• Enabling Technologies

The Organizing Committee of the HUPO 2019 consists of the committee members of the Australasian Proteomics Society (APS) plus a number of prominent Australian Proteomics Scientists:

HUPO 2019 Organizing Committee

Prof. Stuart Cordwell (Co-Chair, APS President)
Prof. Peter Hoffmann (Co-Chair and LOC Chair, APS Vice President))
Prof. Anthony Purcell (APS Treasurer)
Prof. Mark Molloy (APS Secretary)
Prof. Marc Wilkins (APS Committee)
Dr. Michelle Colgrave (APS Committee)
Dr. Morten Thaysen-Andersen (APS Committee)
Dr. Andrew Webb (APS Committee)
Additional HUPO 2019 Organizing Committee
Prof. Mark Baker (HPP)
A/Prof. Michelle Hill (HUPO EC Secretary)
A/Prof. Vera Ignjatovic (HPP)
Prof. Ed Nice (HPP and social event committee)
Prof. Nicolle Packer (Glycoscience)
Prof. Paul Haynes (Plant and Food Proteome)
Prof. Gavin Reid (Multi-omics)

Visit the conference website www.hupo2019.org for more details.

We look forward to welcoming you to Adelaide in 2019 for an unforgettable HUPO World Congress.

Sanjeeva Srivastava, IIT Bombay, India

Proteomics is the study of entire protein complement of an organism. Advancements in proteomics have been phenomenal over the last decade with several promising high-throughput technologies emerging at the forefront of various applications. Owing to the rapid advancements in state-of-the-art proteomics technologies, continuous expansion of our scientific understanding, and challenges associated with omics research, it has become essential to keep up with current trends and advances in proteomics research. In this light, we conducted three workshops at IIT Bombay, where eminent scientists and researchers from India and abroad had shared their knowledge and expertise to train the participants and familiarize them to the vast applications of proteomics.

Basics and Advanced Proteomics Approaches (December 3 to 14, 2018)

The DST supported programme was specially designed for Scientists/Technologists who are actively involved in research and development activities. The overall goal of the programme was to develop an educational training program on diverse proteomic technologies and offer hands-on training on the cutting edge proteomics technology to benefit the scientists in their research skill enhancement and keeping them abreast with the last technological advancements in the field of science. 25 scientists were selected for this program.

Cancer Proteogenomics Workshop (December 6 to 11, 2018)

This training program utilized advanced genomic & proteomic technologies and their data from high-quality human biospecimens to identify potentially actionable therapeutic molecular targets. This IUSSTF funded training program was a collaborative effort by experts in the fields of proteomics and proteogenomics in cancer research from the Broad Institute of MIT and Harvard (Convener, USA: D. R. Mani) and Indian Institute of Technology Bombay (Convener, India: Sanjeeva Srivastava). The program comprised interactive lectures with case studies, hands-on sessions and demonstrations on proteogenomics aimed at accelerated understanding of cancer. 200+ participants attended this training program.

Caner proteogenomics workshop Group 

Cancer Moonshot India Program – December 7, 2018

The Cancer Moonshot aims to accelerate cancer research to make effective therapies available to more patients, while also improving early and accurate detection.

https://www.cancer.gov/research/key-initiatives/moonshot-cancer-initiative

Similar to the Cancer Moonshot project of USA, to expedite cancer diagnosis and treatment, we have initiated the Cancer Moonshot India project. India has now become the 12th country to join the International Cancer Proteogenome Consortium (ICPC) of the National Cancer Institute (NCI), U.S. The Indian Institute of Technology Bombay (IITB) aims to study proteomics and the Tata Memorial Hospital (TMH), Mumbai, aims to study the genomics of three cancers, breast, cervix and oral. Dr. Henry Rodriguez, Director, NCI Office of Cancer Clinical Proteomics Research inaugrated this event and delivered a speech to the gathering, which included distniguished clinicians from ACTREC, TMC and KEM hospitals; key industry leaders; and scienitsists working in genomics and proteomics area.

