Dr. Javier Alfaro uses a variety of different molecular profiling strategies to interrogate the relationship between the tumour and the immune system. Javier believes that while cancer is a disease of the genome, the selection pressures that support the development of cancer hallmarks act on the expressed phenotypic traits of the cancer cell. This means that a comprehensive molecular portrait of the tumour must include the proteome and the metabolome, which are significant endpoints of gene processing. Javier’s work focuses on the development of proteogenomic pipelines for neoantigen discovery, integrative -omics with a focus on Oesophageal cancer and Sarcomas, a bioinformatic interrogation of immune-editing in cancer, and supporting the clinical translation of new proteomics technologies. He has a PhD in Medical Biophysics (University of Toronto), specializing in computational proteomics, a Masters in Biochemistry specializing in bioinformatics (Dalhousie University) and a double major in Biochemistry and Computer Science (University of Victoria).

What is your professional background?

I have graduated from Intercollegiate Faculty of Biotechnology of University of Gdansk and Medical University of Gdansk in 2019. During my master thesis I have worked on characterization of spectrum of phenotypes in context of epithelial to mesenchymal transition (EMT) in circulating tumour cells in early breast cancer. During EMT, epithelial cancer cells gain mesenchymal-like features and are more likely to immune escape, what corelates with worse prognosis. I became really interested in the interactions between cancer cells and the immune system, what led me to pursuing PhD in this field.

What led you to work in the ICCVS?

I believe that the interdisciplinary approach towards cancer treatment in ICCVS makes it an excellent place to pursue PhD. The perspective of working with top researchers in an international setting seemed like a great opportunity to learn a variety of new skills and extend my knowledge.

What are you working on just now?

Right now, I am investigating the role of B cells in cancer, as they have the ability to both promote and inhibit the tumour progression.

What is your professional background?

Dominika completed her undergraduate studies at Robert Gordon University in Aberdeen, Scotland. Her passion for laboratory work led her to choosing Bioscience with Biomedical Sciences program. During her studies, Dominika wrote a research proposal to study effects of sleep deprivation in Alzheimer Disease rat models. The quality of her work led to her being given the possibility to start internship at the Laboratory of Synaptogenesis at Nencki Institute of Experimental Biology in Warsaw, Poland. In the final year of her studies, Dominika joined Laboratory of Parasitology at Instituto de Investigacao e Inovacao em Saude in Porto, Portugal, where she carried a project on in vitro cytotoxicity and antiparasitic activity of new hydroxamic and mononaphthalimde derivatives. After graduating with Hons BSc Diploma, Dominika completed an MSc programme in Applied Neuroscience at King’s College London. At the same time, she was offered a biologist position at the Laboratory of Cytoskeleton and Cilia Biology at Nencki Institute of Experimental Biology. There, she gained experience in molecular biology techniques and carried a research project on roles of Fap246 and Spef2 in ciliary motility. Due to Dominika’s rising interest in the field of neuroscience, she has decided to pursue her scientific career as a PhD student at ICCVS. Dominika is studying mechanisms which lead to neurodegenerative diseases and cancer, using SH-SY5Y cell line and patient derived Induced Pluripotent Stem Cells as her models.

What led you to work in the ICCVS?

I’ve been looking to join the team of diverse and highly motivated professionals coming from different scientific backgrounds. The collaborative, inclusive and innovative nature of ICCVS encouraged me to join them as a PhD student.

What are you working on just now?

I am currently working on understanding factors that lead to neurodegenerative diseases using patient derived Induced Pluripotent Stem Cells models.

What is your professional background?

I did my PhD in the Laboratory of Bioinformatics and System Biology (CeNT, Warsaw), where I devoted myself to the development of a new, direct, high-resolution method for DSBs labelling. This work resulted in a specific, ultra-sensitive, and universal DSB detection technique called i-BLESS. After that time, I worked in the Laboratory of Functional and Structural Genomics (CeNT, Warsaw), where I was involved in research on the relationship between replication, transcription, and genome three-dimensional organization. In general, over these years I have been seeking a better understanding of the genome sensitivity to double-strand breaks and ways for maintaining genome stability under stress conditions, including replication stress, in relation to higher-order chromatin organization. Before joining ICCVS I worked in the Experimental and Translational Immunology Group at the Intercollegiate Faculty of Biotechnology, where I was involved in more applied research, trying to increase T cell ability to fight cancer or virus-infected cells using artificial exosomes.

What led you to work in the ICCVS?

I have always wanted to be involved in research that could directly benefit society, e.g. by the development of new treatments, therapies, and diagnostic methods. During the first years of my career, the projects I participated in were not directly linked to cancer but related to processes that can lead to carcinogenesis, such as genetic instability. Later I was more directly involved in cancer research, trying to develop a novel tool for cancer treatment using artificial exosomes. I believe that in ICCVS I will be able to use the knowledge and experience I gained so far in a more practical way, helping to develop immunotherapies for the treatment of non-small cell lung cancer patients.

What are you working on just now?

Immunosuppressive conditions within the tumour microenvironment (TME) can strongly influence the function of immune cells, resulting in the escape of the tumour from immune surveillance and, subsequently, the progression of its growth. One way in which the tumour exerts its immunosuppressive effect is through small extracellular vesicle-mediated cell communication. Currently, my goal is to gain more insight into how tumour-derived small extracellular vesicles (sEV) contribute to the immunosuppressive effect of TME.

