Biology subjects

Skorski, T.

Publications and source records attributed to Skorski, T..

6 recordsLinked to original sources

bioRxiv2026

DNMT1-Mediated Epigenetic Reprogramming Drives KMT2A Amplifications and Rearrangements

MLL/KMT2A amplifications and rearrangements are prevalent in infant, adult, and therapy-induced leukemia; however, the molecular contributors controlling these alterations remain elusive. Here, we reveal that rapid CTCF degradation generates local genome structure alterations at KMT2A and copy gains and rearrangements. We then established a conserved, coordinated interplay between DNA and histone methylation pathways that control CTCF occupancy, and in turn, KMT2A locus stability. For example, DNMT1 overexpression promotes increased H3K9 methylation, reduced CTCF occupancy, and causes KMT2A alterations. However, DNMT1 inhibition suppresses these events and KMT2A alterations caused by topoisomerase II inhibition. Locus-specific epigenome targeting demonstrated that DNA or H3K9 methylation promotes KMT2A copy gains and rearrangement, whereas targeted TET activity suppresses these events upon methylation perturbation or doxorubicin treatment. These findings identify a conserved, coordinated DNA-histone methylation axis governing KMT2A amplifications and rearrangement susceptibility, revealing biomarkers and therapeutic targets to predict and intercept these events in cancer.

cancer biology↗

bioRxiv2026

Targeting Cellular Pseudo-Senescence to Overcome PARP inhibitors Resistance in BRCA1 -Mutated Breast Cancer

Poly (ADP-ribose) polymerase (PARP) inhibitors (PARPi) are a mainstay therapy for homologous recombination (HR)-deficient cancers; however, resistance remains a major clinical challenge. Previously, through a genome wide CRISPR screen, we identified ZNF251 haploinsufficiency as a novel driver of PARPi resistance. In BRCA1-mutant (BRCA1mut) cells, ZNF251 deficiency led to HR hyperactivation, conferring PARPi resistance that could be reversed by RAD51 inhibition. In this study, we further show that ZNF251 deficiency induces replication stress and a pseudo-senescence state, in which cells exhibit molecular and phenotypic markers of senescence while retaining proliferative capacity. Because senomorphic and senolytic therapies can target senescent cells, we tested whether these approaches could overcome PARPi resistance in ZNF251-deficient breast cancer cells. Critically, targeting this senescence-like state with either senomorphic agents, such as cytokine inhibitors, or senolytic agents, such as BCL-2 and BCL-XL inhibitors, overcame PARPi resistance ex vivo and in vivo. Importantly, pseudo-senescence was also observed in other PARPi-resistant contexts driven by HR hyperactivation, including 53BP1- and Shieldin-mutant cells, suggesting that it may represent a broader mechanism underlying PARPi resistance in breast cancer. Furthermore, in two olaparib-resistant, BRCA-mutant triple-negative breast cancer organoid models, treatment with DT2216, a BCL-XL-targeting PROTAC, sensitized both models to olaparib. Together, our work defines a novel pathway linking HR hyperactivation, replication stress, and pseudo-senescence, and positions both senomorphic and senolytic therapies as promising strategies to overcome PARPi resistance in BRCA1mut breast cancer. HighlightsO_LIZNF251 deficiency drives PARP inhibitor resistance through HR hyperactivation, replication stress, and pseudo-senescence in BRCA1-mutant breast cancer. C_LIO_LISenomorphic and senolytic therapies overcome PARP inhibitor resistance in vitro, in vivo, and in patient-derived organoid models. C_LIO_LIPseudo-senescence represents a shared vulnerability of HR-hyperactivated PARPi-resistant cancers and can be therapeutically targeted. C_LI

Cancer Biology↗

bioRxiv2026

TIAR-dependent coordination of alternative splicing and lipid peroxidation is required for CML cell resistance to imatinib in the bone marrow stroma

Chronic myeloid leukemia (CML) is treated with Abl1 tyrosine kinase inhibitors (TKIs). Quiescent cancer cells residing in the bone marrow (BM) can survive the treatment and cause CML relapse. We previously found that a subset of alternative splicing (AS) changes detected in CML cells surviving months of therapy are initiated within hours of treatment onset. Here, we investigated how AS in CML cells is modulated by the human BM microenvironment. By incorporating humanized BM niche models in vivo, we uncovered stroma-induced transcriptome adaptation that influences transcriptional regulation, transmembrane transport, lipid metabolism, the tricarboxylic acid cycle, and respiratory electron transport. We identified RNA-binding protein TIAR (T-cell intracellular antigen-related protein) as a key mediator of CML survival under TKI imatinib treatment. Our data show TIAR-dependent coordination of RNA processing with the metabolic program induced by stromal interaction. Quantitative nascent proteome analysis revealed that TIAR silencing affects the synthesis of metabolic enzymes and proteins involved in imatinib-induced erythroid differentiation. Besides, TIAR knockdown increased lipid peroxidation in untreated cells and decreased reduction potential in cells upon imatinib treatment. Taken together, TIAR deficiency reduces CML survival, possibly by inducing ferroptosis. These findings identify TIAR-dependent RNA processing within the BM niche as a previously unrecognized mechanism of CML therapy resistance and a potential therapeutic vulnerability.

cancer biology↗

bioRxiv2025

Selective Sensitivity of Ph-like B-ALL to BRG1 Inhibition Reveals a Novel Targeted Therapy Strategy

