Biology subjects

Everts, M.

Publications and source records attributed to Everts, M..

8 recordsLinked to original sources

bioRxiv2025

TAOK1 regulates chemo- and radiosensitivity in BRCA1/2-deficient tumors

BRCA1/2-deficient cells are hypersensitive to replication stress- and DNA-damage-inducing agents such as poly(ADP-ribose) polymerase inhibitors (PARPi), platinum drugs, and ionizing radiation (IR), largely due to impaired homologous recombination repair and replication fork (RF) protection. The precise mechanisms underlying RF vulnerability in the absence of BRCA1/2 remain incompletely understood, however. Here, we identify Thousand And One Amino Acid Kinase 1 (TAOK1) as a novel regulator of RF dynamics that sensitizes BRCA1/2-deficient cells to both PARPi and IR. Unlike established DNA repair factors, such as PARG or the 53BP1-RIF1-shieldin-CST pathway, which mediate PARPi sensitivity while protecting cells against IR, TAOK1 promotes RF degradation and suppresses post-replicative damage repair. TAOK1 depletion stabilizes RFs and reduces replication-associated DNA damage in BRCA1/2-deficient cells, thereby conferring therapy resistance. Interestingly, we found that TAOK1 functions in RF regulation to be independent of its kinase activity. Instead, it interacts with PCNA and regulates ISG15 levels and thereby affects RF stability. Our findings reveal TAOK1 as a non-canonical mediator of therapy sensitivity in BRCA1/2-deficient tumors. TeaserTAOK1 controls replication fork stability through PCNA and ISG15, affecting therapy response in BRCA1/2-deficient cancers.

cancer biology↗

bioRxiv2025

CIP2A is required for mitotic recruitment of the SLX1/XPF/MUS81 tri-nuclease complex to replication stress-induced DNA lesions to maintain genome integrity

Perturbed DNA replication can lead to incompletely replicated DNA when cells enter mitosis and can interfere with chromosome segregation. Cells therefore require mechanisms to resolve these lesions during mitosis. The CIP2A-TOPBP1 complex is described to function as a molecular tether that connects fragmented DNA molecules. However, whether CIP2A also functions in processing of incompletely replicated DNA remained unclear. We show that CIP2A-TOPBP1 forms large filamentous structures at sites of incomplete DNA replication during mitosis, which recruit the SMX tri-nuclease complex members SLX4, MUS81 and ERCC1/XPF. These structures form in proximity to sites of mitotic DNA synthesis, although CIP2A is not required for mitotic DNA synthesis. In addition to its globular and coiled-coil domain, the unstructured C-terminal domain of CIP2A is essential for CIP2A-TOPBP1 filamentous structure formation and recruitment of the SMX complex. BRCA1-/- and BRCA2-/- cells have increased mitotic DNA lesions that recruit CIP2A and SLX4. We show that the C-terminal part of CIP2A is required for survival of BRCA2-/- cells. Moreover, SLX4 is crucial for genome stability in BRCA2-/- cells. Combined, we demonstrate that CIP2A-TOPBP1 recruits the SMX complex during mitosis, which is required to resolve mitotic DNA lesions, allows faithful chromosome segregation and maintain viability of BRCA2-/- cells.

cell biology↗

bioRxiv2025

WEE1 inhibitors trigger GCN2-mediated activation of the integrated stress response

The WEE1 kinase negatively regulates CDK1/2 to control DNA replication and mitotic entry. Genetic factors that determine sensitivity to WEE1 inhibitors (WEE1i) are largely unknown. A genome-wide insertional mutagenesis screen revealed that mutation of EIF2A, a translation regulator, sensitized to WEE1i. Mechanistically, WEE1i treatment triggers a translational shut-down, which is lethal in combination with the reduced translation of EIF2AKO cells. A genome-wide CRISPR-Cas9 screen revealed that inactivation of integrated stress response (ISR) kinases GCN1/2 rescued WEE1i-mediated cytotoxicity. WEE1i induced GCN2 activation, ATF4 upregulation, and altered ribosome dynamics. Loss of the collided ribosome sensor ZNF598 conversely increased sensitivity to WEE1i. Notably, the ISR was not required for WEE1i to induce DNA damage, premature mitotic entry or sensitization to DNA-damaging chemotherapeutics. ISR activation was independent of CDK1/2 activation. Importantly, WEE1i-mediated ISR activation was independent of WEE1 presence, pointing at off-target effects, which are shared by multiple chemically distinct WEE1i. This response was also observed in peripheral blood mononuclear cells. Importantly, low-dose WEE1 inhibition did not induce ISR activation, while it still synergized with PKMYT1 inhibition. Taken together, WEE1i triggers toxic ISR activation and translational shutdown, which can be prevented by low-dose or combination treatments, while retaining the cell cycle checkpoint-perturbing effects.

