Zbigniew Korwek, Ph.D.

Department of Biosystems and Soft Matter (ZBiMM)
Division of Modelling in Biology and Medicine (PMBM)
position: assistant professor
telephone: (+48) 22 826 12 81 ext.: 326
room: 221
e-mail: zkorwek
personal site: http://pmbm.ippt.pan.pl/web/Zbigniew_Korwek

Doctoral thesis
2013-09-28Mechanizm śmierci i starzenia ludzkich limfocytów T – rola ścieżki sygnalizacyjnej odpowiedzi na uszkodzenia DNA (DDR)  (IBD PAN)
supervisor -- Prof. Ewa Sikora, Ph.D., Dr. Habil., IBD PAN
1322
 
Recent publications
1.Korwek Z., Tudelska K., Nałęcz-Jawecki P., Czerkies M., Prus W., Markiewicz J., Kochańczyk M., Lipniacki T., Importins promote high-frequency NF-κB oscillations increasing information channel capacity, Biology Direct, ISSN: 1745-6150, DOI: 10.1186/s13062-016-0164-z, Vol.11, No.61, pp.1-21, 2016
Abstract:

BACKGROUND:
Importins and exportins influence gene expression by enabling nucleocytoplasmic shuttling of transcription factors. A key transcription factor of innate immunity, NF-κB, is sequestered in the cytoplasm by its inhibitor, IκBα, which masks nuclear localization sequence of NF-κB. In response to TNFα or LPS, IκBα is degraded, which allows importins to bind NF-κB and shepherd it across nuclear pores. NF-κB nuclear activity is terminated when newly synthesized IκBα enters the nucleus, binds NF-κB and exportin which directs the complex to the cytoplasm. Although importins/exportins are known to regulate spatiotemporal kinetics of NF-κB and other transcription factors governing innate immunity, the mechanistic details of these interactions have not been elucidated and mathematically modelled.
RESULTS:
Based on our quantitative experimental data, we pursue NF-κB system modelling by explicitly including NF-κB-importin and IκBα-exportin binding to show that the competition between importins and IκBα enables NF-κB nuclear translocation despite high levels of IκBα. These interactions reduce the effective relaxation time and allow the NF-κB regulatory pathway to respond to recurrent TNFα pulses of 45-min period, which is about twice shorter than the characteristic period of NF-κB oscillations. By stochastic simulations of model dynamics we demonstrate that randomly appearing, short TNFα pulses can be converted to essentially digital pulses of NF-κB activity, provided that intervals between input pulses are not shorter than 1 h.
CONCLUSIONS:
By including interactions involving importin-α and exportin we bring the modelling of spatiotemporal kinetics of transcription factors to a more mechanistic level. Basing on the analysis of the pursued model we estimated the information transmission rate of the NF-κB pathway as 1 bit per hour.

Keywords:

Karyopherins, Nucleocytoplasmic transport, Negative feedback, Channel information capacity, Mathematical modelling

Affiliations:
Korwek Z.-IPPT PAN
Tudelska K.-other affiliation
Nałęcz-Jawecki P.-University of Warsaw (PL)
Czerkies M.-IPPT PAN
Prus W.-IPPT PAN
Markiewicz J.-IPPT PAN
Kochańczyk M.-IPPT PAN
Lipniacki T.-IPPT PAN
2.Kijewska M., Kocyk M., Kloss M., Stępniak K., Korwek Z., Polakowska R., Dąbrowski M., Gieryng A., Wojtas B., Ciechomska I.A., Kamińska B., The embryonic type of SPP1 transcriptional regulation is re-activated in glioblastoma, Oncotarget, ISSN: 1949-2553, DOI: 10.18632/oncotarget.14092, pp.1-16, 2016
Abstract:

Osteopontin (SPP1, a secreted phosphoprotein 1) is primarily involved in immune responses, tissue remodelling and biomineralization. However, it is also overexpressed in many cancers and regulates tumour progression by increasing migration, invasion and cancer stem cell self-renewal. Mechanisms of SPP1 overexpression in gliomas are poorly understood. We demonstrate overexpression of two out of five SPP1 isoforms in glioblastoma (GBM) and differential isoform expression in glioma cell lines. Up-regulated SPP1 expression is associated with binding of the GLI1 transcription factor to the promoter and OCT4 (octamer-binding transcription factor 4) to the first SPP1 intron of the SPP1 gene in human glioma cells but not in non-transformed astrocytes. GLI1 knockdown reduced SPP1 mRNA and protein levels in glioma cells. GLI1 and OCT4 are known regulators of stem cell pluripotency. GBMs contain rare cells that express stem cell markers and display ability to self-renew. We reveal that SPP1 is overexpressed in glioma initiating cells defined by high rhodamine 123 efflux, sphere forming capacity and stemness marker expression. Forced differentiation of human glioma spheres reduced SPP1 expression. Knockdown of SPP1, GLI1 or CD44 with siRNAs diminished sphere formation. C6 glioma cells stably depleted of Spp1 displayed reduced sphere forming capacity and downregulated stemness marker expression. Overexpression of the wild type Spp1, but not Spp1 lacking a Cd44 binding domain, rescued cell ability to form spheres. Our findings show re-activation of the embryonic-type transcriptional regulation of SPP1 in malignant gliomas and point to the importance of SPP1-CD44 interactions in self-renewal and pluripotency glioma initiating cells.

Keywords:

osteopontin, glioma initiating cells, transcription factors, stemness factors, self-renewal

Affiliations:
Kijewska M.-other affiliation
Kocyk M.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Kamińska B.-other affiliation
Kloss M.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Stępniak K.-other affiliation
Korwek Z.-other affiliation
Polakowska R.-other affiliation
Dąbrowski M.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Gieryng A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Wojtas B.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Ciechomska I.A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
3.Alster O., Bielak-Żmijewska A., Mosieniak G., Moreno-Villaneuva M., Dudka-Ruszkowska W., Wojtala A., Kusio-Kobiałka M., Korwek Z., Burkle A., Piwocka K., Siwicki J.K., Sikora E., The Role of Nibrin in Doxorubicin-Induced Apoptosis and Cell Senescence in Nijmegen Breakage Syndrome Patients Lymphocytes, PLOS ONE, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0104964, Vol.9, No.8, pp.e104964-1-13, 2014
Abstract:

Nibrin plays an important role in the DNA damage response (DDR) and DNA repair. DDR is a crucial signaling pathway in apoptosis and senescence. To verify whether truncated nibrin (p70), causing Nijmegen Breakage Syndrome (NBS), is involved in DDR and cell fate upon DNA damage, we used two (S4 and S3R) spontaneously immortalized T cell lines from NBS patients, with the founding mutation and a control cell line (L5). S4 and S3R cells have the same level of p70 nibrin, however p70 from S4 cells was able to form more complexes with ATM and BRCA1. Doxorubicin-induced DDR followed by cell senescence could only be observed in L5 and S4 cells, but not in the S3R ones. Furthermore the S3R cells only underwent cell death, but not senescence after doxorubicin treatment. In contrary to doxorubicin treatment, cells from all three cell lines were able to activate the DDR pathway after being exposed to γ-radiation. Downregulation of nibrin in normal human vascular smooth muscle cells (VSMCs) did not prevent the activation of DDR and induction of senescence. Our results indicate that a substantially reduced level of nibrin or its truncated p70 form is sufficient to induce DNA-damage dependent senescence in VSMCs and S4 cells, respectively. In doxorubicin-treated S3R cells DDR activation was severely impaired, thus preventing the induction of senescence.

Affiliations:
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Bielak-Żmijewska A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Siwicki J.K.-Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology (PL)
Sikora E.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Mosieniak G.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Moreno-Villaneuva M.-University of Konstanz (DE)
Dudka-Ruszkowska W.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Wojtala A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Kusio-Kobiałka M.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Korwek Z.-other affiliation
Burkle A.-University of Konstanz (DE)
Piwocka K.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
4.Bielak-Żmijewska A., Wnuk M., Przybylska D., Grabowska W., Lewinska A., Alster O., Korwek Z., Cmoch A., Myszka A., Pikula S., Mosieniak G., Sikora E., A comparison of replicative senescence and doxorubicin-induced premature senescence of vascular smooth muscle cells isolated from human aorta, BIOGERONTOLOGY, ISSN: 1389-5729, DOI: 10.1007/s10522-013-9477-9, Vol.15, pp.47-64, 2014
Abstract:

Senescence of vascular smooth muscle cells (VSMCs) contributes to aging as well as age-related diseases of the cardiovascular system. Senescent VSMCs have been shown to be present in atherosclerotic plaques. Both replicative (RS) and stress-induced premature senescence (SIPS) accompany cardiovascular diseases. We aimed to establish the signature of RS and SIPS of VSMCs, induced by a common anticancer drug, doxorubicin, and to discover the so far undisclosed features of senescent cells that are potentially harmful to the organism. Most of the senescence hallmarks were common for both RS and SIPS; however, some differences were observed. 32 % of doxorubicin-treated cells were arrested in the G2/M phase of the cell cycle, while 73 % of replicatively senescing cells were arrested in the G1 phase. Moreover, on the basis of alkaline phosphatase activity measurements, we show that a 7-day treatment with doxorubicin (dox), does not cause precocious cell calcification, which is a characteristic feature of RS. We did not observe calcification even though after 7 days of dox-treatment many other markers characteristic for senescent cells were present. It can suggest that dox-induced SIPS does not accelerate the mineralization of vessels. We consider that detailed characterization of the two types of cellular senescence can be useful in in vitro studies of potential anti-aging factors.

Keywords:

Senescence, VSMCs, Doxorubicin, Aging, Cardiovascular diseases, Calcification

Affiliations:
Bielak-Żmijewska A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Wnuk M.-other affiliation
Mosieniak G.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Sikora E.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Przybylska D.-other affiliation
Grabowska W.-other affiliation
Lewinska A.-other affiliation
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Korwek Z.-other affiliation
Cmoch A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Myszka A.-other affiliation
Pikula S.-other affiliation
5.Korwek Z., Alster O., Rola szlaku indukowanego uszkodzeniami DNA w apoptozie i starzeniu komórkowym, Postępy Biochemii, ISSN: 0032-5422, Vol.60, No.2, pp.248-262, 2014
Abstract:

Materiał genetyczny każdego organizmu jest ciągle narażony na uszkodzenia spowodowane fizjologicznymi procesami zachodzącymi w komórce, jaki i działaniem szkodliwych czynników pochodzących z otaczającego środowiska. W komórkach eukariotycznych został rozwinięty system monitorujący integralność genomu, nazwany szlakiem odpowiedzi na uszkodzenia DNA (DDR). Odpowiedź komórek na działanie czynnika indukującego uszkodzenia DNA może prowadzić do starzenia, naprawy uszkodzeń DNA, bądź śmierci komórkowej. Kluczowym elementem szlaku DDR, jest białko p53. W wyniku licznych modyfikacji potranslacyjnych zaangażowane może ono być w aktywację wielu genów i białek, prowadzących do przeżycia lub śmierci komórki. W starzeniu komórkowym białko p53 prowadzi do indukcji p21, czego konsekwencją jest zatrzymanie komórek w cyklu. W apoptozie białko p53 bierze udział w aktywacji kaspaz, które odpowiedzialne są za degradację wielu białek. Decyzja o tym, która ze ścieżek będzie aktywowana zależy od stopnia uszkodzenia DNA.

Keywords:

starzenie komórkowe, apoptoza, szlak odpowiedzi na uszkodzenia DNA, autofagia, naprawa uszkodzeń DNA

Affiliations:
Korwek Z.-IPPT PAN
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
6.Alster O., Korwek Z., Znaczniki starzenia komórkowego, Postępy Biochemii, ISSN: 0032-5422, Vol.60, No.2, pp.138-146, 2014
Abstract:

Starzenie jest złożonym procesem związanym z nieodwracalnym zatrzymaniem komórek w cyklu. Wyróżnić można starzenie replikacyjne, zależne od skracania telomerów, i starzenie przyspieszone, które jest niezależne od ich skracania. Starzenie replikacyjne obserwowane jest w hodowli jako skończona liczba podziałów komórek, co może trwać od kilku tygodni do miesięcy, w zależności od typu komórek. Starzenie przyspieszone zachodzi już po kilku dniach od zadziałania czynnika je indukującego. Nie ma jednego uniwersalnego znacznika procesu starzenia komórkowego. Badanie starzenia komórkowego możliwe jest dzięki występowaniu szeregu znaczników tego procesu, które pozwalają obserwować zmiany zarówno na poziomie molekularnym jak i biochemicznym. Dopiero ich współwystępowanie pozwala na uzyskanie pewności, że komórki uległy starzeniu.