What is your professional background?

I obtained my PhD in Chemistry at the Faculty of Chemistry, University of Gdańsk. I worked mainly as an analytical chemist in research project realized at University of Gdańsk and in the Institute of Oceanology Polish Academy of Sciences. I worked also in industry, as a member of Environmental Protection Team of “Remontowa” Shiprepair Yard. In 2024 I joined the team of the International Center for Cancer Vaccine Science.

What led you to work in the ICCVS?

The main motivating factor was to learn something new and to gain new experience which will broaden my portfolio. Therefore I took the opportunity to work in an international and multidisciplinary research team.

What are you working on just now?

As a member of the ICCVS Research Support Team I help to create a smoothly run place to conduct research.

What is your professional background?

Vast majority of my professional career I have worked in the area of EU grants, I understand the role of grants as a mechanism to improve the situation of European citizens, and to equalize chances for a better life for all people in Europe. I am experienced in programme management, I was part of all the project and programme cycle steps, from opening calls, through assessment, implementation and closure. For more than 15 years I gained cross-cutting practice working as an administration, communication and promotion manager, project then financial officer and head of the Joint Secretariat of the Interreg South Baltic Programme. I graduated from the Gdańsk University of Technology (Faculty of Chemistry) as an engineer of Environmental Protection and Management and from post-graduate studies in Cooperation with European Union Structures.

What led you to work in the ICCVS?

The main motivating factor has always been the opportunity to develop, to learn something new, to gain new experience and broaden my portfolio. At the same time, I always try to make sure my skills and all the years of experience can bring some added value to the institution and society. I enjoy working in international organization, it gives me the understanding, respect, and sensitivity necessary for cooperation with people of different cultural backgrounds.

What are you working on just now?

I joined the ICCVS research support team to work on EU project management, grant writing and administration duties within the Centre.

What is your professional background?

I have strong background in protein biochemistry. Till 2016 I studied the mechanism of function of molecular chaperones in disaggregation and refolding of aggregated proteins. In the course of my PhD studies (Intercollegiate Faculty of Biotechnology, University of Gdańsk) I explored the mode of action of bacterial small heat shock proteins. Having completed my PhD, I studied the mechanism of cooperation between Hsp70 and Hsp100 chaperones.
I also have some work experience in the industry. I held the Scientist position in Selvita (Kraków), a drug discovery company, where I developed protein production and purification methods, which resulted in providing high-quality recombinant proteins for several pharmaceutical companies from Europe and the United States. Subsequently, I worked as a Downstream Process Development Specialist in biopharmaceutical company Polpharma Biologics (Gdańsk), where I performed experiments aimed at optimization of purification process of therapeutic antibodies, which are in the company’s portfolio.

What led you to work in the ICCVS?

While working in the industry I found it gives me great satisfaction to contribute to the projects aimed at drug development. However, I also realized that participating in early stage of these research projects, when ideas are born, before being transformed into products, would be much more exciting for me. I am particularly interested in cancer immunology. Therefore, I decided to seek for a job opportunity, which would enable me to explore the interactions between cancer and immune cells and the mechanisms enabling tumour cells to evade immune system. The ICCVS happened to be just a perfect match for me.

What are you working on just now?

I have recently started a research project on the role of type I interferons (IFNs) in cancer. It was shown that cancer cells suppress type I IFNs signalling, which results in tumour growth and metastasis. My goal is to gain more insight into the mechanisms enabling tumour cells to suppress type I IFNs secretion. Moreover, I plan to investigate how lack of these cytokines production may lead to tumour progression. I will analyse direct effects of type I IFNs signalling suppression on cancer cells as well as its impact on the crosstalk between cancer and immune cells.

What is your professional background?

I obtained my MSc Medical Biotechnology degree at Collegium Medicum Nicolaus Copernicus University in Bydgoszcz, Poland. At the beginning of my research carrier I worked in wet-lab being focused on analytical chemistry i.e. liquid chromatography/gas chromatography and sample preparation procedures. During my PhD, I had an opportunity to work at the Technical University of Braunschweig in the field of pharmaceutical chemistry and at the Molecular Epidemiology Group in the Spanish National Cancer Research Center (CNIO, Madrid). The experience related to data analysis gained in CNIO (Madrid) has led me to develop computational skills on data modeling so that my PhD thesis defended at the Medical University of Gdańsk was focused on metabolomics data analysis using Bayesian statistics. Apart from metabolomics studies I also have experience in analyzing micro RNA and SNP data.

What led you to work in the ICCVS?

Mainly my intuition, but my goal was also to look for an opportunity to develop new skills outside my comfort zone.

What are you working on just now?

Integration of proteomics data (within Horizon 2020 consortium), HLA typing in sarcoma, occurrence of flu type A/B and its association with SARS-CoV-2 disease.

What is your professional background?

I obtained my MSc Medical Biotechnology degree at the Intercollegiate Faculty of Biotechnology of the University of Gdansk and Medical University of Gdansk in 2018. At the same year I started to work in the LIDER “Vaccine against the virus Zika – innovative preparation of subunit antigens“ project. The main goal of my work was overproduction and purification of recombinant variants of Zika virus E protein in bac to bac and mammalian system and the analysis of the obtained proteins.