Enchanting dance performances by Faizal Kahan and his group

Trans-Proteomic Pipeline (December 12 to 14, 2018)

The TPP workshop was scheduled from 12th to 14th December 2018. This advanced mass spectrometry data analysis workshop was supported by IUSSTF joint virtual center grant and conducted by Institute for Systems Biology scientists.

Click here for more: http://www.bio.iitb.ac.in/~sanjeeva/cpg2018/

HUPO President (2017-2018), Mike Snyder, California, USA

It has been a true honor to have served as HUPO President for the past two years. The field of proteomics has never been more exciting with numerous advances in technology, transformational research findings, and improved integration into systems biology and medicine. We can now profile thousands of proteins at rapid speed and with instrument sensitivities that enable single cell proteomics. Through the efforts of the Human Proteome Project (HPP) the number of uncharacterized proteins has rapidly diminished (to under 3,000) and the Human Protein Atlas has mapped the expression and subcellular localization of the majority of human proteins. Our annual HUPO meetings continue to present the very best science in proteomics and attract the very best practitioners of our field. Most importantly, we have welcomed many new scientists at our annual meeting and benefited from their outstanding contributions on numerous committees. We have undertaken many bold initiatives such as the launch of the international Human Proteomics Moonshot project. The international influence and stature of the organization is evidenced by the enthusiastic participation of former US Vice President Joseph Biden at our annual meeting. The HPP continues to make great progress as our flagship project, with Mark Baker assuming the helm after the Herculean efforts of Gil Omen to get the HPP launched and running smoothly.

Despite our many successes, there remains much to be done and we cannot afford to be complacent—this is the same as falling behind. We still cannot profile all proteins and isoforms with low sample amounts and with high throughput. Depth and speed will be important for large studies, similar to other omics fields. Single cell proteomics is promising but still in its infancy. As leaders in the field, HUPO members need to educate our peers and funding agencies about the significant value of incorporating proteomics into all major projects going forward. Many researchers and some funding agencies are beginning to recognize that understanding biological systems requires proteomics, which is closer to phenotypes than nucleic acid assays, and this has shaped the scope of some newer initiatives, for example the MoTrPAC consortium. Finally, I believe that medicine of today using large sample volumes and visits in the clinic will be replaced by small “finger prick” sample collection and mail-in assays. HUPO and the field of proteomics needs to be at the forefront of this. I anticipate major advances in the field of proteomics in the coming years and believe HUPO will play a pivotal role in making these happen. I think we are in terrific hands under Steve Pennington’s leadership. My heartfelt thanks for everyone‘s contributions during my term.

György Marko-Varga, Sweden

Focusing on Patient-Relative-Friend Aspects in the 2018 Summit

Photo by Karl Melin.

The European Cancer Moonshot Symposium was held in Lund May 23rd. The primary goal of the meeting was to invite and discuss cancer research from the perspective of patients, relatives, and friends. Patients and relatives from the US and different parts of Europe told their stories and about their experiences from treatment of various cancer forms (https://www.facebook.com/europencancermoonshotlund/ ).

Honest and emotional lectures were given on the factual circumstances that a patient and a close relative face when dealing with tough messages, treatments, and decisions. The mental trainer, Igor Ardoris, shared his experience of how to deal with these situations, controlling the mind and imaginational part, that can be trained to overcome and ease pain and disease pressure.

The former athlete and world record holder in high jump Patrik Sjöberg gave a deeply touching talk about a child’s perception of having cancer. Mr Sjöberg is now working part time advocating for children with cancer, through the Tuva’s Day Foundation (Varberg för Liv/Tuvas Dag). Martin Bekken from BEWi, has been a strong support to the European Cancer Moonshot Lund Center, by getting the word out on the build of the PRF-group-that was the focus of our meeting this year.

