NewS

C-HPP Workshop
Sunday, October 20th, 2024
Seminar Room 7, International Congress Center Dresden, Germany

Session One: C-HPP Update and Business Meeting (Chair, Chris Overall)

9:00: Welcome, C-HPP Annual Report and Update (Chris Overall)
“Gender and Geographic Diversity in the C-HPP and Team Renewal.”

9:30: Elections for C-HPP EC positions vacant: We welcome nominations from the floor or by email prior to the Workshop.

(a) Chair 2025-2028 (Nominations: Gong Zhang; )
(b) Co-Chair (if Gong Zhang is elected Chair, a Co-Chair position becomes vacant. If so, nominations for the Co-chair: Fernando Corrales; )
(c) Secretary General (Nominations Heeyoun Hwang; ) (if Heeyoun Hwang is elected Secretary General, a Co-Chair position becomes vacant. If so, nominations for the CoChair: Josh Labaer; )
(d) Member-at-large (Nominations Gilberto Domont; )
(e) ECR Member (Nominations from HUPO ECR Committee)

9:45: ECR Talk “Discovery of a Novel Player in ER-Mitochondria Interactions by DARTS-LC-MS/MS Proteomics Analysis” (Minjeong Ko, Korea)

10:00: "Unlocking the Secrets of Chromosome 2: The Critical Role of Associated Proteins in Health and Disease – Now a Danish Contribution” (Allan Stensballe + Louise Bundgaard) 

10:15-10:45: Biobreak/Coffee

Session Two: C-HPP Team Updates (Chair Gong Zhang)

10:45: Mitochondria team: “Humanin-Like Peptides” (Viviana Greco)

11:00: ECR talk “TMEM160, a Protein Belonging to Chromosome 19 with no Assigned Function, Promotes Tumoral Growth in Non-small Cell Lung and Cervical Cancer Cell Lines” (Gloria Angelina Herrera-Quiterio)

11:15: Chr 20 Team China “An Enquiry Towards the Identification Criteria of Missing Proteins” (Yuxin Li)

11:30: "Celebrating 10 Years of the C-HPP with a Regrouping Ceremony and Plaque Presentations” (Heeyoun Hwang + Chris Overall)

12:00-12:30: Working Lunch

Session Three: Functionalization of PTMs and Proteins (Chair Ho Jeong Kwon)

12:30: “The HPP Portal (HP3) Compiling GO + HPA + Uniprot” (Gong Zhang)

12:50: “FE Classification Update” (Eric Deutsch)

13:10: “GO Consortium and the C-HPP” (Pascale Gaudet)

13:20: General Discussion

14:00: Workshop Close

20:00: C-HPP Workshop Dinner

Congratulations to the finalists of the 2024 Poster Competition for both the Postdoctoral and the Graduate Student Category.

Postdoctoral Category:

• Anna Pagotto, ETH Zurich
• Enes Ugur Max Planck Institute of Biochemistry
• Fabian Frommelt CeMM
• Heather Murray The University of Newcastle
• Hsiang-En Hsu Academia Sinica
• Jan N. Hansen Stanford University
• Jonas P. Becker German Cancer Research Center
• Magdalena Kuras Lund University
• Malte Sielaff University Medical Center of the Johannes Gutenberg-University Mainz
• Matthew The TU Munich
• Rebecca Herzog Medical University of Vienna
• Thierry M. Nordmann Max Planck Insitutue of Biochemistry
• Tristan Cardon INSERM U1192 Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM)
• Vishnu Mohan Weizmann Insitute of Science
• Yaoting Sun Westlake University

Graduate Student Category:

• Adele Nel University of Pretoria
• Aigerim Kassym Jena University hospital
• Alicia-Sophie Schebesta Max Planck Institute of Biochemistry
• Alireza Nameni VIB-UGent
• Amy George Newcastle University
• Jan Simonik Masaryk University
• Johannes P. Zimmermann Univeristy of Würzburg
• Julian Müller Technical University of Munich
• Lucas Rodrigues-Ribeiro National Institute of Science and Technology in Nanobiopharmaceutics
• Maximilian Zwiebel MPI of Biochemistry
• Melissa S Vorster Stellenbosch University
• Nicolai Bjødstrup Palstrøm Odense University Hospital
• Pinar Altiner Institute of Pharmacology and Structural Biology (IPBS)
• Sophia Steigerwald Max Planck Institute of Biochemistry
• Tilman Werner University Medical Center Freiburg
• Vivien Wiltzsch Fraunhofer Institute for Cell Therapy and Immunology
• Yan Zhou Westlake University

Congratulations to the following PhD candidates who will be presenting their research in just 3 minutes during HUPO 2024 world congress in Dresden!

Alireza Nameni
I am currently a third-year PhD student at VIB-UGent Belgium, with a background in artificial intelligence and engineering. My research includes various projects with a primary focus on iDeepLC, a deep learning-based retention time predictor for modified peptides, and the Mokapot project, which enhances peptide-spectrum match identification using nonlinear machine learning algorithms.

Johanna Wallner
Hi there, I am Johanna. I studied Biochemistry at TU Munich and developed a passion for proteomics towards the end of my master's studies. This led me to pursue a PhD at OmicScouts GmbH, a company specializing in proteomics-based research. I am also affiliated with the Sieber Chair at TU Munich. The project I will present here is a collaboration with the Bundeswehr Institute of Microbiology. Our goal is to develop an easy-to-use model system for studying a variety of viral infections.

Julian Müller
Hi! I'm Julian, a PhD student at the Chair of Proteomics and Bioanalytics at TUM, Germany. I'm a bioinformatician by training and fell in love with proteomics during my masters, so you will find me either at a PC or in front of a mass spec. My PhD project revolves around cellular signaling cascades, particularly those involving phosphorylation. Our group uses phosphoproteomics and kinase inhibitors to study these signaling cascades, and my job is to write software that facilitates the analysis and interpretation of these large datasets.

Julia Schessner
After studying molecular biotechnology at the University of Heidelberg for my Bachelor's and Master's degree I returned to my hometown Munich and started my PhD at the Max-Planck-Institute of Biochemistry. Throughout my studies I always worked in the wet-lab, as well as the dry-lab, writing data analysis tools for the data I acquired myself. This was a perfect fit for my work on the subcellular organization of the proteome, where I needed to use all my skills from cell culture to data analysis to drive my projects. What grounds me is my 2 year-old daughter who I hope to inspire to always follow her curiosity and to never stop learning.

Carmen Garcia Duran
I am a PhD student in the Department of Microbiology and Parasitology at Complutense University of Madrid under the supervision of Dr Concha Gil. My research focuses on the study of microbiota in disease using metaproteomics, with special interest in sepsis and long-COVID. The main objective is to gain a deeper understanding of these communities and identify disease biomarkers, such as microbial proteins or microorganisms.

Ericka Itang
Ericka Itang is a third-year PhD student at the Max Planck Institute of Biochemistry in Martinsried, Germany. She has developed a workflow that combines dimethyl-based labeling and sample multiplexing with data-independent acquisition, known as multiplexed-DIA (mDIA). Recently, she applied this mDIA workflow to the proteomics analysis of clinical samples such as urine and plasma to map the landscape of pediatric health and disease. Her research interests also include investigating the role of endogenous peptides in therapeutics. Born and raised in the Philippines, Ericka moved to Germany in 2021 to further her education and expand her horizons in scientific research.

Yu Zong
I am a PhD student from Fudan University, Shanghai, China. My research interest involves applying artificial intelligence to solve important questions in proteomics. My main work focuses on predicting phosphopeptides and glycopeptides spectra using advanced deep learning models.