Despite therapeutic advances, high-risk subtypes of B-cell acute lymphoblastic leukemia (B-ALL) such as Philadelphia chromosome-like (Ph-like) and KMT2A-rearranged (KMT2A-R) remain a formidable clinical challenge. BRG1 (gene name SMARCA4), the ATPase subunit of the SWI/SNF chromatin-remodeling complex, has been extensively studied in solid tumors, where inactivating mutations are linked to aggressive disease and poor prognosis. Although BRG1 is known to be essential for early B cell development, its role in B-ALL remains poorly understood. Therefore, we investigated the therapeutic relevance of BRG1 in high-risk B-ALL. Meta-analysis of gene expression data revealed that BRG1-inactivating mutations are exceedingly rare (0.35%) in B-ALL, suggesting that intact BRG1 function may be critical for leukemogenesis. Subtype-specific analyses revealed that elevated BRG1 expression is associated with significantly shorter overall survival in children with Ph-like B-ALL, while the opposite trend was observed in KMT2A-R B-ALL. We confirmed higher BRG1 expressions in Ph-like compared to KMT2A-R B-ALL via gene expression analysis, RT-PCR, and Western blotting. The pharmacologic inhibition of BRG1 using two selective inhibitors, BRM014 and FHD-286, revealed marked sensitivity in Ph-like B-ALL cell lines, whereas KMT2A-R B-ALL was resistant. Mechanistically, we found that BRG1 inhibition results in cell cycle arrest via downregulation of cell cycle regulators (CCND3, CDK4, CDK6, E2F1, and MYC) and upregulation of the cell cycle inhibitor CDKN1B (p27). Importantly, treatment with FHD-286 significantly prolonged the survival of NSG mice engrafted with Ph-like B-ALL cells. Taken together, these findings establish BRG1 as a critical, subtype-specific dependency in Ph-like B-ALL and demonstrate that its pharmacologic inhibition effectively suppresses leukemic cell proliferation through induction of cell cycle arrest. The pronounced in vitro sensitivity and improved in vivo survival upon BRG1 inhibition provide compelling preclinical evidence for its therapeutic targeting. These results support the advancement of BRG1-directed strategies as a viable treatment approach for patients with Ph-like B-ALL, with the potential to improve outcomes in this high-risk population. HighlightsO_LIHigher levels of BRG1 correlate to poor clinical outcomes in Ph-like but KMT2A-R B-ALL C_LIO_LIInhibition of BRG1 induces cell cycle arrest in Ph-like cells in vitro and extends the survival of mice in pre-clinical in vivo studies C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/661805v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1b0a6cforg.highwire.dtl.DTLVardef@977257org.highwire.dtl.DTLVardef@d3bf7forg.highwire.dtl.DTLVardef@1c12d52_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

DNA polymerase theta-mediated DNA repair is a functional dependency and therapeutic vulnerability in DNMT3A deficient leukemia cells

Myeloid malignancies carrying somatic DNMT3A mutations (DNMT3Amut) may be refractory to standard therapy. DNMT3Amut leukemia cells accumulate toxic DNA double strand breaks (DSBs) and stalled replication forks, rendering them dependent on DNA damage response (DDR). We report here that DNA polymerase theta (Pol{theta}), a key element in DSB repair by end-joining (TMEJ) and in fork restarting, is essential for survival and proliferation of DNMT3Amut leukemia cells. Pol{theta} is overexpressed in DNMT3Amut leukemia cells due to abrogation of PARP1 PARylation-dependent UBE2O E3 ligase-mediated ubiquitination and proteasomal degradation of Pol{theta}. In addition, PARP1-mediated recruitment of the SMARCAD1-MSH2/MSH3 repressive complex to DSBs was diminished in DNMT3Amut leukemia cells which facilitated loading of Pol{theta} on DNA damage and promoting TMEJ and replication fork restart. Pol{theta} inhibitors enhanced the anti-leukemic effects of standard drugs such as FLT3 kinase inhibitor quizartinib, cytarabine +/- doxorubicin, and etoposide in vitro and in mice with DNMT3Amut leukemia. Altogether, Pol{theta} is an attractive target in DNMT3Amut hematological malignancies.

cancer biology↗

bioRxiv2022

Loss of ZNF251 stimulates NHEJ resulting in PARP inhibitor resistance in BRCA1-mutated cancer cells

Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a promising new class of agents that have demonstrated efficacy in treating various cancers, particularly those with BRCA1/2 mutations. Cancer-associated BRCA1/2 mutations disrupt DNA double-strand break (DSB) repair by homologous recombination (HR). PARP inhibitors (PARPis) have been used to trigger synthetic lethality in BRCA1/2-mutated cancer cells by promoting the accumulation of toxic DSBs. Unfortunately, resistance to PARPis is common and can occur through multiple mechanisms, including the restoration of HR and/or stabilization of replication forks. To gain a better understanding of the mechanisms underlying PARPis resistance, we conducted an unbiased CRISPR-pooled genome-wide library screen to identify new genes whose deficiency confers resistance to the PARPi olaparib. Our research revealed that haploinsufficiency of the ZNF251 gene, which encodes zinc finger protein 251, is associated with resistance to PARPis in various breast and ovarian cancer cell lines carrying BRCA1 mutations. Mechanistically, we discovered that ZNF251 haploinsufficiency leads to stimulation of RAD51-mediated HR repair of DSBs in olaparib-treated BRCA1-mutated cancer cells. Moreover, we demonstrated that a RAD51 inhibitor reversed PARPi resistance in ZNF251 haploinsufficient cancer cells harboring BRCA1 mutations. Our findings provide important insights into the mechanisms underlying PARPis resistance by highlighting the role of RAD51 in this phenomenon.

cancer biology↗