NewS

Chromosome Team Leadership
Good news: Drs. Allan Stensballe and Louise Bundgaard, both excellent scientists, will lead the Chromosome 2 team representing Denmark. Now all our chromosomes have a team!!!

C-HPP Workshops
We are announcing two Chromosome-Centric Human Proteome Project (C-HPP) Workshops for 2024 and one for 2025:

• 26th C-HPP Workshop: (0.5 day), Dresden, Sunday 20th October 2024, 10:00 AM – 15:00 PM (before HUPO Congress).
• 27th C-HPP Workshop on the new Human Proteome Project Portal, China, November 2024.
• 28th C-HPP Workshop: The HPP Grand Challenge, Saint-Malo, France, June 13-15, 2025 (before EUPA).

Elections in Dresden for C-HPP EC Members
Please send nominations for the following positions to the C-HPP Secretary General, Dr Peter Horvatovich (p.l.horvatovich@rug.nl).

1. Chris Overall will be stepping down as Chair of the C-HPP at the end of 2024, and we invite nominations for the new Chair.
2. Gilberto Domont is a current member, and we invite nominations to fill this position for three years starting in January 2025.
3. We are creating a new ECR position on the C-HPP EC; the individual will be elected in Dresden to sit on this EC from January 2025 for 3 years.
4. Election for a member-at-large of the C-HPP EC.

Our goal is to have equal female and male representation on the C-HPP EC.

Current C-HPP EC

• Christopher M. Overall, Canada (to December 31, 2024), Chair.
• Gong Zhang, China (to December 31, 2027), Co-Chair.
• Heeyoun Hwang, Korea (to December 31, 2028), Co-Chair.
• Peter Horvatovich, The Netherlands (to December 31, 2025), Secretary General.
• Gilberto Domont, Brazil (to December 31, 2024), Member-at-Large.
• Fernando Corrales, Spain (to December 31, 2025), Member-at-Large.
• Sergio Encarnación-Guevara, Mexico (to December 31, 2027), Member-at-Large.

November 18-19, 2024
Location: Aerial UTS Function Centre, Ultimo, Sydney, Australia
Organized By: Children Medical Research Institute, ProCan

Through this two-day meeting, internationally renowned experts in proteomics, genomics, cancer management, biomarker and drug discovery will share their progress towards addressing the challenges and opportunities of multi-omic data integration in cancer management, with a special focus on the role of proteomics in advancing biomarker development and drug discovery.

More details here....

In recognition and appreciation of the significant support, participation and guidance provided by HUPO's Industrial Advisory Board (IAB), one IAB member will be highlighted each month. We encourage you to connect with these companies directly for further information about their involvement in HUPO, and their products and services.

Pelago Bioscience is a CRO supporting all phases of drug discovery, with expertise in target engagement in biologically relevant assay systems. We believe that all drug discovery projects should know their target(s) before entering the clinic. To fulfill this mission, we utilize our patented core technology, CETSA® (Cellular Thermal Shift Assay), essential for early decision-making throughout the entire drug discovery pipeline.

CETSA measures the thermal stability of proteins in response to compound binding in a completely label-free manner. It offers multiple assay formats, from confirming target engagement and validating targets to generating hits for challenging targets and elucidating compound mechanisms of action. CETSA also excels in understanding the selectivity profile of compounds in biologically relevant models.

Pelago Bioscience services include among others:

Target Deconvolution with CETSA:

Uncover your drug candidate's interactions with targets through comprehensive, proteome-wide analysis. This combines CETSA with mass spectrometry, delivering unbiased results covering over 7,000 proteins without modifications to your compound or target proteins. Identify both on-target and off-target interactions in biologically relevant cell systems, providing crucial insights for target identification and mechanism of action studies.

Primary Screening with CETSA:

Accelerate your lead generation process by identifying high-quality chemical starting points with high-throughput screening. Benefit from rapid assay development, high-throughput screening for challenging targets, and identification of high-quality hits for further development, saving time and money while reducing attrition rates.