With the patient in focus the meeting also engaged the hospital management of the southern health care district of Sweden, experts and medical doctors from cancer treatment clinics, and prominent cancer researches in the cancer diagnostic field. The Cancer Moonshot research team in Lund hosting the Symposium also had reporting from the Cancer Moonshot Australia activities, was presented by Professor Mark Baker, where major funding and investments for future Cancer research and developments have been made recently, expanding on the US/Australia Cancer Moonshot collaboration. Dr. Henry Rodriguez, from the NIH/NCI (National Instituts of Health/National Cancer Institute), presented the overall progress and activities of the Cancer Moonshot program in the US, and Dr. Thomas Conrads, showed the latest cancer studies within the Cancer Moonshot & US/Apollo developments, which were very impressive.

Statement from professor Johan Malm “When working with front-line clinical research at the European Cancer Moonshot Lund Center, as we are doing, it is very stimulating and inspiring to listen to all the different stories from patient and their relatives. Then you realize that what matters is not you. It is what you are working for, namely a better life for the people facing the consequences of cancer”.

Statement from Ken Miller, Thermo Fisher Scientific “Thermo Fisher is a partner to many global Cancer Moonshot laboratories and we consider the program in Lund to be an exemplar of clinical excellence, biobanking, and analytical expertise. We are confident that this team will help the cancer research field make progress toward the dream of patient phenotyping and precision medicine.”

The Cancer Moonshot was initiated in 2016 by the 47th vice president Joe Biden.

The project team in Lund hosting this year’s international European Cancer Moonshot summit built the theme on Joe Biden’s vision;

“Break down the silos and start to collaborate, involve all disciplines, with one common aim, to defeat cancer.”

Related links:

Watch all 5 sessions of the European Cancer Moonshot Symposium in Lund

Session 1: https://www.youtube.com/watch?v=nsvPAvvqCLA&t=4s

Session 2: https://www.youtube.com/watch?v=ihxSd820lNo

Session 3: https://www.youtube.com/watch?v=Gfp6Ic8pe5U&t=3s

Session 4: https://www.youtube.com/watch?v=vcV5rcnLT7I&t=4s

Session 5: https://www.youtube.com/watch?v=MJe56CHUw_k

Follow the European Cancer Moonshot Lund Center here: http://www.cancermoonshotlund.com/ 

Hear about Eve Kelly's story here: https://www.youtube.com/watch?v=9euomHlFqnY

Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

Post-translational modifications (PTMs) on proteins can play a critical role in function by regulating protein structure, function and/or localization. Although consensus sites for some of the more well-studied PTMs have been established, PTMs are not predictable from the genetic code. Furthermore, PTMs can be either stably attached through the life of a protein, or reversibly added depending on stimulation. Hence, direct interrogation at the protein level is required to fully characterize PTM function in health and disease.

Several B/D-HPP teams have been investigating the biological roles of PTMs and their disease associations, with two recent publications in leading interdisciplinary journals.

Neil Kelleher and his team at Northwestern University used top-down proteomics to characterize proteoforms of KRAS, a gene frequently mutated in human cancer. The novel mass spectrometry-based whole protein assay enabled the team to investigate the effect of genetic mutations in KRAS on PTMs of the protein that are important for proper KRAS regulation. In collaboration with National Cancer Institute, the study, recently published in Proceedings of the National Academy of Science USA, quantified the percentage of mutant KRAS4b present in colorectal cancer tissue, and identified differences in the level of C-terminal carboxymethylation, which is critical for KRAS function. Such detailed characterization and quantification of KRAS proteoforms was only possible with the novel top down mass spectrometry-based assay. In the future, targeted assays such as this will be extended to characterize proteoforms within specific cell types to increase their sensitivity and selectivity and inform cancer prognosis and personalized therapy selection.

