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Laboratory of Bioinformatics and Protein Engineering

Laboratory of Bioinformatics and Protein Engineering

Leader
Janusz M. Bujnicki, PhD, Professor

Leader

We explore the universe of RNA, not just as a messenger of genetic blueprints but as a dynamic entity that shapes life at the molecular level. Our work treats RNA as a puzzle, where each piece is a clue to its myriad roles from catalysts to regulators within the cell. With advanced computational models and experimental techniques, we decode RNA's complex structures and interactions, especially with proteins and small molecules.

Research Summary 

Our work is focused on the development and applications of new methods for RNA structure determination and modeling RNA interactions, combining computational predictions with experimental analyses. This approach is vital for delving into RNA's role in biological processes, contributing significantly to the fields of molecular biology, bioinformatics, and structural biology. Our contributions include software tools like ModeRNA and SimRNA, which have become essential for researchers globally. We investigate the three-dimensional structures of RNA from viruses, bacteria, and humans, focusing on potential targets for small molecules. Our research is enriched by interdisciplinary collaborations with various research groups and with commercial partners in Poland and worldwide.

Scientific Impact 

- Tools for RNA modeling & small molecule interactions
- Determined structures of viral & bacterial RNAs (e.g., coronavirus 5' regions)
- Collaborated with Molecure to validate tools in drug discovery (inhibiting cancer protein translation)

Future Goals

We aim to deepen our understanding of RNA structure and function, particularly by studying molecules with therapeutic potential. Our advances in computational methods, integrated with experimental studies, are geared towards contributing to both fundamental research and future practical applications, with the ultimate goal of positively impacting scientific knowledge and human health.

Collaborations

- Cryo-EM & RNA structure: S. Glatt (Poland), Z. Su (China) 
- RNA dynamics & AFM: F. Moreno-Herrero (Spain) 
- RNA CD and FTIR: V. Arluison, F. Wien (France) 
- RNA-targeting drugs: Molecure (Poland)

Comment

“Our aim is to determine RNA structures and interactions, and design new molecules with functions with potential for applications in medicine and biotechnology”, says Prof. Janusz Bujnicki.

 

fot lab JB copy

Determination of RNA 3D structure and dynamics, using a combination of computational and experimental methods. Example for the 5′-proximal region in SARS-CoV-2 RNA.

 

Visit the laboratory website for more details: https://genesilico.pl/ 

About the lab

 bujnicki j

Janusz M. Bujnicki, PhD, Professor 

Correspondence address:
Laboratory of Bioinformatics and Protein Engineering
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
www: iimcb.genesilico.pl
tel: +48 (22) 597 0750; fax: +48 (22) 597 0715

DEGREES

2009 - Professor of Biological Sciences, nomination by the President of the Republic of Poland
2005 - DSc Habil in Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
2001- PhD in Biology, University of Warsaw, Faculty of Biology, Poland
1998 - MSc in Microbiology, University of Warsaw, Faculty of Biology, Poland

PROFESSIONAL EXPERIENCE

2002-present - Professor, Head of Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Poland (100% appointment)
2019-present - Scientific Advisor, Łukasiewicz Research Network - PORT Polish Center for Technology Development (25% appointment)
2006-2020 - Associate Professor (extraordinarius), Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
2010-2011 - Deputy Director, International Institute of Molecular and Cell Biology in Warsaw (1 year rolling position)
2008 - Visiting Professor, University of Tokyo, Japan(sabbatical)
2004-2006 - Assistant Professor, Adam Mickiewicz University, Poznań, Poland
2001 - Visiting Scientist, National Center for Biotechnology Information,National Institutes of Health, Bethesda, Maryland, USA
1999-2002 - Research Scientist, Bioinformatics Laboratory, International Institute of Molecular and Cell Biology in Warsaw, Poland
1998-2000 - Senior Research Assistant, Henry Ford Hospital, Detroit, Michigan, USA

SELECTED PROFESSIONAL AFFILIATIONS

2019-2022 - Member, Committee for Science Evaluation, Ministry of Science and Higher Education
2020 - Member, Advisory Group on Preventing, Counteracting and Combating COVID-19, Ministry of Science and Higher Education
2019-present - Member, University Council, University of Warsaw (Chairman, 2019-2020)
2018-present - Member, Academia Europaea
2018-present - Member, European Molecular Biology Organization
2017-present - Member, European Science Advisors Forum
2016-present - Corresponding Member, Polish Academy of Sciences
2016-2017 - Member, Council of the National Science Congress
2015-2020 - Member, Group of Chief Scientific Advisors, European Commission’s Scientific Advice Mechanism
2014-2018 - Member, Scientific Policy Committee, Polish Ministry of Science and Higher Education
2013-present - Executive Editor, Nucleic Acids Research
2013-2016 - Member, Scientific Committee of the Innovative Medicines Initiative
2013-2015 - Member, Science Europe: Life, Environmental and Geo Sciences (LEGS) Scientific Committee
2011-2016 - Member, Polish Young Academy, Polish Academy of Sciences
2007-present - Member, Polish Bioinformatics Society (founding member; Vice-President, 2007-2010; President, 2011-2013)
2007-present - Member, RNA Society
2001-present - Member, International Society for Computational Biology (Senior Member, 2015-)