Hit Confirmation with CETSA:

Validate your selected target protein's binding to a compound in its native state. This service assesses compound binding without modifications to the protein or compound, ensuring accurate target engagement assessment and helping you prioritize promising drug candidates.

By partnering with Pelago Bioscience, you tap into:

Robust Target Engagement Assessment: Gain confidence in your drug targets, ensuring candidates engage with intended targets in a biologically relevant context.

Breakthroughs for Challenging Targets: Identify promising drug candidates for targets traditionally deemed "undruggable," unlocking new therapeutic possibilities.

Deep Mechanistic Insights: Understand the precise mechanisms of action of your compounds, illuminating interactions with targets and broader cellular pathways.

Comprehensive Selectivity Profiling: Assess compound specificity against potential off-targets in biologically relevant models, minimizing unwanted side effects.

Pelago Bioscience's team of seasoned scientists collaborates closely with you to deliver actionable insights, enabling confident asset prioritization in your drug discovery pipeline. Our expertise, over a decade of experience with more than 220 customers including leading pharmaceutical companies, and powerful CETSA technology make us your trusted partner in accelerating drug discovery.

Sunday, October 20th 19:30-22:30

Early career researchers and senior scientists are all welcome to join this exciting event, which aims to bridge digital, cultural, and continental gaps. The ECR Networking Evening provides a fantastic opportunity for early-stage researchers to meet, share, and connect with colleagues and senior researchers.

This year, the evening will feature a scenic boat ride around Dresden, offering stunning views, drinks, and a chance to mingle in a relaxed atmosphere. It's the perfect setting to network with peers and mentors from around the world.

Be ready to meet new people and participate in engaging activities!

Register here for the ECR Networking Evening and reserve your ticket now, as space is limited!

The manuscript competition is a unique opportunity for early career researchers to gain visibility in the proteomics community, as it serves as a platform to highlight the important contributions that postdoctoral fellows, young clinicians and junior faculty members make to the proteomics field. Three finalists have been selected to present their publications in a dedicated plenary session at HUPO 2024, where an expert committee will evaluate the oral presentations to determine the “Proteomics Highlight of the Year” by an ECR. Congratulations to all finalists:

1. Leyuan Li (Beijing Proteome Research Center, CN)- Revealing proteome-level functional redundancy in human gut microbiome using ultra-deep metaproteomics
2. Stacy Malaker (Yale University, USA) - Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE
3. Marc van Oostrum (Max Planck Institute for Brain Research, Germany.) - The proteomic landscape of synaptic diversity across brain regions and cell types

Highlighting a member of HUPO, we invite a diverse group of researchers from different career stages, disciplines, geographical locations, and ethnicities to submit a profile for our monthly spotlight. This initiative aims to improve visibility of HUPO members, advertise research, and enhance the HUPO community. This month we are featuring:

Mariette Matondo, Paris, France

What is your current position and location?

I am the head of the Proteomics Core Facility at the Institut Pasteur in Paris, in the Department of Structural Biology and Chemistry (DBSC) (https://research.pasteur.fr/en/team/proteomics/ )

How did you get started in the field of proteomics?

I began my journey in proteomics in 2005 as a Master's student with Anne Gonzalez de Peredo in the Mass Spectrometry and Proteomics Laboratory led by Dr. B. Monsarrat at IPBS-CNRS in Toulouse. This was the only research and proteomics facility in Toulouse at the time. I continued in this lab as a Ph.D. student under the supervision of Dr. B. Monsarrat and Dr. O. Burlet-Schiltz. I was fortunate to work with one of the first Orbitrap mass spectrometers. My Ph.D. project focused on determining differentially regulated proteins upon proteasome inhibition in AML cell lines through a combination of large-scale and targeted quantitative proteomics. After earning my Ph.D., I joined Dr. Ruedi Aebersold’s lab at ETH Zurich as a postdoc, where I further specialized in targeted proteomics using SRM and continued my research in the field of MS-based proteomics. Since September 2013, I have been leading the Proteomics Core Facility at the Institut Pasteur.

