Supervisors from Nencki Institute of Experimental Biology

 a.pekowska@nencki.edu.pl

@ https://pekowskalab.github.io

Aleksandra Pękowska is a head of the Dioscuri Centre for Chromatin Biology and Epigenomics at the Nencki Institute of Experimental Biology in Warsaw. Dioscuri is a program initiated by the Max Planck Society, managed jointly with the National Science Centre (Poland) and mutually funded by the Polish Ministry of Science and Higher Education and the German Federal Ministry of Education and Research.

In 2006, Dr. Pękowska graduated from the University of Lodz with a MS in biology (spec. biophysics). For her PhD in immunology and epigenomics, she joined the lab of Dr. Pierre Ferrier at the CIML in Marseilles (Marie Curie RTN). In 2011, Dr. Pękowska obtained a prestigious EIPOD fellowship (EMBL/Marie Curie actions) and joined groups of Dr. Wolfgang Huber, Dr. Lars Steinmetz, and Dr. Paul Bertone at EMBL/EBI for an interdisciplinary postdoc. In 2016, she joined the team of Dr. Rafael Casellas at NIAMS (NIH) in Bethesda. In 2019, Dr. Pękowska moved back to Poland to establish her group.

Dr. Pękowska’s lab combines cutting-edge genomics technologies (Hi-C, ChIP-seq, RNA-seq), CRISPR-Cas9 – based (epi)genome engineering, with computational tools to provide new insights into the genetic bases of brain evolution (Dioscuri, and EMBO Installation Grants; 1.5M, 130k EUR respectively). Using these techniques, Dr. Pękowska’s group is also investigating the mechanisms orchestrating genome topology during the development of the central nervous system (OPUS17 grant 450k euros).

Dr. Pękowska has established several international collaborations: with Prof. Martin Vingron, (director of MPI, Berlin), Prof.  Jeroen Krijgsveld, (DKFZ, Heidelberg), Dr. Rafael Casellas (NIAMS/NIH Bethesda, also as part of the NIH Regulome Project), Dr. Erez Aiden (Baylor, Huston), Dr. Salvatore Spicuglia (TAGC, Marseilles); as well as national collaborations (Dr. Bartosz Wilczynski, University of Warsaw, Fac. of Mathematics, Informatics and Mechanics, Prof. Jakub Wlodarczyk, Nencki Institute).

 

Research interests:

Chromatin biology, evolutionary genomics, genome topology

 

Major publications:

Pękowska A., Klaus B, Xiang W., Severino J., Daigle N., Klein F.A., Oleś M., Casellas R., Ellenberg J., Steinmetz L.M.S., Bertone P., Huber W. (2018 ). “Gain of CTCF-anchored chromatin loops marks the exit from naive pluripotency”, Cell Systems, Nov. 28; 7(5):482-495.

Vian L., Pękowska A., Rao SSR., Kieffer-Kwon K-R, Jung S, Baranello L., Huang SC., El Khattabi L., Dose M., Pruett N., Sanborn AL., Canela A., Maman Y., Oksanen A., Resch W., Li X., Lee B., Kovalchuk AL., Tang Z., Nelson S., Di Pierro M., Cheng RR., Machol I., St Hilaire B.G., Durand N.C., Shamim M.S., Stamenova EK., Onuchic JN., Ruan Y., Nussenzweig A., Levens D., Aiden EL., Casellas R. (2018 ).  “The energetics and physiological impact of cohesin extrusion”, Cell, May 17;173(5):1165-1178.e20.