SELECTED AWARDS AND FELLOWSHIPS

2019 - André Mischke Young Academy of Europe Prize for Science and Policy Honorary Award "For Merits for Inventiveness," Prime Minister at the request of the Polish Patent Office
2019 - Award for Organizational Achievements, Ministry of Science and Higher Education
2017 - Crystal Brussels Sprout Award
2015 - Jan Karol Parnas Award of the Polish Biochemical Society
2014 - National Science Centre Award for outstanding scientific achievements
2014 -Master Award, Foundation for Polish Science
2014 - Prime Minister’s Award for outstanding scientific achievements
2014 - Selected as one of “25 leaders for the next 25 years” by Teraz Polska magazine of the Polish Promotional Emblem Foundation
2014 - Knight's Cross of the Order of Polonia Restituta
2014 - Award in the Science category of the national plebiscite “Poles with Verve”
2013 - ERC Proof of Concept Grant
2012 - Award for Outstanding Research Achievements, Ministry of Science and Higher Education
2010 - ERC Starting Grant (2011-2015)
2009 - Scholarship for Outstanding Young Scientists, Minister of Science and Higher Education
2009 - Award for Research Achievements, Ministry of Science and Higher Education
2006 - Prime Minister Award for habilitation thesis
2006 - Young Researcher Award in Structural and Evolutionary Biology, Visegrad Group Academies of Sciences
2003, 2004 - START Scholarship for Young Scientists, Foundation for Polish Science
2002-2005 - EMBO/HHMI Young Investigator Award
2002 - Award for best Polish genetics-related publication in 2002, Polish Genetics Society
2001 - Award for best Polish publication on nucleic acid biochemistry in 2000, Polish Biochemical Society and Sigma-Aldrich

DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION

A. Żylicz-Stachula, A. Chmiel, I. Cymerman, A. Czerwoniec, M. Gajda, M. Pawłowski, J. Sasin-Kurowska, J. Kosiński, A. Obarska-Kosińska, S. Pawlak, E. Purta, K. Tkaczuk, Ł. Kościński, M.Rother, W. Potrzebowski, I. Korneta, T. Puton, J. Kasprzak, I. Tuszyńska, Ł. Kozłowski, M. Werner, A. Kamaszewska, A. Philips, K. Milanowska, M. Piętal, D. Matelska, K. Majorek, M. Domagalski, T. Osiński, M. Machnicka, M. Magnus, K. Szczepaniak, M. Zielińska, Astha, I. Foik, D. Toczydłowska-Socha.

Group members

 team2019

 

Lab Leader:

  • Janusz M. Bujnicki, PhD, Professor

Senior Researchers:

  • Elżbieta Purta, PhD

  • Filip Stefaniak, PhD

Postdoctoral Researchers:

  • Sunandan Mukherjee, PhD

  • Tales Rocha de Moura, PhD

  • Satyabrata Maiti, PhD

  • Gregory Nikolaev, PhD

  • Rui João Loureiro, PhD

  • Kuntal Mondal, PhD

Research Assistants:

  • Agata Bernat, MSc

  • Dominik Sordyl, MSc

Research Technicians:

  • Masoud Amiri Farsani, MSc

  • Seyed Naeim Moafinejad, MSc

PhD Students:

  • Nagendar Goud Badepally, MSc

Lab Technician:

  • Iwona Ptasiewicz (part-time)

Laboratory Support Specialist:

  • Katarzyna Grzelak, MSc

Laboratory of Neurodegeneration

Laboratory of Neurodegeneration

Leader
Jacek Kuźnicki, PhD, Professor

Leader

We study molecular processes, which degenerate neurons in Alzheimer’s (AD), Parkinson’s (PD) and Huntington’s (HD) diseases. We use cultured human and animal cells as well as fish and mouse models of these diseases. Recently we have shown that the disappearance of neurons in the PD zebrafish model can be stopped by inhibiting the influx of calcium ions to mitochondria. We plan to identify calcium sensitive proteins that take part in the development of this disease.

Research Summary

Parkinson disease (PD) is an incurable neurodegenerative disorder. Its pathological hallmarks include the aggregation of α-synuclein and loss of dopaminergic neurons. In various PD animal models and in cells from PD patients, perturbations of calcium homeostasis occur. Our major focus are on Ca2+ dependent mechanisms involved in the development of PD. Its three types can be distinguished: most prevalent sporadic with a late onset, familial that is caused by mutations of genes such as PINK1 or LRRK2, and environmentally-induced by drugs such as MPTP. Our published data show that degeneration of dopaminergic neurons in zebrafish PD models as a result of a pink1 mutation or MPTP toxicity is rescued by inactivation of the mitochondrial calcium uniporter (MCU). Others showed that MCU inhibition rescues neurons with mutation in LRRK2. If different factors that cause PD have a common denominator that is related to MCU activity, then what is it? Our hypothesis is that specific genes are turned on or off when MCU inactivation exhibits protection of dopaminergic neurons. The aim of our work is to identify those genes, proteins and cells in which they are expressed to understand how they provide neuronal protection.