After working at the Univerisity I joined Prochimia Surfaces company where I participated in two projects. I synthesised and characterised gold nanoparticles with anticancer drugs or fluorophores as ligands on the surface.  Furthermore, I developed gold nanoparticles that will effectively bind proteins as Cas9.

After two years of working at a private company, I joined the ICCVS.

What led you to work in the ICCVS?

ICCVS offers a great opportunity to work in an international and multidisciplinary research team.  Scientists with different scientific backgrounds and approaches encourage innovating thinking of cancer immunology and expanding knowledge in other fields of biotechnology.

What are you working on just now?

As a Cell biologist I am interested in dissecting the interplay between immune and cell proliferation pathways in the NSCLC ( non-small cell lung cancer). I am working on a project focusing on the role of transcription factor Nrf2 pathway in tumor formation and progression in NSCLC. I am also investigating the interaction between different proteins  (including Nrf2) and MHC class I.

What is your professional background?

Katarzyna is a pharmacist, who graduated from the Medical University of Lodz and a PhD student in ICCVS. Several years spent in multiple laboratories, ensured her to pursue a scientific path. Katarzyna’s first scientific project was held at the University of Central Lancashire and utilized a 3D printing as a tool in personalized medicine design. To complete her masters’ thesis, she spent 6 months at Charles University in Prague, performing cytotoxicity studies using compounds, which she had previously synthesized. After learning those laboratory skills, she applied for the Visiting Graduate Traineeship Program and worked for a year at The Oklahoma Medical Research Foundation (USA). Katarzyna’s multidisciplinary research experience, including pharmaceutical sciences, cytotoxicity studies, genetics and cellular biology only confirmed that being a researcher is the right choice for her.

What led you to work in the ICCVS?

The idea of creating ICCVS was to bring scientific excellence into polish science. In parallel, its mission is to solve the most disturbing problem in the field of biomedical sciences – defeating cancer. My decision to join ICCVS was driven by a strong believe that international collaboration with worldwide recognized scientists and multidisciplinary approach is a key to great success.

What are you working on just now?

Canine osteosarcoma occurs spontaneously in companion animals, especially dogs. It carries many similarities to human disease, making it a perfect model for identification of novel treatment approaches benefiting both dogs and humans. Immune checkpoints have recently been recognized as crucial regulatory pathways that maintain immune homeostasis by modulating effector mechanisms in favor of immunogenic tolerance and cancers exploit them to evade antitumor immunity. Programmed cell death 1 (PD-1) is a prominent checkpoint receptor that, upon engagement by its ligands (PD-L1), dampens T effector functions by inhibiting signaling downstream of the T cell receptor (TCR). Thus, expression of PD-1 ligands, particularly PD-L1, in the tumor microenvironment (TME) protects cancers from immune-mediated rejection. Recent reports identified, that these proteins are involved in tumor pathogenesis and affect cellular proliferation, autophagy or induce epithelial to mesenchymal transition. However, little is known regarding this phenomenon in osteosarcoma. Our aim is to further characterize the effects of PD-1/PD-L1 axis on cellular phenotype in canine osteosarcoma cell lines as a model for human disease.

What is your professional background?

Currently, I work as a postdoctoral researcher in International Centre for Cancer Vaccine Science with the main research focus on proteomics of mutated protein/peptide sequences in biological material. I actively work in the field of biochemistry and proteomics for past 9 years. My first experiences in proteomics came from bachelor and master studies at Masaryk University, Brno. During this period I was focused on targeted quantitation of p53 in complex biological matrices and on cell membrane proteins as a potential target of anti-metastatic treatment of breast cancer. My skills in proteomics and mass spectrometry broadened greatly during my doctoral and postdoctoral studies at Masaryk Memorial Cancer Institute (MMCI). I spent there 6 years conducting various mass spectrometry analyses using TripleTOF 5600+ mass spectrometer. My work involved mainly proteomic sample preparation, method preparation to manipulate proteomic sample complexity, mass spectrometry of proteins, proteomic data analysis and interpretation. I have acquired experience in designing new workflows to solve biological questions. My research interests are mass spectrometry of mutated proteins, SWATH/DIA proteomic quantitation for differential biology and proteomics of cell membrane.

What led you to work in the ICCVS?

I see ICCVS as a multidisciplinary center where many fields such as molecular biology, proteomics, genomics, immunology, bioinformatics meet up to solve questions in cancer vaccine science. I see ICCVS as a place, where I could apply my previous knowledge and extend it further.

What are you working on just now?

Currently, I am involved in development of technologies for proteomic research of a cell subpopulations or LCM dissected tissue sections, where patient’s sample amount is limited. The strength of this method could be utilized in cancer proteomics as it could serve to compare different functional parts of a tumor and define relative protein quantity across a tumor.

I am involved in setting up data-independent mass spectrometry (DIA) to enable precise and reproducible label-free proteome comparison across multiple biological samples (e.g. tumor tissue, variously treated cell lines). Combination of DIA and microPOTS has a potential to describe what are the mutated proteome changes across the tumor which might shed a light on processes leading to tumor antigen presentation.