A collaboration between Jenny Van Eyk’s team at Cedars-Sinai Medical Center and Shengbing Wang and David Kass at Johns Hopkins University School of Medicine, determined the functional consequences of a redox-regulated PTM on glycogen synthase kinase 3b (GSK3b). S-nitrosylation is the attachment of nitric oxide to sulfhydryl residues of proteins, and is involved in redox-based cell signaling. The study, published in Circulation Research, reported the novel finding that GSK3b can be modified by S-nitrosylation at specific sites in models of heart failure and sudden cardiac death. S-nitrosylation of GSK3b overrides the classical phospho-regulation and sends it to the nucleus, away from its usual cytoplasmic location. The result is that the S-nitrosylated GSK3b now phosphorylates a completely different repertoire of proteins in the nucleus compared to its known cytoplasmic substrates, implying that drugs meant to target cytoplasmic GSK3b may inhibit complete different nuclear pathways if the GSK3b is S-nitrosylated. “Knowing the PTM status of drug targets and the functional effect is key to next generation therapies.” Says Jenny.

Together, these studies exemplify the work of B/D-HPP teams and clinical collaborators on apply and developing advanced proteomics methods to understanding disease. Future work of the B/D-HPP teams will be to translate the findings into the pathology or clinical chemistry laboratories, to make an impact on patients lives.

Péter Horvatovich, University of Groningen, Netherlands

The Chromosome-Centric Human Proteome Project (C-HPP) plans to identify all elements of the human proteome, their proteoforms and determine their functions. C-HPP efforts are summarized as protein evidence status and functional and other annotations of human protein coding genes by neXtProt. The C-HPP is organized as an international consortium based currently on a per chromosome basis and is open to the entire scientific community for contribution. Besides individual publications, other scientific contributions are summarized in the C-HPP special issues appearing each year in the Journal of Proteome Research. On an ongoing basis, the main C-HPP achievements are highlighted in C-HPP Newsletters published every year. The C-HPP has initiated a community information sharing Wiki page, to enable sharing C-HPP–related information directly by member teams. The C-HPP Wiki includes the following sections:

- Representation of team members information, resources, expertise, projects and results on a chromosome basis

- Protocols, guidelines and central resources of the C-HPP project

- The program of C-HPP workshops organized each year at HUPO congresses and at C-HPP workshops, which includes presentations with authors permission and other workshop related information

- C-HPP news items, which includes announcement of new achievements, new guidelines and yearly appearing C-HPP Newsletters

C-HPP Wiki is a live non-centralized information sharing platform of C-HPP members and has as its goal to share as much information as possible for C-HPP members, for the proteomics scientific community and for interested readers. The web page for C-HPP Wiki is at https://c-hpp.webhosting.rug.nl/tiki-index.php?page=HomePage

Péter Horvatovich, University of Groningen, Netherlands

On February 21, 2018 the new release of neXtProt was published, which serves as the definitive reference database of the human proteome and is used by the Human Proteome Project (HPP) to assess the progress of completing the map of Human Proteome. The new version of neXtProt updated the human proteome evidence using the latest data from PeptideAtlas (release Human 2018-01) and resulted in 17,470 validated human proteins (PE1), 393 more compared to the previous version of January 17, 2017, leaving 2,186 missing proteins with status PE2+PE3+PE4 and 574 uncertain proteins (PE5). In this new release a total of 51 PeptideAtlas data sets was included from cancer tissues and cell lines, with over 1.4 million peptides detected by mass spectrometry. Data from UniProtKB, Ensembl, IntAct, GOA, and GeneIDs, have been also updated. The data have been complemented with GO molecular function, biological process and cellular component annotations for most of the human protein kinases, as well as expression information, mutagenesis and variant phenotype data. The number of validated proteins with unknown function (uPE1) is now 2,271 which can be obtained with SPARQL query NXQ_00022.

Two new rules have been implemented to reflect protein existence:

- proteins with PE2, PE3 or PE4 status have been upgraded to evidence at protein level (PE1) status if the entry has GOLD binary interaction data from neXtProt.