Schwarzer W., Abdennur N., Goloborodko A., Pękowska A., Fudenberg G., Loe-Mie Y., Fonseca N.A., Huber W, Haering C., Mirny L., Spitz F. (2017). “Two independent modes of chromosome organization are revealed by cohesion removal”, Nature, Nov 2;551(7678):51-56.

 a.filipek@nencki.edu.pl

@ en.nencki.gov.pl/laboratory-of-calcium-binding-proteins

After receiving her PhD degree from the Nencki Institute of Experimental Biology, Anna Filipek spent a year as a post-doc at the Oregon Health Science University in the United States. Since 2009 she has been a professor and laboratory head at the Nencki Institute. Her group’s recent research is focused on: 1) the role of heat shock protein 90 (Hsp90) and its co-chaperones (Sgt1, ChP-1, CacyBP/SIP, p23, Aha-1) in abnormal protein folding/aggregation associated with neurodegenerative diseases, 2) the effect of ribosome biogenesis inhibition on the process of oligodendrocyte differentiation and myelination, 3) the role of calcium binding proteins of the S100 family in cytoskeleton organization and 4) transcriptional and epigenetic regulation of genes encoding S100 and other proteins involved in epidermal differentiation. Her lab has expertise in various biological and biochemical methods such as culturing primary cells and cell lines, establishment of stable cell lines with overexpression or silencing of selected proteins, immunoprecipitation, SDS-PAGE, 2D electrophoresis, Western blotting, affinity chromatography, chemical crosslinking, ELISA, plasmid construction, recombinant protein purification, immunocyto/-histochemical and immunofluorescence staining, confocal and electron microscopy, and real time-quantitative PCR (RT-qPCR).

 

Research interests:

Cell/molecular biology, biochemistry, cell proteostasis, neurodegeneration.

 

Major publications:

Bohush A, Niewiadomska G, Weis S, Filipek A. (2019). “HSP90 and Its Novel Co-Chaperones, SGT1 and CHP-1, in Brain of Patients with Parkinson's Disease and Dementia with Lewy Bodies”, J Parkinsons Dis., 9, 97-107.

Rosińska S, Filipek A. (2018). “Interaction of CacyBP/SIP with NPM1 and its influence on NPM1 localization and function in oxidative stress”, J Cell Physiol. , 233, 8826-8838.

Topolska-Woś A, Shell S, Kilańczyk E, Szczepanowski R, Chazin W, Filipek A. (2015). “Dimerization and phosphatase activity of CacyBP/SIP: the influence of oxidative stress”, FASEB J. , 29, 1711-1724.

Wasik U, Schneider G, Mietelska-Porowska A, Mazurkiewicz M, Fabczak H, Weis S, Zabke C, Harrington C, Filipek F, Niewiadomska G. (2013). “CacyBP/SIP in Alzheimer disease pathology: neuronal localization and possible function”, Neurobiol Aging, 34, 1380e1388.

Kilańczyk E, Graczyk A, Ostrowska H, Kasacka I, Leśniak W, Filipek A. (2012). “S100A6 is transcriptionally regulated by β-catenin and interacts with a novel target, lamin A/C, in colorectal cancer cells”, Cell Calcium, 51, 470-477.

 a.szewczyk@nencki.edu.pl

@ http://en.nencki.edu.pl/laboratory-of-intracellular-ion-channels

Adam Szewczyk has been a group leader (Laboratory of Intracellular Ion Channels) at the Nencki Institute since 1999. He earned his PhD from the Nencki Institute, then he spent postdoctoral fellowship at the University of Bern (Angelo Azzi’s lab); University of Nice (Michel lazdunski’s Lab) and Johns Hopkins University (Eduardo Marban’s Lab).

 

Research interests:

Bioenergetics, mitochondria, membranes, pharmacology, mitochondrial potassium channels

 

Major publications:

Laskowski M., Augustynek B., Bednarczyk P., Żochowska M., Kalisz J., O'Rourke B., Szewczyk A., Kulawiak B. (2019). “Single-Channel Properties of the ROMK-Pore-Forming Subunit of the Mitochondrial ATP-Sensitive Potassium Channel”, Int J Mol Sci. 20, pii: E5323.