Research in a Nutshell

Cancer progression is driven in part by the mutation of genes that mediate immortality, angiogenesis, metastasis, changes in energy metabolism, and evasion of the immune system. P53 mutation is one of the most common genetic changes in cancer development that leads to a re-wiring and selective survival advantage to the developing cancer cell. This genetic re-wiring involves changes in the transciptome, the proteome, and the phenotype of the cell within a specific microenvironmental niche in vivo. The lab is using biophysical, biochemical, and proteomic approaches to develop novel molecular insights into clinically relevant cancer progression pathways; particularly cancers of unmet clinical need including oesophageal adenocarcinoma, gliomas, and sarcomas. Emerging therapeutic strategies being developed include drugging protein-protein interactions; biologics and immunotherapeutics; and proteogenomics platforms that define mutated neoantigen landscapes to facilitate cancer vaccine developments.

Biography

Ted Hupp obtained a dual BSc degree in microbiology & chemistry at the idyllically named Bowling Green State University in Ohio, USA. Following a PhD in Biochemistry at Michigan State University, enzymology principles were then applied to the cancer research field in Dundee (UK) to develop the paradigm that the tumour suppressor p53 could be activated by antibodies. His current position of Professor is as the Chair of Experimental Cancer Research at the University of Edinburgh and aims to spearhead the formation of novel, interdisciplinary research programmes in cancer biomedicine. Topics include as Drug Discovery programmes in the Ubiquitin-Proteasome system and the development of therapeutic monoclonal antibodies. It is during these European Union wide collaborations that Ted and colleagues set up the International Center for Cancer Vaccine Science (ICCVS); at the University of Gdansk forming a joint research unit with the University of Edinburgh to seed inter-disciplinary collaborations within the European Union and around the world.

Publications

1             Maurel, M. et al. Control of anterior GRadient 2 (AGR2) dimerization links endoplasmic reticulum proteostasis to inflammation. EMBO Mol Med 11, doi:10.15252/emmm.201810120 (2019).

2             Gu, X. et al. Copy number variation: A prognostic marker for young patients with squamous cell carcinoma of the oral tongue. J Oral Pathol Med 48, 24-30, doi:10.1111/jop.12792 (2019).

3             Gomez-Herranz, M. et al. The effects of IFITM1 and IFITM3 gene deletion on IFNgamma stimulated protein synthesis. Cell Signal 60, 39-56, doi:10.1016/j.cellsig.2019.03.024 (2019).

4             Coufalova, D. et al. An inter-subunit protein-peptide interface that stabilizes the specific activity and oligomerization of the AAA+ chaperone Reptin. J Proteomics 199, 89-101, doi:10.1016/j.jprot.2019.02.012 (2019).

5             Mohtar, M. A. et al. The sequence-specific peptide-binding activity of the protein sulfide isomerase AGR2 directs its’ stable binding to the oncogenic receptor EpCAM. Mol Cell Proteomics, doi:10.1074/mcp.RA118.000573 (2018).

6             O’Neill, J. R. et al. Quantitative Shotgun Proteomics Unveils Candidate Novel Esophageal Adenocarcinoma (EAC)-specific Proteins. Mol Cell Proteomics 16, 1138-1150, doi:10.1074/mcp.M116.065078 (2017)

Collaborations

The ICCVS has formed a centre of excellence in inter-disciplinary research that aims to improve human health by establishing discovery science programmes focused on the immune-cancer synapse. Several inter-disciplinary collaborations with academic and industry colleagues are focused on (i) identifying genes that regulate the expression of MHC  Class I molecules, (ii) identifying oncogenic receptors at cancer-immune synapse; (iii) developing therapeutic antibodies to targets in the cancer secretory system; (iv) using proteogenomics and kinomics platforms to develop preclinical models in cancers of high unmet clinical need.

Technology expertise

Protein-protein interactions; kinase signal transduction; ubiquitination and protein degradation; synthetic monoclonal antibody and peptide bacteriophage libraries

What is your professional background?

dr inż. Umesh Kalathiya is currently pursuing his postdoc at ICCVS, University of Gdansk, Poland, after completing PhD from Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdansk University of Technology, Poland. He graduated his Master of science and engineering in biotechnology (bioinformatics) from Wroclaw University of Technology, Poland and Bachelor of science in bioinformatics from Christ College, Saurashtra University, India. During PhD studies, he was awarded scholarships for the best PhD student from the rector of Gdansk University of Technology. Applying computational and theoretical methods (molecular modelling/docking/dynamics, quantum calculations, protein-protein/drug interactions) to understand biomolecular systems is his area of expertise. His previous research involved designing and identifying novel drug like molecules (using ligand- and structure- based in silico virtual screening approach) for telomerase and telomere proteins. Furthermore, he also participated in different projects where he applied molecular dynamics simulation approach to trace the structural behavior of different proteins.

What led you to work in the ICCVS?

For a person with my expertise (in computational and theoretical methods) ICCVS is the best platform to work, a multidisciplinary center where I get different opportunities to apply my techniques to understand the molecular properties of proteins involved in cancer immunology.

What are you working on just now?

At ICCVS, my research will be surrounding the nonsense-mediated mRNA decay (NMD) components. NMD pathway is a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with truncated open reading frames due to the presence of a premature termination codon. Objective of my work is to investigate the druggable proteins from the set of NMD components. Moreover, using computational approach will try to understand the effect of mutations (coming from different types of cancer) on the structural and dynamic properties of the NMD components.

What is your professional background?