Shaufa Shareef
As a final-year PhD student, I am researching biomarker discovery for infectious diseases such as COVID-19, and investigating the mechanistic basis of immune responses to such conditions. I am a biochemist by training, with a focus on clinical biochemistry and the relationship between scientific discovery and how that translates to clinical practice.  I grew up in Maldives, studied in the UK, and have worked in various aspects of the Maldivian health sector. As such, I also have a keen interest in health inequalities and the disproportionate effect of infectious diseases in this context. I look forward to gaining more insights in the field during HuPo 2024.

Linus Wollenweber
Linus is a second year PhD student in Albert Heck's lab at Utrecht University. Coming from a background in Molecular Biotechnology, he is working on the mass spectrometric analysis of intact Antibody fragments (Fabs). He is currently expanding the toolbox required to measure antibodies from human specimen with clonal resolution. This requires method development in sample preparation, purification, and work on appropriate LC-MS methods to analyze the complex samples.

Robbe Devreese
I am a first-year PhD student in the CompOmics group at the VIB-UGent Center for Medical Biotechnology in Ghent, Belgium. My research focuses on enhancing the prediction of collisional cross-sections of peptides in ion mobility-assisted LC/MS-MS. The aim of my PhD project is to utilize these improved predictions for more sensitive and specific analysis of (clinical) DIA proteomics data.

Annica Preikschat
My name is Annica Preikschat, I graduated from Friedrich Alexander University Erlangen in the field of immunology and I am now working at AG Tenzer in the Core facility of proteomics in the Institute of Immunology at the Unimedical Center of Mainz. My PhD is supported by the Transmed Training program and connects both, immunology and mass spectrometry. The project aims to identify peptides which are important for the adaptive immune response in rheumatoid arthritis patients. This will help to better characterize arthritis and might result in the development of a treatment.

Dominik Lux
Dominik Lux is a computer scientist pursuing his PhD in Bioscience at the Medical Proteome Center, Ruhr-University Bochum, Germany. He focuses on unidentified mass spectrometry data by incorporating besides well-known protein sequences, mutations, variants, and more. By utilizing graphs and established methods, he aims to identify such entries. His PhD research focuses on gaining a deeper understanding of Parkinson's disease, though his approach and tools can be broadly applied.

Daniel Flender
Daniel Flender is a PhD candidate at the University of Antwerp and the Flemish Institute for Technological Research ( VITO), specializing in immunopeptidomics in non small cell lung cancer (NSCLC). His research aims to identify and analyze peptide antigens, with the goal of developing targeted immunotherapies and advancing cancer treatment strategies. By uncovering specific peptides that can trigger immune responses, Daniel's work aims to enhance the precision and effectiveness of cancer treatments. His contributions are pivotal in advancing our understanding of immune system interactions with cancer, ultimately striving to improve patient outcomes and innovate therapeutic approaches in oncology.

Dr. Marc van Oostrum is one of the three finalists selected to present their manuscripts during the manuscript competition in a dedicated plenary session at HUPO2024. Their talks will be evaluated by a panel of experts to select the “Proteomics Highlight of the Year”. Dr. Marc van Oostrum will be presenting his work: The proteomic landscape of synaptic diversity across brain regions and cell types. 

Dr. Marc van Oostrum is currently an SNSF Ambizione Junior Group Leader in Prof. Peter Scheiffele’s laboratory at the Biozentrum of the University of Basel. His research focuses on employing spatial proteomics to unravel the molecular organization and diversity of neuronal synapses. Marc completed his Master’s in Biochemistry at ETH Zürich, where he conducted his thesis research in Prof. Paola Picotti’s lab. He pursued his PhD at the Institute for Molecular Systems Biology at ETH Zürich under Prof. Bernd Wollscheid, specializing in cell surface and spatial proteomics. His postdoctoral work, carried out in Prof. Erin Schuman’s lab at the Max Planck Institute for Brain Research in Frankfurt am Main, explored the molecular diversity of synapses.

