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).

Biography

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.

Biography

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.

Georges Bedran is a bioinformatician recently graduated from the university of Rouen, France. His previous work was focused on developing a bioinformatic workflow to asses biological mutations considering the flow of information from the genome to the proteome. He recently joined the ICCVS as a PhD student to work on developing computational strategies for neo-epitope discovery.

Biography

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.

Biography

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.

Biography

Dr. Daskalogianni did her PhD at Paris Diderot University in France. The work was focused on understanding the molecular mechanisms whereby the Epstein-Barr Virus (EBV)-encoded EBNA1 evades the immune system. Since 2010 she works as a lab and project manager in Robin Fahraeus lab at INSERM, France and she is in charge of a project aiming to develop candidate drugs displaying activity against EBV. In 2018 Chrysoula joined ICCVS, where her main task is to supervise PhD students.

What led you to work in the ICCVS?

New exciting field, great projects, international environment and very nice motivated people!

What are you working on just now?

We have recently shown in our lab that the production of PTPs (Pioneer Translation Products) derived from a nuclear non-canonical translation event is independently regulated from the synthesis of full-length proteins. We are now trying to identify the translation complex that is responsible for non-canonical translation of PTPs. In parallel we are studying these alternative sources of antigenic peptides for MHC class I, by working on a mouse model (Hbb mouse) in which an antigenic peptide is presented from an intron in the β-globin gene.

Finally, we are interested in developing new therapies against EBV related cancers.

Research in a Nutshell

Viral evasion of the immune system is crucial for oncogenic viruses to survive in the host cell environment. By understanding the molecular mechanisms whereby oncogenic viruses suppress the production of antigenic peptide substrates for the major histocompatibility (MHC) class I pathway we hope to discover new targets for immune-based therapies against virus-carrying cancers as well as to discover the cell biological pathways that governs the production and presentation of peptides for the MHC class I pathway. This approach has led us to the characterization of cellular factors that control antigen presentation from the Epstein-Barr virus-encoded EBNA1 and to an alternative mRNA translation event for the production of peptide substrates for the MHC class I pathway. Outside the antigen presentation and EBNA1 fields, we work on the role of the p53 mRNA in regulating the activity of the encoded p53 tumour suppressor protein under different cellular conditions.

Biography

M.D. and PhD at the Karolinska Institute 1993 followed by pos doc at the Dundee University until 2004. From there on director of research at the French INSERM in Paris. Guest professor at Umea University, Sweden.

Collaborations

University of Umea, Sweden; University of San Luis Potosi, Mexico; RECAMO, Brno, Czech Republic; University of Montevideo, Uruguay; Mount Sinai, NY, USA.

Scientific Themes

mRNA translation control & MHC class I antigen presentation.

Biography

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.

Biography

Maria was awarded a BSc Hons in Biochemistry and a MSc in Molecular Biotechnology at the University of Barcelona. She then pursued her studies in cancer biology and obtained a PhD in Molecular Medicine at the University of Edinburgh. There, she developed a strong interest in cancer biology and cell signalling. Her main project studied an interferon induced protein that is implicated in cancer progression and also identified as a restriction factor; it is fascinating how the immune system is capable to eliminate virus as well as malignant cells. Afterwards, she joined the ICCVS.

What led you to work in the ICCVS?

The ICCVS offers a vibrant opportunity to collaborate with a multidisciplinary and international group of researchers that have different backgrounds and interests.

What are you working on just now?

She is working as a postdoc at the Intercollegiate Faculty of Biotechnology, University of Gdańsk. Her work is focused on understanding the interferon pathway, in particular the IRDS response, a small group of genes consistently expressed in patience with resistance to chemotherapy. Currently she is investigating how this signal may also be implicated in viral suppression and how it may mediate the inhibition of SARS-CoV-2.