I completed my Masters in Bioinformatics at the Institute of Bioinformatics and Applied Biotechnology (IBAB) at Bangalore, India. During my Master’s thesis project, my research team and I developed and validated a platform-independent R-based pipeline for the analysis and visualization of transcriptomic microarray data. This work led to a publication “Panga V, Kallor AA, Nair A, Harshan S, Raghunathan S (2019) Mitochondrial dysfunction in rheumatoid arthritis: A comprehensive analysis by integrating gene expression, protein-protein interactions and gene ontology data. PLOS ONE 14(11): e0224632. https://doi.org/10.1371/journal.pone.0224632” in 2019. After my master’s, I worked at Glaxosmithkline Pharmaceuticals Pvt Ltd (GSK) in Bangalore, India, as a Clinical SAS Programmer, where I performed analysis, visualization and reporting on a wide range of drug trials, from Respiratory diseases to Oncology. During my time at GSK, I participated in national level industrial conferences and won the 1^st prize for analytics at the Conference of Statistics and Programming in Clinical Research in 2018, in addition to being awarded performance-based Bronze awards on multiple occassions.

What led you to work in the ICCVS?

With my multi-disciplinary background, spanning microbiology, immunology, biostatistics and bioinformatics, the ICCVS was a natural choice for me given how academicians from diverse backgrounds work and collaborate on projects, while exchanging ideas and technological know-how in the process. Having worked on immunotherapy trials for over two years in GSK, I became curious about the immunological mechanisms behind immunotherapy and the concept of personalized immunotherapy. My curiosity was driven by questions such as why certain patients exhibited severe adverse reactions to immunotherapy while other patients were refractory to the same therapy at the same dosage. Could an analysis of these patient’s genome/transcriptome/epigenome/proteome explain these differences? If so, could immunotherapy be targeted specifically to each patient? It was my quest to find answers to these questions that led me to apply for a position at the ICCVS.

What are you working on just now?

My research focuses on the identification and functional characterization of the so-called “crytptic” or “non-canonical” peptides within the human proteome using computational methods that include protein database searching, validation, deconvolution and visualization. The aim is to characterize the comprehensive non-canonical peptide landscape presented by the Major Histocompatibility Complex proteins in both healthy and cancerous tissues and to identify focal regions of antigen presentation. I am also currently extending our methods to identify and characterize peptides of bacterial origins and the regulatory roles played by them, if any, in the progression of cancer.

What is your professional background?

Currently, I am a 3rd year medical student at the Medical University of Gdańsk.

What led you to work in the ICCVS?

The possibility to extend my knowledge and opportunity to work in laboratory, with the chance to learn something new as well as to develop my own ideas, was tempting enough to join the team.

What are you working on just now?

I work under the supervision of dr Wojciech Siwek on researching the field of transcriptional memory induced by INF-y, how it is established, and the importance of this process for the phenomenon of trained immunity.

What is your professional background?

I’m postdoctoral researcher and currently working in the area of neoantigen discovery and mass spectrometry (MS) at the newly formed International Centre for Cancer Vaccine Science (ICCVS), University of Gdansk, Poland (https://iccvs.ug.edu.pl/). I have specialized in proteomics & I have been working in the area of proteomics concerning health, environment and safety for the past 10 years. I started my research career as research project assistant in the proteomics laboratory, at the National Chemical Laboratory (NCL), India. Herein, I have developed a strong interest on proteomics, MS and biomarker discovery.

Afterwards, I moved to Italy for doctoral studies focusing on invitro and invivo nanobiointeractions, biomarker findings for nanoexposure and nanotoxicology by using advanced proteomics tools. During my first postdoctoral studies at the Istituto Italiano di Tecnologia (IIT), Genova, Italy, I have developed protein nanoparticles for nanomedicine applications & dissolution test for risk assessment of nanomaterials. Additionally, I have background in Bioinformatics, Clinical Research & Clinical Data Management (CRCDM) and Diploma in Medical Laboratory Technology (DMLT).

What led you to work in the ICCVS?

ICCVS is the complete package in one pocket. It provides an exceptional opportunity to work in internationally and multidisciplinary fields such as molecular, biochemical and cell biology with proteogenomics, bioinformatics, synthetic biology, cancer and immunology. This is the place where scientists are dealing with fundamental questions in biology. My prior interest to work in biology, immunology with advanced techniques like mass spectrometer, mass cytometer etc. are attracted to me to work here at ICCVS. My prior multidisciplinary experience in proteomics, toxicoproteomics, nanomedicine will serve me well in my new endeavors in peptide neoantigen discovery.

What are you working on just now?

My research focus at the ICCVS follows few tracks; (1) optimizing cancer cell culture and peptide immune-purification i.e. immunoprecipitation (IP) and acid elution based enrichment of major histocompatibility complex (MHC), and (2) MHC-peptide sequencing by tandem mass spectrometry. This work will utilize tandem MS based sequence analysis of MHC peptides in order to discover peptide neoantigens that may be used as vaccines in personalized cancer therapies. Comprehensive knowledge of the MHC class-I and class-II peptides presented to T-cells is crucial for designing innovative therapeutics against cancer, cancer vaccine development and other diseases. (3) I’m actively involves in Biodiversity for Survival via Biomedicine (Bio2Bio), which is a global, cross-disciplinary initiative to support scientists working to prevent the loss of biodiversity.

What is your professional background?