cancer biology↗

bioRxiv2022

The FIGNL1-interacting protein C1orf112 is synthetic lethal with PICH and mediates RAD51 retention on chromatin.

Joint DNA molecules are natural by-products of DNA replication and repair. Persistent joint molecules give rise to ultrafine DNA bridges (UFBs) in mitosis, which compromise sister chromatid separation. The DNA translocase PICH (ERCC6L) plays a central role in UFB resolution. A genome-wide loss-of-function screen was performed to identify the genetic contexts in which cells become dependent on PICH. In addition to genes involved in DNA condensation, centromere stability and DNA damage repair, we identified the uncharacterized protein C1orf112. We find that C1orf112 interacts with and stabilizes the AAA+ ATPase FIGNL1. Inactivation of either C1orf112 or FIGNL1 resulted in UFB formation, prolonged retention of RAD51 on chromatin, impaired replication fork dynamics, and consequently impaired genome maintenance. Combined, our data reveal that inactivation of C1orf112 and FIGNL1 dysregulates RAD51 dynamics at replication forks, resulting in DNA replication defects, and a dependency on PICH to preserve cell viability.

cancer biology↗

bioRxiv2022

White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern

The spillover of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from humans into white-tailed deer (WTD) and its ability to transmit from deer-to-deer raised concerns about the role of WTD in the epidemiology and ecology of the virus. In the present study, we conducted a comprehensive investigation to assess the prevalence, genetic diversity, and evolution of SARS-CoV-2 in WTD in the State of New York (NY). A total of 5,462 retropharyngeal lymph node (RPLN) samples collected from free-ranging hunter-harvested WTD during the hunting seasons of 2020 (Season 1, September-December 2020, n=2,700) and 2021 (Season 2, September-December 2021, n=2,762) were tested by SARS-CoV-2 real-time RT-PCR. SARS-CoV-2 RNA was detected in 17 samples (0.6%) from Season 1 and in 583 (21.1%) samples from Season 2. Hotspots of infection were identified in multiple confined geographic areas of NY. Sequence analysis of SARS-CoV-2 genomes from 164 samples demonstrated the presence multipls SARS-CoV-2 lineages as well as the co-circulation of three major variants of concern (VOCs) (Alpha, Gamma, and Delta) in WTD. Our analysis suggests the occurrence of multiple spillover events (human-to-deer) of the Alpha and Delta lineages with subsequent deer-to-deer transmission of the viruses. Detection of Alpha and Gamma variants in WTD long after their broad circulation in humans in NY suggests that WTD may serve as a wildlife reservoir for VOCs no longer circulating in humans. Thus, implementation of continuous surveillance programs to monitor SARS-CoV-2 dynamics in WTD are warranted, and measures to minimize virus transmission between humans and animals are urgently needed. SIGNIFICANCEWhite-tailed deer (WTD) are highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and are known to efficiently transmit the virus to other susceptible animals. Evidence of natural exposure or infection of wild WTD in North America raised significant concerns about their role on the ecology of the virus and its impact on the control of the coronavirus disease 2019 (COVID-19) pandemic. This comprehensive study demonstrates widespread infection of SARS-CoV-2 in the WTD populations across the State of New York. Additionally, we showed co-circulation of three major SARS-CoV-2 variants of concern (VOCs) in this wildlife population, long after their broad circulation in humans. These findings indicate that WTD - the most abundant large mammal in North America - may serve as a reservoir for variant SARS-CoV-2 strains that no longer circulate in the human population.

microbiology↗

bioRxiv2021

Sister chromatid exchanges induced by perturbed replication are formed independently of homologous recombination factors