Kampa R.P., Kicinska A., Jarmuszkiewicz W., Pasikowska-Piwko M., Dolegowska B., Debowska R., Szewczyk A., Bednarczyk P. (2019). “Naringenin as an opener of mitochondrial potassium channels in dermal fibroblasts”, Exp Dermatol. 28, 543-550.

Walewska A., Kulawiak B., Szewczyk A., Koprowski P. (2018). “Mechanosensitivity of mitochondrial large-conductance calcium-activated potassium channels”, Biochim Biophys Acta Bioenerg. 1859, 797-805.

Bednarczyk P., Kicinska A., Laskowski M., Kulawiak B., Kampa R., Walewska A., Krajewska M., Jarmuszkiewicz W., Szewczyk A. (2018). “Evidence for a mitochondrial ATP-regulated potassium channel in human dermal fibroblasts,”, Biochim Biophys Acta Bioenerg. 1859, 309-318.

Frankenreiter S., Bednarczyk P., Kniess A., Bork N.I., Straubinger J., Koprowski P., Wrzosek A., Mohr E., Logan A., Murphy M.P., Gawaz M., Krieg T., Szewczyk A., Nikolaev V.O., Ruth P., Lukowski R. (2017). “cGMP-Elevating Compounds and Ischemic Conditioning Provide Cardioprotection Against Ischemia and Reperfusion Injury via Cardiomyocyte-Specific BK Channels”, Circulation. 136, 2337-2355.

 d.wloga@nencki.edu.pl

@ http://en.nencki.gov.pl/laboratory-of-cytoskeleton-and-cilia-biology

Dorota Wloga received her MSc and PhD in biology from the University of Warsaw. After a 7-year postdoctoral fellowship in Dr. Jacek Gaertig’s Laboratory at the University of Georgia, she came back to Poland where she joined the Laboratory of Cell Movement Physiology at the Nencki Institute. There, supported by a Marie Curie International Reintegration Grant (2011-2015) and EMBO Installation Grant (2012-2016), she started to investigate ciliary proteins. Since 2015 Dorota Wloga has led the Laboratory of Cytoskeleton and Cilia Biology. Her laboratory is interested in the identification and functional analyses of novel, as-yet uncharacterized, evolutionarily conserved ciliary proteins, and in discovering their role in the motile cilia assembly and beating generation and regulation. One of the main goals is to identify proteins or small complexes that regulate and/or connect main ciliary complexes, and thus to find the “missing links” in the chain of signal transduction in cilia, from the central apparatus to dynein arms.

 

Research interests:

Cilia beating regulation, microtubules, cytoskeleton

 

Major publications:

Joachimiak E., Waclawek E., Osinka A., Niziolek M., Fabczak H, Gaertig J., Wloga D. (2020). “LisH domain-containing N-terminal fragment is important for localization, dimerization and stability of Katnal2 in Tetrahymena”, Cells. 25;9(2):292.

Urbanska P., Joachimiak E., Bazan R., Fu G., Poprzeczko M., Fabczak H., Nicastro D., Wloga D. (2018). “Ciliary proteins Fap43 and Fap44 interact with each other and are essential for proper cilia and flagella beating”, Cell Mol Life Sci. 75(24):4479-4493.

Joachimiak E., Jerka-Dziadosz M., Krzemień-Ojak Ł., Wacławek E., Jedynak K., Urbanska P., Brutkowski W., Sas-Nowosielska H., Fabczak H., Gaertig J., Wloga D. (2018). “Multiple phosphorylation sites on g-tubulin are essential and contribute to the biogenesis of basal bodies in Tetrahymena”, J Cellular Physiology 233(11):8648-8665.