Jacek Kowalski, MD, is the 1st year PhD International Centre for Cancer Vaccine Science (ICCVS) student and is a board-certified pathologist as a staff member at the Department of Pathomorphology at the Medical University of Gdansk. He has practical knowledge of pathological techniques from a variety of different material, including cytology samples, according to the current WHO classification systems. He is focused on thoracic pathology and participates in multidisciplinary program at the Medical University of Gdansk for thoracic malignancies. He participates in several clinical trials as investigator pathologist (ongoing clinical immunotherapy trials in oncology) and is involved in cooperation with external research partners, such as European Thoracic Oncology Platform. He is a coauthor of several case reports and patient series articles and is a member of several organisations dedicated to pathology, thoracic oncology and immunotherapy.

What led you to work in the ICCVS?

I am willing to extend knowledge about interactions between the immune system and tumour, and the possibilities of their use in cancer immunotherapy, especially in lung cancers.

What are you working on just now?

I am currently working on the use of methods of cellular composition analysis in lung cancer for potential immune-based therapies.

What is your professional background?

I obtained my MSc in Molecular Biology  at the Faculty of Biology, Geography and Oceanology of the University of Gdańsk.  The same year I started to work for the company Immunolab as a Laboratory Manager. We were focused on the production of immunological products, including polyvalent and monovalent rabbit antibodies, and the production of rabbit sera for serological diagnosis of Salmonella bacteria. After 4 years I moved to Malbork to work for Eurofins Polska as Team Leader of Microbiology Lab and Team Leader of the Logistics Department. Working in these positions has taught me how to manage time and collaborate with the entire team to achieve the intended goal.  However, I missed my research work and thus returned to the University of Gdańsk, where I worked on a project entitled “Metagenomic studies of plasmids from environmental samples” in the framework of doctoral studies. In the meantime, I also started to work as a high school biology teacher to develop a passion for science in young people. In 2018 I joined the team of the International Center for Cancer Vaccine Science.

What led you to work in the ICCVS?

The opportunity to work in an international and multidisciplinary research team.

What are you working on just now?

I am member of the ICCVS Research Support Team that helps to create a smoothly run place to conduct research.

Research in a nutshell

Since the beginning of my scientific work I have been working on immune tolerance, cell biology and cellular therapies of human diseases. I am a member of the group that administered for the first time in human in vitro expanded regulatory T cells (Tregs; June 2008), as well as a co-inventor of the first Treg based therapy of type 1 diabetes in children (since 2011).
Studding autoimmunity and following recent biological and cellular therapies I came to the conclusion that autoimmunity and cancer are two sides of the same coin. Immunosuppressive therapies used to be linked to an increased risk for cancer, while anti-cancer strategies are found to induce autoimmune responses against healthy tissues. In addition, immune cell populations used as therapeutic tool in autoimmunity play deleterious role in cancer and vice versa. Therefore, I think that knowledge gathered at the field of autoimmunity can be very useful at the cancer area.
The leading project of Cancer Immunology Group is focused on elaboration of antigen specific T cell based therapy of non-small cell lung cancer (NSCLC). My Group is focused on detailed characterization of phenotype and activation status of tumor infiltrating lymphocytes (Tc, Th, Treg, NK and B cells). We all together have been looking for, isolate and expand the immune cell subsets that will the most effective in anti-cancer response in the particular patient (personalized medicine). We have been also studding mechanisms that can potentiate anti-tumor responses of these cell soldiers.
I believe and try to prove with my studies that we have all the tools for the treatment of multiple diseases in our bodies. We have just to look and listen to intently to understand how we can use them in a proper manner.

Biography

VMD at University of Warmia and Mazury in Olsztyn (2005), PhD (2010) and habilitation (2013)- Medical University of Gdańsk (MUG), postdoc at University of Chicago (2010-2011; Kosciuszko Foundation grant), Prof. of medical sciences (2019)- MUG and University of Gdańsk; involved in realization of 13 international and national projects; author of 1 patent and 2 international patent applications (under evaluation); teacher of immunology (Faculty of Medicine, Faculty of Pharmacy with Subfaculty of Laboratory Medicine); laureate of several national and international awards, i.a.: 2 Scientific Awards of European Federation of Immunological Societies (EFIS; Vienna and Glasgow), Award of Polish- American Medical Society (PAMS; Chicago), Young Investigator Award- International Society for Pediatric and Adolescent Diabetes (ISPAD; Istanbul), 2 Scientific Awards of The International Pancreas and Islet Transplant Association (IPITA, Prague), Stipend of Minister of Science and Higher Education for Outstanding Young Scientists

Collaborations

Germans Trias i Pujol University Hospital and Research Institute, Universitat Autònoma Barcelona, Barcelona, Spain; University of Amsterdam, Academic Medical Center, Amsterdam, Netherlands; National University of Ireland, Galway, Ireland; Charité – Universitätsmedizin Berlin, Berlin, Germany; Medical University of Gdańsk, Gdańsk, Poland; Tor Vergata University of Rome, Rome, Italy. University of Chicago, Chicago, USA; Koc University, Istanbul, Turkey.

What is your professional background?

At the time I studied Applied Microbiology, my main areas of concern included bioremediation processes and antimicrobial food properties. I began to be interested in biopharmaceuticals which led me to work in Mabion S.A. as a bioprocess technician. There, I learned primarily the downstream processes of biosimilar drug production involving affinity and ion-exchange chromatography, ultrafiltration, formulation etc. Pursuing my growing interest in the development of immunotherapies and, most importantly, medical research, I applied for PhD program in medical sciences at Intercollegiate Faculty of Biotechnology UG & MUG in 2021.