Scientific Impact

- We expect to identify genes that are turned on or off when calcium ions cannot enter mitochondria via uniporter.
- We will identify cells in which proteins that are encoded by these genes operate.
- The identified genes and proteins might have potential diagnostic value for pre-symptomatic stages of PD and provide a basis for novel anti-PD treatments.   

Future Goals

After identifying gene(s) that are turned on or off when calcium ions cannot enter mitochondria via their uniporter and cells in which it takes place to preserve neuronal protection, the goal will be to confirm this mechanism in animal models such as zebrafish.

Comment

"In various animal models of Parkinson’s (PD), as well as of Alzheimer’s (AD) and Huntington’s (HD)  diseases and in cells from PD, AD and HD patients, perturbations of calcium homeostasis occur. Studying these processes may identify common pathological mechanism in neurodegenerative diseases", says Prof. Jacek Kuźnicki.


Fig JK Lab

Graphical abstract of project hypothesis to explain how inactivation of mitochondrial calcium uniporter protects dopaminergic neurons. Illustration by Dr. Ewelina Latoszek

About the lab

 jkuznicki

Jacek Kuźnicki, PhD, Professor 

Correspondence address:
Laboratory of Neurodegeneration
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

DEGREES

1993 - Professor, awarded by the President of the Republic of Poland
1987 - DSc. Habil., Nencki Institute of Experimental Biology PAS, Warsaw, Poland
1980 - PhD in biochemistry, Nencki Institute of Experimental Biology PAS, Warsaw, Poland
1976 - MSc in biochemistry, Faculty of Biology, University of Warsaw, Poland

PROFESSIONAL EXPERIENCE

2001-present - Professor, Head of Laboratory of Neurodegeneration, International Institute of Molecular and Cell Biology in Warsaw, Poland
2020-2022 - President of the National Science Centre Council, member 2018-2022
2001-2018 - Director, International Institute of Molecular and Cell Biology in Warsaw, Poland; Feb-Dec 2018 Acting Director, International Institute of Molecular and Cell Biology in Warsaw, Poland
2017-2018 - Deputy Chair of the Council of Provosts, 2nd Division: Biological and Agricultural Sciences, Polish Academy of Sciences
2000-2001 - Director, Centre of Excellence Phare Sci-Tech II, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1999-2001 - Acting Director, International Institute of Molecular and Cell Biology in Warsaw, Poland; Organizer and Director, Centenarian Program
1996-2002 - Head, Laboratory of Calcium Binding Proteins, professor 2002- 2014 Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1992-1995 - Visiting Professor, NIMH, Bethesda, MD, USA
1991-1992 - Deputy Scientific Director, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1986-1992 - Associate Professor and Head of Laboratory of Calcium Binding Proteins, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1984-1985 - Research Associate, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1981-1984 - Visiting Fellow, NIH, Bethesda, MD, USA
1980-1981 - Post-doctoral Fellow, Nencki Institute
1976-1980 - PhD Student, Nencki Institute of Experimental Biology PAN, Warsaw

PROFESSIONAL TRAINING

2018, July - Visiting Professor, Laboratory of H. Burgess, National Institute of Child Health and Human Development, Bethesda, MD, USA
2015, July - Visiting Professor, Laboratory of W. Harris, University of Cambridge, UK 
2014, July - Visiting Professor, Laboratory of B.E. Snaar-Jagalska, Leiden University, The Netherlands
1992-1995 - Visiting Professor, Laboratory of D. Jacobowitz, National Institute of Mental Health, Bethesda, MD, USA
1981-1984 - Visiting Fellow (postdoc), Laboratory of E.D. Korn, National Institute of Heart, Lung and Blood, Bethesda, MD, USA