Biography

Prof Goodlett has spent his career using mass spectrometry to solve biomedical problems via novel technology and software developments. He has been active in a variety of fields including medicine, oceanography, pharmacy, microbiology, proteomics (including clinical applications), lipidomics, and often through the lens of protein & glycolipid structure-function relationships producing > 250 publications. He is a Professor at the University of Maryland (2013-present) and previously at the University of Washington (2004-2012) as well as first Director of Proteomics at the Institute for Systems Biology (2000-2003). From 2012-2016 he was a Finland Distinguished Professor; https://www.youtube.com/watch?v=jfOOMNJivvY. He is an Editor at Rapid Communications in Mass Spectrometry who recently published an interview with him https://onlinelibrary.wiley.com/doi/abs/10.1002/rcm.8187. Since 2007 he has been a co-organizer of www.msbm.org, a mass spectrometry course. He has also founded two companies: Deurion (Seattle WA) who make ion sources and Pataigin (Baltimore MD) who are developing a microbial diagnostic platform.

What led you to work in the ICCVS?

One of the PIs, Prof Hupp who I met in Scotland during the RASOR (UK funding: BBC5115721 BBSRC/EPSRC IRColl) program proteomic technology development, invited me to help with writing the original ICCVS proposal. After it was funded it made sense to us to continue my association.

What are you working on just now?

I’m helping one of the Group Leaders, Dr Dapic, generally as a mentor and specifically the ICCVS to sort through the process of identifying MHC peptides via mass spectrometry. In my early career, and notably before search engines and useful databases circa 1996, I worked at Bristol-Myers Squibb sequencing MHC peptides.

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

Biography

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.

Biography

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.

Biography

In 2010 I enrolled in the Intercollegiate Faculty of Biotechnology in Gdańsk, Poland, on the course led by University of Gdańsk and Medical University in Gdańsk, which provided me with interdisciplinary biomedical education. After attaining a BSc, I continued my studies and in 2015 I earned an MSc degree with honours in biotechnology, based on my research – concerning deleterious health effects of endocrine disrupting chemicals present in common plastic products – which I conducted on UNIVPM, Italy.

During my studies I performed a development project for a leading medical diagnostics company and gathered some additional experience in topics of biological weapons countermeasure, non-coding RNAs and reducing chemotherapy toxicity. Following graduation, I spent two productive years in a leading Polish biopharmaceutical R&D company, participating in a successful development of a therapeutic antibody product, working in an international, GMP/GLP/GDP-focused environment, learning about various aspects of industrial antibody production and commercial operations.

What led you to work in the ICCVS?

Passionate about biotherapeutics, I joined newly-forming ICCVS in 2017, looking to develop innovative cancer treatment modalities and to further my skills in biological drug discovery and development.

What are you working on just now?

Currently I work on adapting proprietary murine antibodies for use in different species and characterizing the properties of novel biotherapeutic leads.

Biography

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 (http://www.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.

Biography

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.

Biography

Małgorzata was originally educated in veterinary medicine from University of Life Sciences in Wrocław and Copenhagen University and subsequently practiced in veterinary clinics in Poland, Germany, Holland and Malta. This experience led here to develop an interest in immunology research as a more innovative approach to impact on animal health. She worked towards her PhD degree at the National University of Singapore (NUS) at two labs: in the department of biological sciences, drug discovery lab of Kim Chu-YoungYong Loo Lin School of Medicine and in the department of microbiology with immunology programme at Paul Macary’s (PAM) lab. In PAM lab she worked on an anti-dengue antibody (14c10), which was found to have remarkable neutralizing activity of Dengue Virus 1 (DV1) in vitro and in vivo and is currently under clinical development by GSK. She has defined the role of Fc region of 14c10 and investigated the impact of 14c10-based antibody therapy upon the ability of the treated hosts to generate their own protective immune response where the virus has been rapidly neutralized and cleared from circulation. As a result, she obtained PhD degree in the area of antibody engineering to equip herself with the education to develop research projects.