The 33^rd HBPP Workshop took place from May 22^nd to 24^th 2024, in Naas, just outside Dublin, in Ireland. It was a very successful, small but intense meeting with participants from Australia, Brazil, Germany, Ireland, Saudi Arabia, Sweden, United Kingdom, and the USA.

The meeting addressed clinical, animal, and cellular findings for neurodegeneration (e.g. Alzheimer’s disease, Parkinson’s disease, Multiple Sclerosis) and neuropsychiatric conditions such as Schizophrenia, Bipolar disorder and Autism. Whilst most of the work presented employed mass spectrometry-based proteomics, there was a trend of employing large-scale protein arrays of different kinds as well as combination of proteomics with other –omics platforms. Advanced statistical analyses including multivariate machine learning as well as Mendelian randomization of GWAS findings were elegantly combined with proteomics findings. Pathway analyses and investigations of posttranslational modifications were also presented.

Christopher Whelan from Johnson and Johnson presented an update from the findings of the open-access proteomics resource profiling on blood plasma samples collected from over 50,000 UK Biobank participants to elucidate the biological mechanisms underlying proteo-genomic discoveries (Nature. 2023 Oct;622(7982):329-338. doi: 10.1038/s41586-023-06592-6. Epub 2023 Oct 4.PMID: 37794186.).

In addition, we welcomed PreOmics at the meeting to display their latest products. We also discussed lab sustainability actions and accreditation (My Green Lab).

There was ample time for networking at the meeting, and it was exciting to hear about related lab exchanges that are ongoing and planned.

The discussions and continuing work done by HBPP is significant and helps to advance the development and roll out of neuroproteomic methods to acquire holistic insights of the brain proteome in health and disease.

The 34th HUPO HBPP workshop will take place in Toledo, USA, in 2025. Further details will be announced on the HBPP website https://hupo.org/Brain and https://x.com/BrainProteomics in due course.

For more information regarding this workshop or the Human Brain Proteome Project, please visit the HUPO website here and/or contact: Melanie Föcking (mfocking@rcsi.ie, current chair of HBPP) or Darragh O’Brien (darragh.obrien@ndm.ox.ac.uk, HBPP communications officer).

Stacy Malaker is one of the three finalists selected to present their manuscripts during the manuscript competition in a dedicated plenary session at HUPO2024. A panel of experts will evaluate their talks to select the “Proteomics Highlight of the Year”. Stacy Malaker will be presenting her work: Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. 

Dr. Malaker is an Assistant Professor in the Department of Chemistry at Yale University. Her laboratory is focused on establishing methods and technology to study mucins, a class of densely O-glycosylated extracellular proteins, by mass spectrometry. Additionally, the laboratory studies mucins in a biological context, since these proteins play integral, yet poorly understood, roles in numerous diseases. Prior to her appointment at Yale, she received her B.S. from the University of Michigan in Biochemistry and Anthropology-Zoology. Dr. Malaker then went on to receive her PhD in Chemistry from the University of Virginia in the laboratory of Professor Donald Hunt. She continued to investigate the role of aberrant glycosylation in cancer as an NIH postdoctoral fellow in Professor Carolyn Bertozzi’s laboratory at Stanford University before starting at Yale in 2021.

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
Upcoming workshops for 2024 and 2025:

• 26^th C-HPP Workshop: (0.5 day), Dresden, Sunday 20^th October 2024, 9:00 AM – 14:00 PM (before HUPO Congress).
• 27^th C-HPP Workshop on the new Human Proteome Project Portal, Guangzhou LEDY Life and Health City, China, November 28 & 29th 2024.
• 28^th 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. C-HPP Secretary General Dr Peter Horvatovich will be stepping down at the end of 2024, and we invite nominations to fill this position for three years starting in January 2025.
4. We are creating a new ECR position for the C-HPP EC, and we will elect in Dresden a new ECR to sit on the EC from January 2025 for 3 years. Please self nominate.
5. Election for a member-at-large of the C-HPP EC for three years starting in January 2025.

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.