- As a consequence of UniProtKB demerging entries encoded by multiple genes, some neXtProt entries now have exactly the same protein sequence and are indistinguishable at protein level. The list can be retrieved using SPARQL query NXQ_00231. Peptides matching uniquely on such indistinguishable entries are now labeled “pseudo-unique” rather than "Found in other entries" and were used to validate protein existence if they complied with the HPP guidelines.

The Proteomics view for entries has been revamped and now loads faster. In addition, it is now possible to search the positional annotations listed in the feature table for a specific category or for text found in the feature description. For instance, searching for "SRM" returns the number of SRM peptides mapping to the isoform and allows to the users to rapidly browse the data for all SRM peptides.

New advanced search SPARQL queries have been added, such as to identify proteins with high proline content in the SnorQL interface (NXQ_00225), to list proteins with at least 2 uniquely mapping peptides larger than 9 amino acid lengths found in blood plasma, urine or cerebrospinal fluid to support markers research (NXQ_00226) and to identify proteins with experimentally determined lengthy alpha-helices (length larger than 75 amino acids) illustrating query of proteins with specific secondary structure (NXQ_00230).

New letter format of Journal of Proteome Research to report missing proteins

Discovery of a missing protein or new proteins can now be published in the Journal of Proteome Research December 2018 Special Issue as a short definitive report, submitted in the Letters format. To be considered for publication as a Letter, the missing protein(s) must meet the HUPO Data Interpretation Guidelines version 2.1 and be cast in the context of both the HPP and biological setting in which they were discovered. We anticipate this format will encourage many teams, particularly of the B/D-HPP and the general proteomics community, to highlight such protein discoveries when found in disease and biological sample analyses. Such side findings in a more biological focused analysis may otherwise may be lost or not further detailed as they were an incidental finding.

Letters have a maximum length of four journal pages and should contain sufficient experiment detail for the research to be reproduced. There should be no more than 3 figures, 2 tables and 20 references. A separate Table of Contents Graphic is required, but does not count toward the 4-page or Figure limit. Reporting of missing proteins must meet both the Journal of Proteome Research technical and the HUPO Data Interpretation Guidelines (see further details in Deutsch et al. PMID 27490519) including figure(s) of the annotated spectra and the data uploaded to ProteomeXchange with a PXD number included in the abstract. To be reviewed the HPP Checklist items must be fulfilled and submitted.

Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

The last decades saw a steady increase in the incidence of rheumatic and autoimmune diseases such as osteoarthritis (OA) rheumatoid arthritis (RA), multiple sclerosis (MS), inflammatory bowel diseases (IBD) and systemic lupus erythematosus (SLE). Rheumatic and autoimmune diseases (RAD) are characterised by inflammation of joints, muscles, and connective tissues around joints and bones. Apart from the debilitating mobility and pain, RAD patients are also at increased risk of cardiovascular and neurodegenerative diseases. Given the huge socioeconomic impact of RAD, broad research efforts have been dedicated these diseases worldwide.

The RAD B/D-HPP initiative was launched in 2017 by Francisco J. Blanco (Rheumatology Department, INIBIC-Complejo Hospitalario Universitario A Coruña in Spain) with co-chair Paul J. Utz from Stanford Department of Medicine, USA). Currently, 6 research groups from 5 countries participate in RAD-HPP, but the collaborative network has already extended to Cardiovascular-HPP and Chromosome 16-HPP .

After establishing the networks and promoting visibility of the new initiative, the immediate scientific goals of RAD-HPP are to define the proteome of human joint tissues (cartilage, synovial membrane, subchondral bone), and to assemble prioritized lists of proteins clinically relevant in RAD using the ‘popular proteins’ strategy with text mining tools. Collaborations within the RAD-HPP have already resulted in several publications in 2017, including circulating biomarkers for knee radiographic osteoarthritis , use of protein array to discover and validate biomarkers for Osteoarticular Pathologies , and anti-citrullinated protein antibodies in rheumatoid arthritis.