MEMBERSHIP IN SCIENTIFIC SOCIETIES, ORGANIZATIONS, AND PANELS

2020-present - External expert in biotechnology, Łukasiewcz Research Network - PORT Polish Center for Technology Development
2020-present
- Ordinary Member, Polish Academy of Sciences
2016-2021 - Member, International Advisory Board, Małopolska Centre of Biotechnology, Jagiellonian University
2011-present - Member, International Expert Council of the Research and Education Center, State Key Laboratory of Molecular and Cellular Biology, Ukraine
2011-2014 - Member, Science Policy Committee, and Rotating President (Jul-Dec 2012), Ministry of Science and Higher Education
2008-2022 - Board Member, European Calcium Society, member since 1997
2008-2018 - Member, Board of Directors, and Rotating President (Jul-Dec 2016, Jul-Dec 2013, Jul-Dec 2010), Biocentrum-Ochota Consortium
2006-2011 - Member, Advisory Group, 7FP HEALTH, European Commission
2004-2019 - Corresponding Member, Polish Academy of Sciences
2004-present - Honorary Chair and co-founder, BioEducation Foundation
2002-present - Head of Program Board, Centre for Innovative Bioscience Education
1993-2014 - Member, Scientific Council, Nencki Institute of Experimental Biology, Polish Academy of Sciences
1996-1998 & 2000-2002 - Vice-President, Biotechnology Committee, Polish Academy of Sciences
1989 - 1991 - General Secretary, Polish Biochemical Society, member since 1977

HONORS, PRIZES AND AWARDS

2018 - Commemorative medal for the 100th Anniversary of the Nencki Institute for outstanding contribution to the development of this Institute, supporting its activities, shaping the image and building a mutual success
2013 - Crystal Brussels Prize for outstanding achievements in 7th Framework Programme of the European Union for Research and Development
2013 - Award from the 2nd Division of Biological and Agricultural Sciences, Polish Academy of Sciences for series of works on β-catenin
2011 - Konorski Award for the best Polish research work in neurobiology awarded by the Polish Neuroscience Society and Committee on Neurobiology of the PAS
2008 - Officer's Cross of the Order of Polonia Restituta awarded by the President of Poland
2004-2007 - Professorial Subsidy Program Award from Foundation for Polish Science
2003 - Prime Minister Award for the scientific achievements, Warsaw
2001 - Award from the Division of Biological Sciences of the PAS for the work on CaBP
1998 - Knight's Cross of the Order of Polonia Restituta awarded by the President of  Poland
1987 - Polish Anatomical Society Award for the article in “Advances in Cell Biology”
1986 - Skarzynski Award from the Polish Biochemical Society for the best review article in “Advances in Biochemistry”
1977 - Mozolowski Award, Polish Biochem. Society for outstanding Polish young biochemist
1977 - Parnas Award from Polish Biochem. Society for the best paper in biochemical research
1976 - MSc, Magna cum laude, University of Warsaw

DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION

A. Filipek, J. Kordowska, U. Wojda, J. Hetman, M. Palczewska, M. Nowotny, K. Billing-Marczak, Ł. Bojarski, W. Michowski, K. Misztal, M. Figiel, K. Honarnejad, A. Jaworska, K. Gazda, F. Maciąg, J. Jędrychowska, I. Wasilewska, RK. Gupta.

Group members

KuznickiLab

Lab Leader
Jacek Kuźnicki, PhD, Professor

Senior Researchers
Vladimir Korzh, PhD, DSc Habil

Postdoctoral Researchers
Weronika Skarżyńska, PhD
Narges Sotoudeh, PhD
Krystyna Żyżyńska-Galeńska, PhD

PhD Students
Razieh Amini, MSc
Sofiia Baranykova, MSc
Mrudula Dileep, MSc

Research Assistants
Aleksandra Moskal, MSc

Volunteers
Magdalena Czeredys, PhD, DSc Habil (from Mossakowski Medical Research Institute PAS)
Iga Wasilewska, PhD (from Mossakowski Medical Research Institute PAS)

Lab Technician
Monika Matuszczyk (part-time)

Laboratory Support Specialist
Dominika Dubicka-Boroch, MSc

Laboratory of Structural Biology

Laboratory of Structural Biology

Leader
Matthias Bochtler, PhD, Professor

Leader

We study epigenetics, i.e. nucleic acid and histone modifications that control cell fate change and maintenance. Our methods range from various flavors of high-throughput sequencing to classical biochemistry and structural biology. We also rely increasingly on “big data”. Our work has implications in oncology, particularly for hematologic malignancies that have a strong epigenetic component.

Research Summary

Our work is focused on chromatin modifications, and on their role in maintaining and changing cell fate. Most of our projects revolve around DNA modifications, particularly DNA maintenance methylation at the replisome, and its reversal by active and active- passive DNA demethylation. We study the links between "epigenetic" and "repair" enzymes, as well as the recruitment and adaptation of DNA repair processes to epigenetic reprogramming. We are also interested in the contributions of histone modifications to cell fate maintenance and change. Specifically, we are investigating COMPASS- like complexes - the mediators of positive genetic memory. 

Scientific Impact

- We have contributed to a better understanding of TET dioxygenases that are the drivers of active and active-passive DNA demethylation.
- We have helped to elucidate the feedback loop that implements positive genetic memory.
- We have discovered and classified a number of reader domains for nucleic acid modifications.
- We have elucidated a chemically novel nucleic acid modification pathway.