Wloga D., Joachimiak E., Louka P.,  Gaertig J. (2017). “Post-translational Modifications of Tubulin and Cilia”, Cold Spring Harbor Perspectives in Biology. 1,9(6).

 e.knapska@nencki.edu.pl

@ https://knapskalab.eu/index.php/en/

Ewelina Knapska is an associate professor at the Nencki Institute of Experimental Biology, Polish Academy of Sciences in Warsaw, where she also obtained her PhD degree in 2006. After 2 years of postdoctoral training at the University of Michigan, Ann Arbor, she returned to the Nencki Institute, where she is now the head of the Laboratory of Emotions Neurobiology. Ewelina Knapska’s research interests include neural mechanisms of socially transferred emotions and impaired social behaviors. She addresses the question of which neurons in the brain are involved in processing of emotions, how they are connected, and how they form  functional networks. In particular, her research focuses on the differences in processing of positive and negative emotions stemming from interactions with others. She also investigates neuronal plasticity within the amygdala – a key brain region related to processing of emotions – with the ultimate goal of applying knowledge gained by studying the malfunctioning of the neurons in rodent models to therapies targeting autism spectrum disorders.

 

Research interests:

Social behavior, social learning, neuronal circuits controlling social interactions, amygdala.

 

Major publications:

Olsson A., Knapska E., Lindström B. (2020). “The neural and computational systems of social learning”, Nat. Rev. Neurosci. 21(4): 197-212.

Meyza K.Z., Bartal I.B., Monfils M.H., Panksepp J.B., Knapska E. (2017). “The roots of empathy: Through the lens of rodent models”, Neurosci. Biobehav. Rev. 76(Pt B): 216-234.

Puscian A., Leski S., Kasprowicz G., Winiarski M., Borowska J., Nikolaev T., Boguszewski P.M., Lipp H.P., Knapska E. (2016). “Eco-HAB as a fully automated and ecologically relevant assessment of social impairments in mouse models of autism”, Elife. 5:e19532.

Knapska E., Lioudyno V., Kiryk A., Mikosz M., Gorkiewicz T., Michaluk P., Gawlak M., Chaturvedi M., Mochol G., Balcerzyk M., Wojcik D.K., Wilczynski G.M., Kaczmarek L. (2013). “Reward learning requires activity of matrix metalloproteinase-9 in the central amygdala”,  J Neurosci. 33(36): 14591-14600.

Knapska E., Macias M., Mikosz M., Nowak A., Owczarek D., Wawrzyniak M., Pieprzyk M., Cymerman I.A., Werka T., Sheng M., Maren S., Jaworski J., Kaczmarek L. (2012). “Functional anatomy of neural circuits regulating fear and extinction”,  Proc Natl Acad Sci US A. 109(42): 17093-17098.

 g.sumara@nencki.edu.pl

@ http://en.nencki.gov.pl/grzegorz-sumara-lab

Grzegorz Sumara has headed the Dioscuri Center for Metabolic Diseases at the Nencki Institute of Experimental Biology PAS since 2020. He started his research carrier with undergraduate student internships at the Institute of Molecular Pathology (IMP), Vienna, Austria, and at the University Hospital of Zürich, Switzerland. Grzegorz received his PhD from the University of Zurich and the ETH Zurich. Afterwards he spent 4 years as postdoctoral HFSP fellow at Columbia University in New York and half a year at the IGBMC in Strasbourg. Prior to coming to the Nencki Institute, Grzegorz was a junior group leader at the Rudolf Virchow Centre in Würzburg, Germany. He received the prestigious Emmy Noether grant from the German Research Foundation for his work on studying hormonally-induced signalling cascades in adipocytes and hepatocytes as well as an ERC Starting Grant, under which he established Protein kinase D (PKD) family members as a crucial regulators of energy metabolism. All of these achievements have allowed Grzegorz to build the scientific program for a Dioscuri Centre of Scientific Excellence in Warsaw, where his research group focuses on unrevealing the cross-talk of different signalling molecules in regulation of adipocytes function during metabolic diseases such as obesity or cancer-associated cachexia.

 

Research interests:

Cancer-associated cachexia; obesity; signaling cascades in health and disease; organ cross-talk; lipolysis.