What led you to work in the ICCVS?

The possibility of learning in international and interdisciplinary team with a focus on important field of cancer science.

What are you working on just now?

I focus on developing a three-dimensional method of non-small cell lung cancer spheroid culture to mimic clinical samples and using it in hypoxia-response proteomic and immunopeptidomic studies with LC-MS technology.

What is your professional background?

Dr inż. Monikaben Padariya, is a postdoc at ICCVS, Gdansk. She obtained her PhD (dr inż.) from Gdańsk University of Technology and Master in engineering (mgr inż.) from Wrocław University of Science and Technology. Poland. She received training from Indian Institute of Technology (IIT), New Delhi, India. Monika received pro-quality award and scholarship for the best PhD student from Gdańsk University of Technology for three consecutive years. In addition, her PhD was funded by Polish National Agency for Academic Exchange (NAWA). She is a author of 25 scientific publications, and in the year 2015 and 2017, she has been awarded “Young scientists with best creative work published” by Polish Academy of Sciences (PAN), Gdansk. Applying bioinformatics and computational structural biology methods (molecular modeling, molecular dynamics, protein-protein/RNA/DNA interactions) to understand different biological molecules in cell is her field of expertise. And also acquires interest in database development, data mining, and web designing. She has an emerging interests in immunopeptidomics research, her recent work involves the understanding of ERp57 and Tapasin from the peptide-loading complex (PLC).

What led you to work in the ICCVS?

ICCVS gives opportunity to collaborate with renowned scientist in the cancer immunology field, and here I can learn how to integrate different techniques to answer a biological question.

What are you working on just now?

At ICCVS my research activities are focused on understanding the peptides presented on the MHC I molecules, and their selectivity in recognition by the T-cell receptors. One of several question, that we are seeking the answer relates to the transporters involved in antigen presentation, TAP1 and TAP2. In addition, to study the immunopeptidome data and their transportation by TAP, we planned to investigate structural properties of the entire PLC (MHC I, β2m, Calreticulin, ERp57, Tapasin, TAP1, and TAP2) .

What is your professional background?

Aleksander Pałkowski obtained his master’s degree in Control Engineering and Robotics at the Gdansk University of Technology in 2012. Subsequently, he finished his PhD degree in the same field and university in 2018. He defended a thesis entitled “Automation of the rehabilitation process for children with cerebral palsy and osteogenesis imperfecta”. During his PhD studies his main research focus was development of machine learning and optimization methods for medical signals analysis. Between 2019 and 2020 he worked as an Assistant Professor at the Gdansk University of Technology. Since 2021 he works as a Postdoctoral Researcher at the International Centre for Cancer Vaccine Science. He collaborated on many occasions with medical centers on projects related to cardiography, myography, and human body surface area. His main fields of interest are artificial intelligence, data science, optimization, and medicine.

What led you to work in the ICCVS?

I was always striving to expand the scope of my knowledge and skills; and bioinformatics were always high on my interests list. ICCVS gave me the opportunity to work in that exciting new field with an international team of experts where I can put my skills to the test and discover a whole new world of science.

What are you working on just now?

Currently I am working on better understanding of the evolution of the immune system and its capabilities to distinguish self from non-self.

What is your professional background?

Ines is graduated DVM from University of Zagreb, Croatia. At the very end of her studies she realized that the knowledge she acquired, and her constant curiosity is leading her into direction of science. Soon after graduation she joined ICCVS (March 2020) as a PhD student. She is spending her free time mostly enjoying outdoor activities and is a proud owner of a dog named Kofi.

What led you to work in the ICCVS?

A vision of inter-disciplinary research approach finally gave us an opportunity to solve problems from many different points of view. ICCVS is not only having innovative approach to science but is also international center, giving you an opportunity to learn from experts from all around the world.

What are you working on just now?

Currently I am working on isolation and characterization of NK cells from patients with non-small cells lung cancer for potential cell-based immunotherapies.

What is your professional background?

I have graduated on Intercollegiate Faculty of Biotechnology, University of Gdansk in a field of protein biochemistry. Now I have started a postdoc position on ICCVS in a field of cancer proteomics & immunopeptidomics.  I have experience with operating a nanoLC/MS system and subsequent data analysis, I have also worked as analytical chemist in GLP-regulated environment. I believe that this knowledge, together with my recent experience with classical in vitro protein analysis will serve as a good starting point to my research in ICCVS.

What led you to work in the ICCVS?

I hope this place will be a good next step in my career, I would like to develop my skills further and apply them to an extremely interesting field of cancer proteomics and immunology.

What are you working on just now?

My current activities will concern proteomic and peptidomic analysis of isolated cellular subpopulations as well as general method development for MS-based proteomics/lipidomics. In the future I would like to investigate peptide processing in proteasomes in a more detailed way.

What is your professional background?

I graduated from University of Gdansk at the Department of Biology where I obtained a MSc degree. My scientific approach to research was formed by the idea of connecting different sources of data to obtain a larger perspective. That drove me to pursue a PhD study in the area of plant biology. I have experience in a range of tasks: research, education and many more.

What led you to work in the ICCVS?

ICCVS is a great international place that brings together a diverse team of open-minded scientists with a shared goal of advancing research in a biomedical field. I found it as a great opportunity to develop my knowledge and skills through the guidance and support of the experts. The mission of the ICCVS highly motivated me to broaden my scientific interests.