Keywords:

znaczniki starzenia, starzenie replikacyjne, starzenie przyspieszone, fenotyp sekrecyjny, β-galaktozydaza związana ze starzeniem

Affiliations:
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Korwek Z.-IPPT PAN
7.Korwek Z., Bielak-Żmijewska A., Mosieniak G., Alster O., Moreno-Villaneuva M., Burkle A., Sikora E., DNA damage-independent apoptosis induced by curcumin in normal resting human T cells and leukaemic Jurkat cells, MUTAGENESIS, ISSN: 0267-8357, DOI: 10.1093/mutage/get017, Vol.4, pp.1-6, 2013
Abstract:

Curcumin, a phytochemical derived from the rhizome of Curcuma longa, is a very potent inducer of cancer cell death. It is believed that cancer cells are more sensitive to curcumin treatment than normal cells. Curcumin has been shown to act as a prooxidant and induce DNA lesions in normal cells. We were interested in whether curcumin induces DNA damage and the DNA damage response (DDR) signalling pathway leading to apoptosis in normal resting human T cells. To this end, we analysed DNA damage after curcumin treatment of resting human T cells (CD3+) and of proliferating leukaemic Jurkat cells by the fluorimetric detection of alkaline DNA unwinding (FADU) assay and immunocytochemical detection of γ-H2AX foci. We showed that curcumin-treated Jurkat cells and resting T cells showed neither DNA lesions nor did they activate key proteins in the DDR signalling pathway, such as phospho-ATM and phospho-p53. However, both types of cell were equally sensitive to curcumin-induced apoptosis and displayed activation of caspase-8 but not of DNA damage-dependent caspase-2. Altogether, our results revealed that curcumin can induce apoptosis of normal resting human T cells that is not connected with DNA damage.

Affiliations:
Korwek Z.-other affiliation
Bielak-Żmijewska A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Mosieniak G.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Moreno-Villaneuva M.-University of Konstanz (DE)
Burkle A.-University of Konstanz (DE)
Sikora E.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
8.Korwek Z., Sewastianik T., Bielak-Żmijewska A., Mosieniak G., Alster O., Moreno-Villaneuva M., Burkle A., Sikora E., Inhibition of ATM blocks the etoposide-induced DNA damage response and apoptosis of resting human T cells, DNA REPAIR, ISSN: 1568-7864, DOI: 10.1016/j.dnarep.2012.08.006, Vol.11, pp.864-873, 2012
Abstract:

It is believed that normal cells with an unaffected DNA damage response (DDR) and DNA damage repair machinery, could be less prone to DNA damaging treatment than cancer cells. However, the anticancer drug, etoposide, which is a topoisomerase II inhibitor, can generate DNA double strand breaks affecting not only replication but also transcription and therefore can induce DNA damage in non-replicating cells. Indeed, we showed that etoposide could influence transcription and was able to activate DDR in resting human T cells by inducing phosphorylation of ATM and its substrates, H2AX and p53. This led to activation of PUMA, caspases and to apoptotic cell death. Lymphoblastoid leukemic Jurkat cells, as cycling cells, were more sensitive to etoposide considering the level of DNA damage, DDR and apoptosis. Next, we used ATM inhibitor, KU 55933, which has been shown previously to be a radio/chemo-sensitizing agent. Pretreatment of resting T cells with KU 55933 blocked phosphorylation of ATM, H2AX and p53, which, in turn, prevented PUMA expression, caspase activation and apoptosis. On the other hand, KU 55933 incremented apoptosis of Jurkat cells. However, etoposide-induced DNA damage in resting T cells was not influenced by KU 55933 as revealed by the FADU assay. Altogether our results show that KU 55933 blocks DDR and apoptosis induced by etoposide in normal resting T cells, but increased cytotoxic effect on proliferating leukemic Jurkat cells. We discuss the possible beneficial and adverse effects of drugs affecting the DDR in cancer cells that are currently in preclinical anticancer trials.

Keywords:

FADU, γH2AX, DSBs, Caspases, KU 55933

Affiliations:
Korwek Z.-other affiliation
Sewastianik T.-other affiliation
Bielak-Żmijewska A.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Mosieniak G.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Alster O.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)
Moreno-Villaneuva M.-University of Konstanz (DE)
Burkle A.-University of Konstanz (DE)
Sikora E.-Nencki Institute of Experimental Biology, Polish Academy of Sciences (PL)