Future Goals

In the future, we plan to extend our chromatin studies, taking into account preventive epigenome maintenance by nucleotide pool control. We want to focus on "epigenome repair" mechanisms that counteract gradual epigenome degradation with age and in disease. Furthermore, we want to better understand how the loss of enzymes with antagonistic roles (DNMT3A, TET2) can have similar, malignancy-promoting effects in cancers with a strong epigenetic component. 
 

Collaborations

Our collaborators come from both academia (e.g. G. Xu, J. Wong, T. Jurkowski, T. Hore, C. Winata, W. Bickmore, A. Wlodawer) and the biotech industry (S. Xu, P. Weigele). Thanks to this strong circle of partners, we have extended our research methods spectrum and we can now ask questions at very different levels, ranging from atomistic to animal studies.
 

Comment

"With minor exceptions, all cells in our body carry the same genetic information and yet they are very different. Much of the difference is epigenetically encoded in the form of DNA and histone modifications. We combine genetics, biochemistry and structural biology to study the maintenance and remodeling of the epigenetic layer of our genomes", says Prof. Matthias Bochtler.

 

Yearbook

The lab works on epigenetic marks on DNA and histones and their effects on cell fate maintenance and change. The picture is an “artistic” representation of the theme of the lab, prepared using generative artificial intelligence.

About the lab

 bochtler m

Matthias Bochtler, PhD, Professor 

Correspondence address:
Laboratory of Structural Biology
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Office: This email address is being protected from spambots. You need JavaScript enabled to view it.
tel: +48 (22) 597 0732; fax: +48 (22) 597 0715

DEGREES

2009 - Professor of Biological Sciences, nomination by the President of the Republic of Poland

2006 - DSc Habil, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

1999 - PhD in Biochemistry, Technical University of Munich, Germany

1995 - MSc in Experimental Physics, Munich University, Germany

PROFESSIONAL EMPLOYMENT

2011-present - Professor, Head of Laboratory of Structural in Biology, International Institute of Molecular and Cell Biology in Warsaw, Poland, and Laboratory of Genome Engineering, Institute of Biochemistry and Biophysics, Polish Academy of Sciences,Warsaw, Poland

2007-2011 - Part-time Director of Structural Biology, Cardiff University, United Kingdom

2001-2010 - Head, Joint MPG-PAS Junior Research Group, International Institute of Molecular and Cell Biology in Warsaw, Poland

2000 - Patent training, Weickmann & Weickmann

1999-2000 - Postdoctoral Fellow, Max Planck Institute of Biochemistry, Martinsried, Germany

RESEARCH TRAINING

1996-1999 - Research Assistant, Max Planck Institute of Biochemistry, Martinsried, Germany

1995-1996 - Internship, Medical Microbiology, University of Regensburg,  Germany

1992-1993 - Guest Student, Cambridge University, United Kingdom

1990-1992 - Studies in Physics, Munich University, Germany

HONORS, PRIZES AND AWARDS

2023 - Minister of Education and Science Award for significant achievements in scientific activities 

2023 - Włodzimierz Krzyżosiak Distinction awarded by the Polish Academy of Sciences

2018 - TEAM Foundation for Polish Science

2018 - International Academic Partnerships Programme, Polish National Agency for Academic Exchange

2018 - DAINA, National Science Centre

2015 - HARMONIA, National Science Centre

2012 - MAESTRO, National Science Centre

2011 - TEAM, Foundation for Polish Science Professor Stefan Pieńkowski Award

2004 - EMBO/HHMI Young Investigator Award

2000 - Crystal Award, Germany

1998 - Crystal Award Germany

1990 – 1992 - Scholarship from Deutsche Studienstiftung and Bavarian State

DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION

R. Filipek, M. Firczuk, M. Lipka, R. Szczepanowski, M. Kaus-Drobek, M. Sokołowska, G. Chojnowski, H. Korza, M. Wojciechowski, W. Siwek, P. Haniewicz, A.A. Kazrani, K. Mierzejewska.

Group members

BochtlerLab copy

Lab Leader:

  • Matthias Bochtler, PhD, Professor

Senior Researcher:

  • Honorata Czapińska, PhD, DSc Habil

PhD Students:

  • Anna Fedenko, Msc

  • Terry Karimi, MSc

  • Natalia Leśniowska, MSc

Lab Technician:

  • Julia Kędzierska, MSc

Laboratory Support Specialist:

  • Katarzyna J. Gromkowska, PhD

Contact:

This email address is being protected from spambots. You need JavaScript enabled to view it.

Former group members


Wet-lab postdoctoral position - coming soon. (Updated: March 13, 2026)

Please inquire at This email address is being protected from spambots. You need JavaScript enabled to view it. 


Current job vacancies at IIMCB are listed here: CLICK TO VISIT.

If you do not see a suitable position but are interested in working with us, please feel free to contact us at This email address is being protected from spambots. You need JavaScript enabled to view it..