 

Major publications:

El-Merahbi R., Viera J.T., Valdes A.L., Kolczynska K., Reuter S., Löffler M.C., Erk M., Ade C.P., Karwen T., Mayer A.E., Eilers M., Sumara G. (2020). “The adrenergic-induced ERK3 pathway drives lipolysis and suppresses energy dissipation”, Genes Dev., Apr 1;34(7-8):495-510.

Mayer A.E., Löffler M.C., Loza Valdés A.E., Schmitz W., El-Merahbi R., Viera J.T., Erk M., Zhang T., Braun U., Heikenwalder M., Leitges M., Schulze A., Sumara G. (2019).The kinase PKD3 provides negative feedback on cholesterol and triglyceride synthesis by suppressing insulin signalling”, Sci Signal., Aug 6;12(593):eaav9150.

Löffler M.C., Mayer A.E., Trujillo Viera J., Loza Valdes A., El-Merahbi R., Ade C.P., Karwen T., Schmitz W., Slotta A., Erk M., Janaki-Raman S., Matesanz N., Torres J., Marcos M., Sabio G., Eilers M., Schulze A., Sumara G. (2018). “Protein kinase D1 deletion in adipocytes enhances energy dissipation and protects against adiposity”,  EMBO J.,  Nov 15;37(22):e99182.

Sumara G., Sumara O., Kim J., Karsenty G. (2012). “Gut-derived serotonin is a multifunctional determinant to fasting adaptation”, Cell Metab., Nov 7;16(5):588-600.

Sumara G., Formentini I., Collins S., Sumara I., Windak R., Bodenmiller B., Ramracheya R., Caille D., Jiang H., Platt K.A., Meda P., Aebersold R., Rorsman P., Ricci R. (2009). “Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis”, Cell, Jan 23;136(2):235-48.

 m.wieckowski@nencki.edu.pl

@ https://wieckowski-mitolab.nencki.edu.pl

Mariusz Wieckowski is a professor at the Nencki Institute, where he completed his PhD in 1999, focusing on the role of mitochondrial megachannel in the uncoupling of oxidative phosphorylation. In 2002 he joined Prof. R. Rizzuto’s laboratory at the University of Ferrara, where as a post-doc he began studies on close interaction between endoplasmic reticulum with mitochondria. Since 2007 he lead his own team continuing work on the molecular composition of mitochondrial megachannel and the physiology of Mitochondria-Associated Membranes (MAM) and Plasma Membrane Associated Membranes (PAM). His recent research is focused on different aspects of intracellular oxidative stress (e.g. in the context of mitochondrial disorders) and resolving the issue of how mitochondrial dysfunction affects mitochondrial and cellular function. Moreover, he investigates the relations between mitochondrial energetic and oxidative stress in tumors as well as pharmacological toxicity to mitochondria. More recently, under the scope of Horizon 2020 projects, he is also investigating hepatic redox alterations and the specific end-points for mitochondrial dysfunction, which drive the progression of in Non-Alcoholic Fatty Liver Disease (NAFLD). Simce January 2020 he heads the Laboratory of Mitochondrial Biology and Metabolism at the Nencki Institute of Experimental Biology.

 

Research interests:

Mitochondrial dysfunction, oxidative stress, nonalcoholic fatty liver disease, mitochondrial permeability transition pore, cancer.

 

Major publications:

Rimessi A., Pozzato C., Carparelli L., Rossi A., Ranucci S., De Fino I., Cigana C., Talarico A., Wieckowski M.R., Ribeiro C.M.P., Trapella C., Rossi G., Cabrini G., Bragonzi A., Pinton P. (2020). “Pharmacological modulation of mitochondrial calcium uniporter controls lung inflammation in cystic fibrosis”, Science Advances 6(19): eaax9093.

Simoes I.C.M., Morciano G., Lebiedzinska-Arciszewska M., Aguiari G., Pinton P., Potes Y., Wieckowski M.R. (2020). “The mystery of mitochondria-ER contact sites in physiology and pathology: A cancer perspective”, Biochim. Biophys. Acta Mol. Basis Dis. 1866(10): 165834.