What are you working on just now?

I am a part of team focused on research in the mechanism of transcriptional memory.

What is your professional background?

I obtained my PhD from the International Institute of Molecular and Cell Biology in Warsaw, Poland. After that I trained as a postdoctoral fellow at the Instituto Gulbenkian de Ciencia in Lisbon, Portugal and University of Oxford, UK. I am now an independent research fellow with a joined appointment between the Massachusetts General Hospital, Harvard Medical School, USA and ICCVS.

What led you to work in the ICCVS?

I am attracted to the focused but ambitious goal of ICCVS on advancement of anti-cancer immunotherapies. I believe that discoveries in this line of research require an intense team effort. I am confident that with my expertise I will be able to collaborate with other scientists at ICCVS and together develop novel ways to harness the immune system to fight cancer.

What are you working on just now?

I am working on a recently discovered phenomenon of transcriptional memory (or innate immune memory) in human cells.

What is your professional background?

I graduated from the Intercollegiate Faculty of Biotechnology  in Gdańsk in  2009 and the same year I started my PhD on pharmacological activation of p53 homolog, TAp73 by small molecules. First post-doctoral research I performed in the INFECT-ERA project where I was investigating the influence of the host genetic background on HBV infection and therapy response. Currently, I am investigating the complex cancer-immune synapse and hope that seeing cancer as an infectious disease will allow us to target it accordingly.

What led you to work in the ICCVS?

A lot of luck, intuition and curiosity.

What are you working on just now?

Topic nr 1: Regulation of MHC class I expression in normal versus cancer cells.

Topic nr 2: Source of antigens for self-presentation in the thymus.

What is your professional background?

Biology and Chemistry have always been my favourite school subjects, which is why I decided to study Biotechnology at the Intercollegiate Faculty of Biotechnology, University of Gdańsk. During my degree I took part in several internships (including Summer Undergraduate Research Programme in Lausanne, Switzerland) and started to work in several research projects. In my Master Thesis I investigated breast cancer stemness markers; I graduated in 2013. I got very interested in differentiation therapy and decided to focus on it in my PhD. I moved to London to pursue my PhD on neuroblastoma as a Marie Curie Fellow in the Institute of Cancer Research. I studied drug combinations that could enhance neuroblastoma differentiation using various cell culture methods. During my PhD I participated in over 10 international conferences and meetings and took part in two internships (NCI NIH in Bethesda, USA and University of Salamanca, Spain); I graduated in 2018.

What led you to work in the ICCVS?

During my PhD I realized differentiation therapy can be used in only few types of tumours and targeted therapy very quickly leads to resistance. Therefore, I wanted to study immunotherapy and cancer vaccines, which are currently the most promising types of cancer treatment.

What are you working on just now?

My main project focuses on characterizing different populations of lymphocytes infiltrating non-small cell lung cancer tumours. I’m also studying how TLR stimulation enhances anti-tumour activity of immune cells. Additionally, in collaboration with other ICCVS researchers, I’m investigating anti-cancer properties of several natural compounds.

What is your professional background?

I have been in bio lab(s) basically as long as I live, as a child of two microbiologists. Having participated in wet lab research since at least very early high school I decided to branch out with my education to broaden horizons and cover a different field, obtaining my Bachelors of Engineering in optoelectronics – in analysis of Raman spectroscopy data on the Gdańsk University of Technology. Following that I obtained my MSc in yet a different domain – industrial pharmaceutics and cosmetics, a MSc curriculum in pharma/cosmetics R&D with a strong focus on the administrative and legal requirements co-led by Polpharma S.A. and Oceanic S.A. on the Medical University of Gdańsk – with my thesis being focused on UPLC-MS method development realized in the API R&D Department of Polpharma in Starogard Gdański. Over the course of my studies I remained active in the wet lab as well as dry lab, performing a range of biochemical, biophysical, phytopathogenic and molecular biology assays as well as acompanying data analysis and bioinformatic analysis in the domains of plant pathogens and cyanobacteria, with a growing focus on multi-omics, in particular metagenomics and inter-species interactions of microbes and their co-habitants or host organisms. In that time I co-authored 10 publications. Recently I had the great honour of joining the computational biology team at ICCVS as a Software Engineer, where I hope to facilitate the communication between wet lab and dry lab researchers, as well as bring in engineering best practices in software tools creation.

What led you to work in the ICCVS?

I wanted to join a multidisciplinary team with some focus on bioinformatics but still tied to real world data. My life goal exiting high school was to build machinery for the people, perhaps more focused on lab equipment, but over the course of my studies I realized that it’s easy to build, but it’s hard to build what people need, and thus it’s extremely important to know the field I want to create for and its needs, which also led to my choice of Masters degree. Software Engineering in biotech research is a natural continuation of that for me, both allowing me to bring my expertise, as well as giving me all so much to learn, and especially collaborate with many different people. It’s also in line with the engineering archetype, creating problems people didn’t even know they have, and sometimes even offering solutions.

What are you working on just now?

My current tasks are mostly focused around creating databases in the domain of immunopeptidomics and cancer patient treatment + follow up, as well as creating ways to visualise and interact with this data. Other than that I participate in defining the data models and help in the creation of AI models serving the grand goal of predicting patient treatment response within the KATY project. In particular I help building common understanding between Bio researchers and AI researchers.