What does being a member of HUPO mean to you?

Being a member of HUPO holds deep significance for me. My first HUPO conference was in Geneva in 2011, and HUPO Boston 2012 was a pivotal event for my career, where I met people who helped me discuss my current position. Over the past years, I have attended most HUPO congresses. Being part of the HUPO community, where I can share my research, gain insights from others, and collaborate with fellow scientists who share a passion for proteomics, truly makes me feel fortunate and valued.

What makes your research program exciting and unique?

In my lab, we use MS-based proteomics to identify and quantify proteins and their modifications, particularly in the context of infectious diseases. To achieve this, we combine multiple proteomics approaches, from bottom-up to top-down proteomics, and from label-free to label-based methods, utilizing both data-dependent acquisition (DDA) and data-independent acquisition (DIA) techniques. As a core facility, our main mission is to develop and implement robust methods to achieve our goals and provide the best results to our collaborators. We actively collaborate with many scientists at the Institut Pasteur and with national and international collaborators, supporting their research endeavors. We recently join the world of single cell proteomics, and I am really looking forward to seeing how this will boost the science and discovery of potential novel candidates’ markers and vaccine.

What are your interests outside the lab?

Outside of the lab, I enjoy every moment spent with my family. I am a mom of two marvelous kids, aged 6 and 9. My kids are full of energy and inspiration, which makes my life very exciting. Besides family time, I read a lot of books and enjoy good movies. From time to time, I also love to indulge in the pleasures of French life: good wine, good meals, and spending time with friends.

Where do you envision the field of proteomics in the next 10 years?

Over the next decade, I anticipate significant transformations and expansions in the field of proteomics, embracing a wider array of non-MS technologies. Innovations such as Olink and nanopore methodologies for single-molecule analysis will become instrumental in the detection and quantification of thousands of proteins within extensive patient cohorts. Nevertheless, I firmly believe that MS-based proteomics will encounter numerous challenges while continuously evolving to unveil myriad new possibilities. Challenges persist, particularly in areas such as post-translational modifications (PTMs), protein complexes, and dynamics.

 

The transition from the bulk proteomics to single-cell proteomics marks a substantial advancement, ushering in fresh perspectives and opportunities. Advancements in single-cell analysis will empower us to intricately characterize the cellular contents of individual cells, elucidating the complexities of cell heterogeneity and addressing pivotal biological inquiries, notably within the realms of cancer and infectious diseases.

 

Furthermore, the advent of AI will catalyze the analysis of the vast and complex datasets generated by mass spectrometry instruments, which are more and more  faster, higher in resolution, and more sensitive. The ongoing development of innovative data analysis and bioinformatics tools will therefore remain a focal point and a pivotal element in shaping the future of proteomics research.

Would you agree to share your Humans of HUPO profile on HUPO social media/ social media tags?

Yes.

The June HUPOST edition is out now! It’s packed with vital news and updates, including information on HUPO 2024 the IAB Spotlight, Council Elections, New Job Postings, ETC and ECR Activities, and more!

In this new monthly feature, we will be highlighting extraordinary HUPO volunteers who lead and support many of HUPO's various Committees, Initiatives and Working Groups. If you would like to volunteer with HUPO, please connect with the HUPO Office.

HUPO Marketing and Outreach Committee (MOC)

The MOC has been at work developing new ways to promote the HUPO mission, the visibility of proteomics within the scientific community and its popularization among the public, as well as gathering funding support. The MOC has been very successful in networking with other HUPO Committees and Initiatives and using a range of tools and activities. The MOC members are from different fields and backgrounds and at various career stages representing the diversity of HUPO.