 

Laboratory of Cell Biology

Laboratory of Cell Biology

Leader
Marta Miączyńska,  PhD, Professor

Leader

We study how cells take up and transport various substances within their interior, focusing on how these logistical rules are altered in cancer cells to support their uncontrolled growth. By understanding the differences in cellular functioning between normal and cancerous cells, we aim to guide the development of therapies that selectively target and eliminate cancer cells. We have already identified one such vulnerability, an “Achilles’ heel,” in certain cancer cells and continue our search for additional therapeutic targets.

Research Summary

We are fascinated by two intracellular processes, endocytosis and receptor signaling, and how they are interlinked. We seek to understand how endosomal compartments contribute to the trafficking and signaling of receptors for growth factors and cytokines in normal and cancer cells.
We investigate the roles of endosomal sorting complexes required for transport (ESCRT) in cell physiology and oncogenesis. Our research has revealed that the dysfunction of endosomes caused by the absence of proper ESCRT function induces an intracellular sterile inflammatory reaction.
We also found out that the ESCRT-I complex is indispensable for the biogenesis and proper functioning of lysosomes, as well as energy metabolism in the cell.
The synthetic lethality we identified between two paralogous ATPases of the ESCRT machinery, VPS4A and VPS4B, revealed a novel pair of druggable targets for personalized oncology.
In another line of research, we focus on the receptor tyrosine kinase AXL, which is overexpressed in late-stage cancers. By identifying the interactome of AXL, we revealed that its activation induces several actin-dependent processes, including macropinocytosis.

Scientific Impact

Our studies provide proof of concept that intracellular trafficking and the molecules regulating it can represent a viable therapeutic target in personalized oncology. For example, the synthetic lethality between VPS4A and VPS4B ATPases provides a rationale for developing VPS4 inhibitors for the precision treatment of VPS4B-deficient cancers. Our ongoing studies of AXL-dependent macropinocytosis aim to uncover ways of blocking this process in metastatic and drug-resistant cancers with AXL overexpression.

Future Goals

We wish to understand how altered expression or mutations in the ESCRT components, observed in cancer or some rare diseases, modify cell physiology. In parallel, we aim to elucidate the mechanisms and effector proteins by which the activated AXL receptor drives macropinocytosis in cancer cells.

Collaborations

We collaborate with partners from the IIMCB and external institutions within the HERO consortium project, which aims to develop the next generation of mRNA-based cancer immunotherapies.

Comment

“We study alterations that occur in signaling and trafficking processes in cancer cells because such changes may represent vulnerabilities of cancer cells to specific therapies”, says Prof. Marta Miączyńska


Figure Miaczynska Lab

Human lung adenocarcinoma cells cultured in vitro, with nuclei stained in blue, actin in green, and endosomes in magenta. Image by Patrycja Daszczuk.

About the lab

mmiaczynska

Marta Miączyńska,  PhD, Professor 

Correspondence address:
Laboratory of Cell Biology
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it. 

DEGREES

2013 - Professor of Biological Sciences, nomination by the President of the Republic of Poland
2008 - DSc Habil in Cell Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1997 - PhD in Genetics, University of Vienna, Austria
1993 - MSc in Molecular Biology, Jagiellonian University, Cracow, Poland
1991 - BSc in Biological Sciences, University of Wolverhampton, UK

PROFESSIONAL EMPLOYMENT

2018-present - Director, International Institute of Molecular and Cell Biology in Warsaw, Poland
2014-2015 - Deputy Director for Science, International Institute of Molecular and Cell Biology in Warsaw, Poland
2013-2014 - Deputy Director, International Institute of Molecular and Cell Biology in Warsaw, Poland
2005-present - Professor, Head of Laboratory of Cell Biology, International Institute of Molecular and Cell Biology in Warsaw, Poland

RESEARCH TRAINING

2001-2005 - Senior Postdoctoral Fellow, Max Planck Institute for Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany
1997-2000 - Postdoctoral training, European Molecular Biology Laboratory, Heidelberg, Germany
1993-1996 - PhD studies, Institute of Microbiology and Genetics, University of Vienna, Austria
1990-1991 - Exchange Student, University of Wolverhampton, UK

HONORS, PRIZES AND AWARDS

2024 - Vice Chair of the EMBO Council
2024 - Co-Chair of EU-LIFE Alliance
2021
- Prime Minister's Award for outstanding scientific achievements
2021 - Member, EMBO Council
2020 - Corresponding Member, Polish Academy of Sciences
2019 - Member, Academia Europaea
2017 - Member, European Molecular Biology Organization
2016-2018 - Member, Council of the National Science Centre
2016 - TEAM, Foundation for Polish Science
2012 - MAESTRO, National Science Centre
2011 - Polish-Swiss Research Programme grant
2007 - Habilitation Fellowship of L’Oréal Poland for Women in Science
2006-2012 - International Senior Research Fellowship, Wellcome Trust
2006-2010 - International Research Scholar, Howard Hughes Medical Institute, USA
2006-2010 - Partner Group grant, Max Planck Society, Germany
2001-2004 - Postdoctoral Fellowship, Max Planck Society, Germany
1999-2000 - Long-Term Postdoctoral Fellowship, Human Frontier Science Program Organization
1998-1999 - Erwin Schrödinger Postdoctoral Fellowship, Austrian Science Fund
1993-1996 - Bertha von Suttner PhD Scholarship, Austrian Ministry of Science
1990-1991 - Studentship, European Community Tempus Scheme

DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION

M. Olchowik, A. Urbańska, A. Hupałowska, Ł. Sadowski, A. Mamińska, A. Toruń, K. Jastrzębski, M. Maksymowicz, K. Wojciechowska, A. Poświata, M. Wróbel.