What led you to work in the ICCVS?

The University of Gdansk is committed to the development of an oncology veterinary institute (OVI) that can form a world-lead in veterinary therapeutics and in developing dog-patient diagnosed with cancer as a superior pre-clinical model for human cancer. This project combines both my veterianary and scientific interests. We are developing parallel dog to human pre-clinical models for cancer therapy, where the dog as a patient itself is treated with recombinant therapeutics engineered for the use in dogs. The double benefit is that except for the development of veterinary therapeutics, which can be used in veterinary practice, we also develop a novel animal model for human cancer research and therefore a new source of pre-clinical data for cancer treatment in human patients.

What are you working on just now?

Monoclonal antibody therapy has become one of alternatives to existing therapies concentrating mostly on symptoms. Administration of specific monoclonal antibodies aims to stimulate the hosts’ immune system to restore the physiological balance in multiple medical conditions including different types of cancer, autoimmune disorders, and infectious diseases. The major limitation of the development of monoclonal therapies is the paucity of clinically relevant models for validation. I aim on development of an antibody biologics platform by focusing on clinical questions and in parallel, development of a model, which can fasten the process of translating our research data into clinics. Right now, we are developing a number of antibodies designed and engineered for a patient –dog diagnosed with lymphoma or melanoma, as well as a tool for brain imaging.

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.

Biography

Marcos carried out a degree in Biochemistry at the University of Castilla-La Mancha (Spain) and decided to specialize in the bioinformatics area by performing the Master studies in Copenhagen (Denmark). He started to work on benchmarking where he designed sequencing tools in collaboration with the Danish Cancer Society (DCRC). Currently he is performing his PhD studies as part of the Bioinformatics team within the ICCVS.

What led you to work in the ICCVS?

After finishing my master studies I was interested in specializing in bioinformatics on the cancer research field. I remember I saw a PhD offer when the ICCVS was recently created and therefore the opportunity of becoming part of this new center. The idea of collaborating with another PhD students entering the same year, and the occasion to work on an international environment brought me to start my PhD studies on this center.

What are you working on just now?

Currently I am working on the integrated proteogenomics field, where I am creating tools for the analysis of deep sequencing data in various types of cancer tissues. This tools will report valuable information of the cancer cells like the number and type of mutations, the state and abundance of transcript isoform and the identification of novel proteoforms.

Biography

I am a first-year PhD student at ICCVS. I was born in Čakovec, Croatia, 8th of December, 1993. I obtained my Master’s degree in Molecular Biotechnology at Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia. On my last year of study, I became the part of the joint master studies of University of Zagreb and University of Orléans for obtaining Double Master’s degree in Molecular Biotechnology and Bioindustrial Techniques. As a part of this program, I was doing my Master 2 Thesis in Chartres, in LBLGC (Laboratoire de Biologie des Ligneux et des Grandes Culture, Université d’Orléans, France). I was active member of research team, working on the project Cells4Life – Lignan Formation in Engineered Cells, with my mentor Dr. Christophe Hano. Except science, my main interest is sport, especially table tennis, which I am actively playing more than 15 years.

What led you to work in the ICCVS?

What attracted me the most, is the idea about ICCVS and research programme that is aimed at supporting the development of new cancer vaccines therapies, very innovative approach, ambitious goals and possibility to work in the different and international environment.

What are you working on just now?

Currently, I am working on project Nrf2 pathway in tumor formation and progression in non-small cell lung cancer. Nrf2 is transcription factor that plays a central role in inducible expression of cytoprotective genes in response to oxidative and electrophilic stresses so research is mainly based on possible role of Nrf2 in immune surveillance and its effect on MHC class I in normal and cancer cells.

Biography

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) .

Biography

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.

Biography

Ines is recently graduated (September 2019) 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.

Biography

Katarzyna Pietrzak 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. Needless to say, it all would not be possible without the guidance of her supervisors.

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.