To spread the word outside of proteomics research circles, RAD-HPP members presented their proteomics work at key RAD clinical meetings around the globe in 2017. These included Osteoarthritis Research Society International (OARSI) World Congress in Las Vegas (USA), the Annual European Congress of Rheumatology-EULAR in Madrid (Spain), Annual Meeting of the American College of Rheumatology in San Diego (USA), and XLIII Congress of the Spanish Rheumatology Society in Bilbao (Spain).

To boost the development and utility of quantitative proteomics assays, RAD-HPP members conducted focused proteomics training sessions in 2017, with highlights being sessions at “Cutting Edge Osteoarthritis” Symposium at Pembroke College, Oxford, and “Proteomics in rheumatic diseases” lecture at a Summer School on Platform Technologies and Big Data applications in Precision Medicine, in Santander, Spain.

With the synergistic international effort and strong clinical translational focus, the RAD-HPP initiative is poised to realise the utility of proteomics in RAD diagnosis and management.

Péter Horvatovich, University of Groningen, Netherlands

The 19th Chromosome Centric Human Proteome Project workshop will be held in Santiago de Compostela (Spain) on June 16-17, 2018 as a companion event of the XII EuPA Congress 2018. We are cordially inviting all scientists and partners interested in discussing the status and future directions of the Chromosome Centric Human Proteome Project. The workshop has the aim to discuss the most pertinent questions of the (chromosome centric) human proteome project, which includes the following topics:

-Completeness of the human proteome and new developments to identify missing proteins, highlights on next-MP50 (50 next missing proteins) program

-Start of the uPE1 project aiming to find function(s) for human proteins identified with high confidence (PE1 category in neXtProt) without any known function

-Discussion on the future directions of the Human Proteome Project focusing on bright (know, HPP PE1 proteome) and dark proteome (unknown, “Missing” proteins, uPE1 proteins and dark structural proteins)

-Inclusion of translated small open reading frames and long non-coding RNAs, sequence variants, splice isoforms and proteins peptides with post-translation modifications

-Bioinformatics infrastructure of the (C-)HPP project

-Recent results and future directions of B/D-HPP and joint actions with C-HPP teams

To follow the status and future paths of C-HPP, the reader is referred to a recent review of the C-HPP Executive Committee members in Expert Review of Proteomics entitled “Advances in the Chromosome-Centric Human Proteome Project: looking to the future”. Questions and suggestions for the workshop can be addressed to the organizer of the workshop, Fernando Corrales (fcorrales@cnb.csic.es, Spanish National Centre for Biotechnology, Madrid, Spain). The continuously updated workshop program is available at C-HPP Wiki. We are looking forward to meet all interested persons at this event.

Michelle Hill, QIMR Berghofer Medical Research Institute, and The University of Queensland, Australia

More than 20 investigators across the globe are working together to unveil the proteins that allow us to see. The B/D-HPP EyeOME initiative began in 2013, under the leadership of Prof Richard Semba (Johns Hopkins University School of Medicine). As for other HPP initiatives, the first task is to identify all of the eye proteins. For this arguably the most complex of organs, this task is far from simple; the human eye consists of diverse specialised tissues and biofluids.

Thanks to the collective efforts of proteomics researchers, the eye proteome database now contains a total of 9,782 non-redundant proteins for 11 eye tissues and biofluids, with the highest number (6,538 proteins) from vitreous humor and the lowest number (827) from aqueous humor. The database was curated under rigorous standards as highlighted in the recent article from the EyeOME team, which also outlined recommendations for human eye proteome studies.

The team is currently preparing a website to facilitate broader dissemination and usage. The international effort in EyeOME will provide a proteomic knowledgebase to increase our understanding of how the eye works at a molecular level. This knowledge will ultimately contribute to improved treatments for disorders of the eye.

The human eye proteome database is available for download here: Supplemental Table S2 xlsx.