Group members

DSC 7105

Lab Leader:
Marta Miączyńska, PhD, Professor

Senior Researcher:
Ewelina Szymańska, PhD
Jarosław Cendrowski, PhD

Postdoctoral Researchers:
Patrycja Daszczuk, PhD
Ranjana Maurya, PhD

PhD Students:
Marta Chwałek, MSc
Malwina Grębowicz-Maciukiewicz, MSc
Bartosz Jary, MSc
Zuzanna Miciak, MSc

Research Assistant:
Agnieszka Świstek, MSc

Master's Students:
Anna Witowska (BSc)

Lab Technician:
Monika Matuszczyk (part-time)

Laboratory Support Specialist:
Renata Wyszyńska, MSc

Laboratory of Molecular and Cellular Neurobiology

Laboratory of Molecular and Cellular Neurobiology

Leader
Jacek Jaworski, PhD, Professor

Leader

Our goal is to understand how nerve cells develop their characteristic shape, critical for the functioning of the brain. Our "gateway" to the world of neurons is the protein mTOR. By utilizing molecular and cellular biology tools, we have come to understand what functions of mTOR are essential for neurons. We want to use this knowledge to diagnose and treat tuberous sclerosis, a disease caused by excessive mTOR activity.

Research Summary 

Since the inception of our laboratory, our goal has been to understand how neurons develop their characteristic shape, which is crucial for brain function. We have sought to identify such mechanisms by studying the mammalian/mechanistic target of rapamycin (mTOR) protein, which is involved in neuronal development and various neuropathologies known as mTORopathies. mTOR is a serine-threonine kinase involved in almost all aspects of mammalian cell function. It forms two protein complexes that were originally thought to regulate translation (mTORC1) or affect the actin cytoskeleton (mTORC2). My postdoctoral work showed that regulating mTOR-dependent translation contributes to dendritogenesis. However, our subsequent work has shown that mTOR functions during neuronal development go beyond the canonical control of translation, e.g., cytoskeleton regulation, intracellular transport or transcription. Our recent studies focus mainly on mTOR functions in neuronal nuclei. An essential part of our work has been to apply our findings in cellular models to clinically relevant models and material. We focused on tuberous sclerosis (TSC), a disease caused by hyperactive mTOR. As a result, we have identified new potential drug targets (TrkB, GCLC) and predictive biomarkers for epilepsy in TSC. In parallel, in recent years we have investigated the mechanisms underlying the stability of neuronal morphology associated with the development of depression.

Scientific Impact 

- Discovery of numerous regulators of neuronal cell morphology, including several mTOR substrates.
- Identification of GCLC and TrkB as new potential therapeutic targets in tuberous sclerosis. 
- Development of predictive biomarkers for drug-resistant epilepsy in children with tuberous sclerosis.

Future Goals

Our primary goal for the coming years is to find out what functions mTOR fulfills in the nucleus of neurons and how they affect their proper development and function. Our current research suggests that destabilizing nuclear mTOR functions, such as controlling transcription factors, can lead to epilepsy. Therefore, we want to test this hypothesis thoroughly.

Collaborations

Our key collaborators include Prof. Kathrin Thedieck, Prof. Sergiusz Jóźwiak, Prof. Katarzyna Kotulska, Prof. David Kwiatkowski, Prof. Eleonora Aronica, Prof. Leszek Kaczmarek and Prof. Ewelina Knapska. We are working to understand how molecular biology translates into clinical features of tuberous sclerosis or depression and how this knowledge can be used to help patients.

Comment

"Our research focuses on the molecular basis of the development and stability of neuronal networks. In particular, we focus on the molecular functions of the mTOR protein, which will enable better diagnosis and potential therapy of mTORopathies, diseases caused by mTOR hyperactivity", says Prof. Jacek Jaworski.