Charlotte Hutchings is a third-year PhD student at the Cambridge Centre for Proteomics, University of Cambridge. She applies expression and subcellular spatial proteomics methods to study the effect of viral production, specifically that of adeno-associated viruses, on cells. Charlotte is also very interested in bioinformatics and big data which has led her to write and teach workflow publications and workshops. Having found a love for proteomics, Charlotte has become an active member of the community and acts as the student representative for the British Society for Proteome Research (BSPR), Vice Chair of Online Activities for the HUPO Early Career Researcher (ECR) Committee and has more recently become involved in the HUPO Marketing and Outreach (MOC) Committee.

Theodora Katsila is a Senior Researcher-Head of the Biomarker Discovery & Translational Research laboratory at the National Hellenic Research Foundation, Greece. Craving for brain teasers (and being loyal to her motto: from information to actionable insights), she is strongly interested in translational biomarkers and proteoform-based drug repurposing. Mining the chemical biology space, Theodora aims to catalyze the transition from serendipity-driven to data-driven translational precision medicine. This paradigm shift comes with a need for biomarker-guided trial design and patient-centric companion diagnostics. For this, Theodora applies mass spectrometry-based multi-omics and data science.

Conor McCafferty is a Program Manager at the Murdoch Children’s Research Institute in Melbourne, Australia, where he coordinates and oversees the body of cancer research performed at the institute and the adjoining Royal Children’s Hospital. He has worked with proteomic technologies to investigate biomarkers of disease and completed his PhD investigating the relationship between thrombosis and COVID-19 in children from the University of Melbourne in 2022, which included proteomic analysis of patients with different COVID-19 outcomes. Conor joined the HUPO Marketing and Outreach Committee in 2019 and additionally sits as a board director of the Australian Society for Medical Research. He has a passion for solving clinical challenges (particularly in pediatrics) and works to develop coordinated research and multi-omic strategies to improve clinical outcomes.

Highlighting a member of HUPO, we invite a diverse group of researchers from different career stages, disciplines, geographical locations, and ethnicities to submit a profile for our monthly spotlight. This initiative aims to improve visibility of HUPO members, advertise research, and enhance the HUPO community. This month we are featuring:

 Yansheng Liu, Connecticut, USA

What is your current position and location?

I am an Associate Professor in the Department of Pharmacology at Yale University School of Medicine, located in New Haven, Connecticut. My lab (https://www.yslproteomics.org/), however, is situated at the Yale Cancer Biology Institute on the Yale West Campus in West Haven, which is about a 15-minute drive from New Haven.

How did you get started in the field of proteomics?

I began my journey in proteomics in 2005 as a Ph.D. student at the Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences. My Ph.D. lab, led by Dr. Rong Zeng, was one of the earliest proteomics laboratories in China. I was fortunate to work with one of the first Orbitrap mass spectrometers. My dissertation was entitled 'Cancer biomarker discovery based on multiplexed quantitative proteomic strategies.' After earning my Ph.D., I joined Dr. Ruedi Aebersold’s lab at ETH Zurich as a postdoc, where I further specialized in DIA-MS and continued my research in the field. So next year will mark my 20th anniversary in proteomics!!

What does being a member of HUPO mean to you?

Being a member of HUPO holds deep significance for me. My first major international conference was HUPO Sydney 2010, not only my first journey outside of China but also the pivotal event where I met Ruedi Aebersold and was accepted as a postdoc in his lab. Over the past 14 years, I have attended most HUPO congresses and now serve on both the HUPO Award Committee and the HUPO Education and Training Committee. I was deeply honored to win the HUPO ECR Manuscript Competition award at HUPO Reconnect 2021. Being part of the HUPO community, where I can share my research, gain insights from others, and collaborate with fellow scientists who share a passion for proteomics, truly makes me feel fortunate and valued. Reflecting on the Chinese proverb, 'The joy of meeting an old friend in a foreign land is one of life’s greatest pleasures,' I resonate with this sentiment each time I attend a HUPO conference.

What makes your research program exciting and unique?