Biography

Magda Pilch is a Ph.D. student in the Prof. Ted Hupp research group. She holds a master’s degree in Biochemistry from the Jagiellonian University in Poland. Her previous research was centered around the mass spectrometric analysis of brain proteome and characterization of molecular mechanisms underlying the therapeutic action of opioids. In summer 2016, Magda took part in Erasmus project and had an internship at the Max Planck Institute of Biochemistry in Munich, where she worked on the improvement of proteome analysis methods.

In October 2017, she joined the ICCVS research programme. In the ICCVS Magda is involved in research of the signaling pathways involved in the interaction between cancer and the immune system.

What led you to work in the ICCVS?

The ICCVS provides an opportunity to work in the international and multidisciplinary research team. The multidisciplinary environment at the center and vast numbers of collaborations with other research groups encourage novel ways of thinking of human cancer immunology and are exciting opportunity to meet experts in many fields including biochemistry, proteomics, bioinformatics, and structural biology.

What are you working on just now?

Magda is involved in research of the interaction between cancer cells and the host’s immune system with the main focus on MHC class I antigen presentation and its role in cancer escape from immune surveillance.

Biography

I have recently 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.

Biography

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.

Biography

I am a 2nd year PhD student at ICCVS and a member of Prof. Robin Fahraeus’s Neoantigen Science Research team. Before starting at ICCVS I graduated from Biotechnology at Poznan University of Life Sciences as well as Drug Discovery and Development at the University of Aberdeen. During the time of my studies, I participated in internships held by Poznan Medical University as well as the Polish Academy of Sciences. In addition to the academic background I had opportunities to gain some industrial experience. As a Master student at Novabiotics Ltd. in Aberdeen UK, I explored topics related to innate immunity and host-pathogen interactions. Later, I was employed as a Research Scientist at Scotia Biologics Ltd, where as part of the team I was focusing on the development of vaccine candidates for the treatment of a wide range of oncology indications.
Gradually, my research interests strengthened within the immune-oncology field and therefore I wanted to continue exploring the subjects within the ICCVS.

What are you working on just now?

The main focus of my current research is to find out alternative sources of antigenic peptides for MHC class I pathway and their impact on the development of immune tolerance. MHC class I presentation pathway plays a crucial role in the immune system and allows to distinguish self from non-self. According to the canonical model of antigen processing and presentation, peptides displayed on the MHC class I molecules origin from the proteasomal degradation products of full-length proteins. Discoveries of alternative sources of antigenic peptides (e.g. DRIPs and PTPs) challenged that notion and shifted the focus of the search for new sources to ribosomal scanning during the pioneer round of translation. Currently, there is much evidence proving the importance of pre-mRNA and mRNA processing in providing antigenic peptides for MHC class I surveillance. My project is focusing on the role of alternative sources of antigenic peptides in the development of central and peripheral tolerance in healthy individuals and in cancer.

Biography

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.

Biography

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.

Biography

Ken studied his BSc in biochemistry at Kenyatta University, where he developed a great passion for science following a few internship opportunities that he received. In 2018, he graduated with a Master’s degree in Clinical Chemistry at the University of Nairobi. Ken spent part of 2017 and 2018 in Toronto (Canada) applying bioinformatics and statistical tools to study how inherited structural variants within DNA-repair genes shape the somatic spectra of localized prostate cancers. Owing to Ken’s immense enthusiasm for science and cancer research, for that matter, he decided to enroll for a PhD to broaden the understanding of this disease

What led you to work in the ICCVS?

In my previous lab, I worked harmoniously with diverse teams and individuals from varied professional backgrounds and nationalities. So, I was looking for something similar, which I found at ICCVS.

What are you working on just now?

Presently, I am working with neuroblastoma cell lines to explore how low oxygen tension shapes the proteome of these cells. Also, I am currently engaged in the development of methods that can aid in the processing of small amounts of samples for proteomic analysis.