The Independent Research Group of Non-coding Parts of the Genome  aims to functionally characterize various non-coding sequences in the genome (miRNA, lncRNA, eRNA, enhancers, promoters and transcription factor binding sites) in basic cellular processes and in cancer pathogenesis.

Currently, the Group implements the following research projects:

  1. “Functional dissection of IGH regulatory regions in B-cell non-Hodgkin lymphoma”, carried out within the FIRST-TEAM programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund (2019-2023).

    Project description: Characteristic feature of B-cell non-Hodgkin lymphoma are recurrent translocations juxtaposing an oncogene (e.g. MYC, BCL2) to the regulatory regions of immunoglobulin heavy chain (IGH) locus. Survival and proliferation of many B-cell lymphomas depends on the expression of the translocated oncogene and on signaling from B-cell receptor expressed from the other functional IGH allele. IGH regulatory elements have been studied in normal B-cell development, but their role in human cancer cells has not been defined. The goal of this project is to identify and characterize the functional elements in IGH regulatory regions and enhancer RNAs (eRNA) essential for B-cell lymphoma cell growth. We will use CRISPR/Cas9 to target all possible sites in IGH regulatory regions and identify the functional sequences. In parallel, GRO-seq will be performed to identify eRNAs expressed from the IGH locus. Intersection of the results and functional follow-up will identify regulatory elements and eRNAs essential for growth of B-cell lymphoma. The results will provide new insights into the role of IGH regulatory regions in malignant cells and may indicate novel therapeutic targets in B-cell lymphoma. This project will be performed in collaboration with scientists from the Netherlands and the US.

    Project budget: 1 952 960,00 PLN
    The project is 100% financed by the Smart Growth Operational Programme 2014-2020


    Woźniak T, Sura W, Kazimierska M, Kasprzyk ME, Podralska M, Dzikiewicz-Krawczyk A. TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. Nucleic Acids Res. 2023 Jul 5;51(W1):W577-W586. doi: 10.1093/nar/gkad355. PMID: 37158253.

    Kasprzyk ME, Łosiewski W, Podralska M, Kazimierska M, Sura W, Dzikiewicz-Krawczyk A. 7-[[(4-methyl-2-pyridinyl)amino](2-pyridinyl)methyl]-8-quinolinol (compound 30666) inhibits enhancer activity and reduces B-cell lymphoma growth – A question of specificity. Eur J Pharmacol. 2021 Nov 5;910:174505. doi: 10.1016/j.ejphar.2021.174505. PMID: 34534532.

    Kasprzyk ME, Sura W, Dzikiewicz-Krawczyk A. Enhancing B-Cell Malignancies-On Repurposing Enhancer Activity towards Cancer. Cancers (Basel). 2021 Jun 29;13(13):3270. doi: 10.3390/cancers13133270. PMID: 34210001.

  2. “Identification and functional characterization of long non-coding RNAs involved in the ATM-dependent response to DNA damage”, carried out within the OPUS programme of the Polish Science Centre (2018-2023).

    Project description: DNA damage repair is essential for the maintenance of genome integrity. Several proteins are involved in the cellular response to DNA damage. Among them, the ATM kinase (ataxia-telangiectasia mutated) plays a crucial role. Mutations in both alleles of the ATM gene lead to the genetic disorder ataxia-telangiectasia (AT), a neurodegenerative disease with increased cancer predisposition. ATM deficient cells demonstrate inefficient DNA repair and hypersensitivity to ionizing radiation. Despite a substantial knowledge of DNA repair processes, still several aspects of DNA damage detection and signaling are not fully understood. In this project we aim to verify the hypothesis that ATM-dependent lncRNAs are essential molecules involved in the DNA damage detection and repair. The study will fullfill three objectives: identification of ionizing radiation-induced lncRNAs, identification of ATM-interacting lncRNAs, and functional characterization of selected lncRNAs in the context of DNA damage response. Results obtained in this project will broaden the knowledge about lncRNAs involved in the detection and repair of DNA damage and will help to better understand the mechanisms of DNA damage response. Moreover, results of functional assays can also indicate lncRNAs as novel factors modulating cells sensitivity to radiotherapy, which may be useful for further applied research.


    Paszkowska A, Kolenda T, Guglas K, Kozłowska-Masłoń J, Podralska M, Teresiak A, Bliźniak R, Dzikiewicz-Krawczyk A, Lamperska K. C10orf55, CASC2, and SFTA1P lncRNAs Are Potential Biomarkers to Assess Radiation Therapy Response in Head and Neck Cancers. J Pers Med. 2022 Oct 11;12(10):1696. doi: 10.3390/jpm12101696. PMID: 36294833.