 

brg1inh w PTZ max intensity

Activity of neurons in zebrafish brain measured using genetic calcium ion sensors after inhibition of chromatin modifying enzymes. Brighter color represents higher activity. Illustration by Roberto Pagano

 

About the lab

 jjaworski

Jacek Jaworski, PhD, Professor

Correspondence address:
Laboratory of Molecular and Cellular Neurobiology
International Institute of Molecular and Cell Biology
4 Ks. Trojdena Street, 02-109 Warsaw, Poland
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
tel: +48 (22) 597 0755; fax: +48 (22) 597 0715

DEGREES

2014 - Professor of Biological Sciences, nomination by the President of the Republic of Poland
2010 - DSc Habil in Molecular Biology, Warsaw University, Poland
2001 - PhD in Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1996 - MSc in Biology, Department of Genetics, Warsaw University, Poland

PROFESSIONAL EXPERIENCE

2018-present - Deputy Director for Science, International Institute of Molecular and Cell Biology in Warsaw, Poland
2010 - 2013 - Deputy Director, International Institute of Molecular and Cell Biology in Warsaw, Poland
2005-present - Professor, Head of Laboratory of Molecular and Cellular Neurobiology, International Institute of Molecular and Cell Biology in Warsaw, Poland

RESEARCH TRAINING

2016 - Research visit (3 weeks) with Prof. William Harris, Cambridge University, Cambridge, UK
2011 - Research visit (2 weeks) with Dr. Carlo Sala, CNR Institute of Neuroscience and Instituto Neurologico Carlo Besta, Milan, Italy
2006 - Research visit (1 month) with Dr. C.C. Hoogenraad, Erasmus Medical Center, Rotterdam, Holland
2002-2005 - Postdoctoral Associate with Prof. Morgan Sheng, Picower Center for Learning and Memory, Massachusetts Institute of Technology and Howard Hughes Medical Institute, Cambridge, MA, USA
2000 - Research training with Dr. J. Guzowski, ARL Division of Neural Systems, Memory and Aging, University of Arizona, Tucson, USA
1997-2001 - Research training (7 months) with Prof. J. Mallet, Laboratoire de Genetique Moleculaire de la Neurotransmission et des Processus Neurodegeneratifs (LGN), UMR 9923 CNRS, Paris, France
1996-2002 - PhD student (until 2001) and Postdoctoral Associate (until May 2002) with Prof. L. Kaczmarek, Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
1995-1996 - Master’s degree, Prof. P. Węgleński, Department of Genetics, Warsaw University, Poland

FELLOWSHIPS AND AWARDS

2018 - TEAM, Foundation for Polish Science
2014 - Master Award, Foundation for Polish Science
2011 - Prime Minister Award for habilitation thesis
2009 - 2nd Division (Biological Sciences) of Polish Academy of Sciences Award for series of publications on MMP9 (together with teams of Prof. Kaczmarek and Dr. Wilczynski)
2005 - Konorski Award for best publication of 2004 in the field of neuroscience (Kowalczyk et al., JCB, 2004, 167:209-213), Polish Neuroscience Society and Polish Academy of Sciences
2002 - Prime Minister Award for PhD thesis
2001 - Foundation for Polish Science National Scholarship for Young Investigators (1 year scholarship)
2000 - EMBO Short Term Fellowship
1999 - Polish Network for Cell and Molecular Biology UNESCO/PAN Scholarship
1997 - Bourse de Stage du Gouvernement Francaise (French Government Scholarship)

MEMBERSHIP IN SCIENTIFIC SOCIETIES, ORGANIZATIONS, AND PANELS

2019 - Member, Scientific Advisory Board of the Institute of Pharmacology, Polish Academy of Sciences
2017 - Vice President, Polish Neuroscience Society (term 2017-2019)
2015 - Corresponding Member, Warsaw Scientific Society
2015 - Member, Scientific Advisory Board of the Nencki Institute of Experimental Biology, Polish Academy of Sciences
2011 - Member, Neurobiology Committee, Polish Academy of Sciences (terms 2011-2014; 2015-2018; 2019-2020)

DOCTORATES DEFENDED UNDER LAB LEADER’S SUPERVISION

Ł. Świech, A. Malik, M. Perycz, M. Urbańska, A. Skałecka, J. Lipka, A. Urbańska, M. Firkowska, K. Kisielewska, A. Kościelny.

 

Group members

 

team2019

 

Lab Leader:

  •  Jacek Jaworski, PhD, Professor

Senior Researchers:

  • Ewa Liszewska, PhD

  • Małgorzata Urbańska, PhD

Postdoctoral Researchers:

  • Roberto Pagano, PhD

Research Specialist:

  • Katarzyna Machnicka, MSc

  • Katarzyna Durczyńska, MSc

  • Karolina Protokowicz, MSc

PhD Students:

  • Olga Doszyń, MSc

  • Shiwani Kumari, MSc

  • Katarzyna Orzoł, MSc

Lab Technician:

  • Alina Zielińska, BSc 

Laboratory Support Specialist:

  • Angelika Jocek, MSc

Volunteers:

  • Julia Łukasiewicz

  • Gabriela Chmurzyńska

  • Wiktoria Kowalska

  • Antonina Ożyńska

 
  1. Laboratory of Protein Structure
  2. Laboratory of Zebrafish Developmental Genomics
  3. Laboratory of Iron Homeostasis
  4. Laboratory of Protein Metabolism

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