Bonora M, Wieckowski MR, Sinclair DA, Kroemer G, Pinton P, Galluzzi L. (2019). “Targeting mitochondria for cardiovascular disorders: therapeutic potential and obstacles”, Nat. Rev. Cardiol. 16(1): 33-55.

Bonora M., Morganti C., Morciano G., Pedriali G., Lebiedzinska-Arciszewska M., Aquila G., Giorgi C., Rizzo P., Campo G., Ferrari R., Kroemer G., Wieckowski M.R., Galluzzi L., Pinton P. (2017). “Mitochondrial permeability transition involves dissociation of F1FO ATP synthase dimers and C-ring conformation”, EMBO Rep. 18(7): 1077-1089.

Giorgi C., Ito K., Lin H.K., Santangelo C., Wieckowski M.R., Lebiedzinska M., Bononi A., Bonora M., Duszynski J., Bernardi R., Rizzuto R., Tacchetti C., Pinton P., Pandolfi P.P. (2010). “PML regulates apoptosis at endoplasmic reticulum by modulating calcium release”, Science 330(6008):1247-1251.

 p.bragoszewski@nencki.edu.pl

@ http://en.nencki.edu.pl/laboratory-of-protein-homeostasis

After succeeding in a Group Leader competition, Piotr Brągoszewski joined the Nencki Institute of Experimental Biology to establish the Laboratory of Protein Homeostasis. Before coming to the Nencki Institute, he was a senior researcher and project leader at the Centre of New Technologies of the University of Warsaw. His post-doctoral experience also includes fellowship and project leader positions at the Laboratory of Mitochondrial Biogenesis headed by Prof. Agnieszka Chacińska at the International Institute of Molecular and Cell Biology in Warsaw.

Since receiving his PhD in 2008 from the Medical Centre of Postgraduate Education in Warsaw, he has developed scientific interests and expertise in protein transportation, folding, quality control, and in mitochondrial biology. He receives funding from the Foundation for Polish Science and the National Science Centre to pursue research projects focusing on the cellular mechanisms that maintain protein homeostasis. His group combines hypothesis based and high throughput screening approaches using molecular and cellular biology, and biochemistry techniques. The dynamic team aims to provide an excellent environment for scientific discoveries and professional development.

 

Research interests:

Protein homeostasis, ubiquitin-proteasome system, protein transport, protein degradation, mitochondria.

 

Major publications:

Kowalski L., Bragoszewski P., Khmelinskii A., Glow E., Knop M., Chacinska A. (2018). “Determinants of the cytosolic turnover of mitochondrial intermembrane space proteins”, BMC Biol. 16(1): p. 66;

Bragoszewski P., Turek M., Chacinska A. (2017). “Control of mitochondrial biogenesis and function by the ubiquitin-proteasome system”,  Open Biol. 7(4).

Bragoszewski P., Wasilewski M., Sakowska P., Gornicka A., Bottinger L., Qiu J., Wiedemann N., Chacinska A. (2015). “Retro-translocation of mitochondrial intermembrane space proteins”, Proc Natl Acad Sci USA. 112(25): p. 7713-8.

Wrobel L., Topf U., Bragoszewski P., Wiese S., Sztolsztener M.E., Oeljeklaus S., Varabyova A., Lirski M., Chroscicki P., Mroczek S., Januszewicz E., Dziembowski A., Koblowska M., Warscheid B., Chacinska A. (2015). “Mistargeted mitochondrial proteins activate a proteostatic response in the cytosol”, Nature. 524(7566): p. 485-8

Bragoszewski P., Gornicka A., Sztolsztener M.E., Chacinska A. (2013). “The ubiquitin-proteasome system regulates mitochondrial intermembrane space proteins”, Mol Cell Biol 33(11):2136-2148.

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