    Kasprzyk ME, Kazimierska M, Sura W, Dzikiewicz-Krawczyk A, Podralska M. Non-coding RNAs: Mechanisms of action. In: Navigating Non-coding RNA: From Biogenesis to Therapeutic Application, Elsevier 2023, pp. 89–138.

    Podralska M, Ciesielska S, Kluiver J, van den Berg A, Dzikiewicz-Krawczyk A, Slezak-Prochazka I. Non-Coding RNAs in Cancer Radiosensitivity: MicroRNAs and lncRNAs as Regulators of Radiation-Induced Signaling Pathways. Cancers (Basel). 2020 Jun 23;12(6):1662. doi: 10.3390/cancers12061662. PMID: 32585857.

  3. “CRISPR/Cas9 screen for identification of functional MYC binding sites and target genes essential for cancer cell growth”, carried out within the SONATA programme of the Polish Science Centre (2017-2022).

    Project description: MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC is a transcription factor that binds to specific E-box sequences in the genome to regulate expression of adjacent genes. To date a comprehensive analysis of direct MYC targets involved in cancer is missing. The aim of this project is to comprehensively identify functional MYC binding sites and corresponding target genes essential for growth of cancer cells using an innovative CRISPR/Cas9-based high-throughput screening approach. We will generate a lentiviral single guide RNA (sgRNA) library to destroy E-box sequences in four cell lines representing different types of MYC-addicted cancers. NGS analysis of sgRNA constructs abundance over time will indicate MYC binding sites essential for growth of cancer cells. For selected E-box sequences and target genes follow-up experiments will confirm their functional relevance in cancer cells. The results will help to understand the mechanisms underlying cancer cell addiction to MYC and may pave the way for novel targeted therapies.


    Kazimierska M, Podralska M, Żurawek M, Woźniak T, Kasprzyk ME, Sura W, Łosiewski W, Ziółkowska-Suchanek I, Kluiver J, van den Berg A, Rozwadowska N, Dzikiewicz-Krawczyk A. CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells. Mol Oncol. 2023 Jul 30. doi: 10.1002/1878-0261.13493. PMID: 37519063.

    Woźniak T, Sura W, Kazimierska M, Kasprzyk ME, Podralska M, Dzikiewicz-Krawczyk A. TransCRISPR-sgRNA design tool for CRISPR/Cas9 experiments targeting specific sequence motifs. Nucleic Acids Res. 2023 Jul 5;51(W1):W577-W586. doi: 10.1093/nar/gkad355. PMID: 37158253.

    Winkle M, Tayari MM, Kok K, Duns G, Grot N, Kazimierska M, Seitz A, de Jong D, Koerts J, Diepstra A, Dzikiewicz-Krawczyk A, Steidl C, Kluiver J, van den Berg A. The lncRNA KTN1-AS1 co-regulates a variety of Myc-target genes and enhances proliferation of Burkitt lymphoma cells. Hum Mol Genet. 2022 Dec 16;31(24):4193-4206. doi: 10.1093/hmg/ddac159. PMID: 35866590.

    Niu F, Kazimierska M, Nolte IM, Terpstra MM, de Jong D, Koerts J, van der Sluis T, Rutgers B, O’Connell RM, Kok K, van den Berg A, Dzikiewicz-Krawczyk A, Kluiver J. The miR-26b-5p/KPNA2 Axis Is an Important Regulator of Burkitt Lymphoma Cell Growth. Cancers (Basel). 2020 Jun 4;12(6):1464. doi: 10.3390/cancers12061464. PMID: 32512858.

    Swier LJYM, Dzikiewicz-Krawczyk A, Winkle M, van den Berg A, Kluiver J. Intricate crosstalk between MYC and non-coding RNAs regulates hallmarks of cancer. Mol Oncol. 2019 Jan;13(1):26-45. doi: 10.1002/1878-0261.12409. PMID: 30451365.

    Kluiver J, Niu F, Yuan Y, Kok K, van den Berg A, Dzikiewicz-Krawczyk A. NGS-Based High-Throughput Screen to Identify MicroRNAs Regulating Growth of B-Cell Lymphoma. Methods Mol Biol. 2019;1956:269-282. doi: 10.1007/978-1-4939-9151-8_12. PMID: 30779039.

The Head of the Independent Research Group:
dr n. med. Agnieszka Dzikiewicz-Krawczyk
phone: +48 61 65 79 219