In my lab, we are dedicated to addressing a fundamental question: Can we measure not only the abundance of any given protein or its modifications but also determine and comprehend their persistence within a cell system? This research focus has catalyzed several exciting directions. First, we have integrated pulse-chase SILAC labeling (pSILAC) with DIA-MS, or plex-DIA, to measure protein turnover rates on a large scale. We've optimized the mass spectrometry methods on our Lumos Orbitrap MS and developed a bioinformatics pipeline to accurately determine protein lifetimes. Second, we ventured into uncharted territory by “marrying” protein turnover measurements with post-translational modification (PTM) profiling, such as phosphoproteomics. This approach allows us to explore how site-specific phosphorylation impacts protein turnover. Interestingly, we've observed that phosphorylation often reduces protein turnover, a phenomenon that was underappreciated in previous studies. Third, we have applied protein turnover measurements across various biological and disease contexts, including cancer aneuploidy, cell starvation, and cell fate decisions. One of our recent discoveries revealed that protein turnover control varies significantly among different 'gain-type' and 'loss-type' lung cancer aneuploidies. Together, our goal is to augment the traditional 'abundance-centric' perspective with a 'lifetime-centric' view on proteins and PTMs, thereby establishing a new paradigm in protein research that spans basic and translational sciences.

In addition to our primary research focus, we are also deeply engaged in understanding biodiversity between human individuals and other species on Earth through proteomics and PTM profiling. Furthermore, we actively collaborate with many local Yale scientists and other global collaborators, supporting their research endeavors, as I firmly believe in the transformative power of proteomics in modern biology.

What are your interests outside the lab?

Outside of the lab, I treasure every moment spent with my wife and our energetic 3.5-year-old son. Besides family time, I dive into the worlds of science fiction novels, classics like 'Dream of the Red Chamber,' and those endlessly fascinating Chinese cultivation and immortal novels—not to mention a good movie binge. These are my favorite ways to blissfully ignore the passage of time. As for exercise, I once wielded a badminton racket, but I've recently traded it in for a home treadmill. I must admit, it’s definitely less smashing!

Where do you envision the field of proteomics in the next 10 years?

Over the next ten years, I envision the field of proteomics expanding to broadly encompass a wider array of non-MS technologies. The detection and quantification of proteins, particularly at the total protein level and in clinical applications, will likely see the emergence of many non-MS technologies. These new methods may compete with, and in some areas surpass, mass spectrometry. Technologies such as multiplex antibody techniques, SomaScan, Olink-like technologies, super-resolution imaging for direct observation of peptide sequences or PTM structures, and nanopore approaches for single-molecule analysis are poised to make significant strides and challenge MS experts.

Additionally, I believe that mass spectrometry will not become obsolete but will continue to develop rapidly. For example, the MS-based analysis of post-translational modifications (PTMs) and protein dynamics, including protein turnover as we are exploring in our lab, will remain essential. Mass spectrometry will continue to generate vast and complex datasets, such as those involving giant patient cohorts, in the future. The development of innovative data analysis and bioinformatics tools will remain a hot topic. Over the next ten years, we might see AI tools like transformers become mainstream in mass spectrometry data analysis and even in routine protein identification and quantification. However, we will also continue to face challenges with data noise, practical issues with sample preparation, and the stability of mass spectrometry system (especially the LC ;-) ).

Moreover, an especially exciting area I foresee is spatial proteomics. My lab recently began incorporating ion mobility separation and MALDI MS imaging into our toolkit. Although these are new territories for us, these emerging spatial 'omics' and spatial proteomics analyses will uncover the cell-type heterogeneity in the disease process, uncovering new disease dependencies and vulnerabilities.

Would you agree to share your Humans of HUPO profile on HUPO social media/ social media tags?

Yes.

The Initiative for Model Organism Proteomics (iMOP) unveils an exciting webinar titled "Exploring New Model Organisms and Unraveling Protein Mysteries."

Mark your calendars for May 21st and get ready to explore the world of proteomics and learn how it's revolutionizing our understanding of molecular mechanisms in a range of new model organisms. Join them on this journey as they shed light on how these discoveries can boost human health, safeguard the environment, and preserve biodiversity. See further webinar details on the flyer below. 

Zoom Meeting Link Here