Sister chromatid exchanges (SCEs) are products of joint DNA molecule resolution, and are considered to form through homologous recombination (HR). Indeed, upon generation of irradiation-induced DNA breaks, SCE induction was compromised in cells deficient for canonical HR factors BRCA1, BRCA2 and RAD51. Contrarily, replication-blocking agents, including PARP inhibitors, induced SCEs independently of BRCA1, BRCA2 and RAD51. PARP inhibitor-induced SCEs were enriched at common fragile sites (CFSs), and were accompanied by post-replicative single-stranded DNA (ssDNA) gaps. Moreover, PARP inhibitor-induced replication lesions were transmitted into mitosis, suggesting that SCEs originate from mitotic processing of under-replicated DNA. We found that DNA polymerase theta (POLQ) was recruited to mitotic DNA lesions, and loss of POLQ resulted in reduced SCE numbers and severe chromosome fragmentation upon PARP inhibition in HR-deficient cells. Combined, our data show that PARP inhibition generates under-replicated DNA, which is transferred into mitosis and processed into SCEs, independently of canonical HR factors.

cancer biology↗

bioRxiv2021

An mRNA expression-based signature for oncogene-induced replication-stress

BackgroundOncogene-induced replication stress characterizes many aggressive cancers, including triple-negative breast cancer (TNBC). Several drugs are being developed that target replication stress, although it is unclear how tumors with high levels of replication stress can be identified. We aimed to develop a gene expression signature of oncogene-induced replication stress. MethodsTNBC and non-transformed RPE1-TP53wt and RPE1-TP53mut cell lines were engineered to overexpress the oncogenes CDC25A, CCNE1 or MYC. DNA fiber analysis was used to measure replication kinetics. Analysis of RNA sequencing data of cell lines and patient-derived tumor samples (TCGA n=10,592) was used to identify differential gene expression. Immunohistochemical validation was conducted on breast cancer samples (n=330). ResultsRNA sequencing revealed 52 commonly upregulated genes after induction of CDC25A, CCNE1 or MYC in our cell line panel. Integration with gene expression data of TGCA samples with amplification of replication stress-inducing oncogenes (CDC25A, CCNE1, MYC, CCND1, MYB, MOS, KRAS, ERBB2, and E2F1), yielded a six-gene signature of oncogene-induced replication stress (NAT10, DDX27, ZNF48, C8ORF33, MOCS3, and MPP6). Expression of NAT10 in breast cancer samples was correlated with phospho-RPA (R=0.451, p=1.82x10-20) and {gamma}H2AX (R=0.304, p=2.95x10-9). Applying the oncogene-induced replication stress signature to patient samples (TCGA n=8,862 and GEO n=13,912) defined the replication stress landscape across 27 tumor subtypes, and identified diffuse large B cell lymphoma, ovarian cancer, TNBC and colorectal carcinoma as cancer subtypes with high levels of oncogene-induced replication stress. ConclusionWe developed a gene expression signature of oncogene-induced replication stress, which may facilitate patient selection for agents that target replication stress.

cancer biology↗

bioRxiv2019

Cyclin E expression is associated with high levels of replication stress in triple-negative breast cancer.

Replication stress entails the improper progression of DNA replication. In cancer cells, including breast cancer cells, an important cause of replication stress is oncogene activation. Importantly, tumors with high levels of replication stress may have different clinical behavior, and high levels of replication stress appear to be a vulnerability of cancer cells, which may be therapeutically targeted by novel molecularly targeted agents. Unfortunately, data on replication stress is largely based on experimental models. Further investigation of replication stress in clinical samples is required to optimally implement novel therapeutics. To uncover the relation between oncogene expression, replication stress and clinical features of breast cancer subtypes, we immunohistochemically analyzed the expression of a panel of oncogenes (Cdc25a, Cyclin E and c-Myc) and markers of replication stress (phospho-Ser33-RPA32 and {gamma}-H2AX) in treatment-naive breast tumor tissues (n=384). Triple-negative breast cancers (TNBCs) exhibited the highest levels of phospho-Ser33-RPA32 (P<0.001 for all tests) and {gamma}-H2AX (P<0.05 for all tests). Moreover, expression levels of Cyclin E (P<0.001 for all tests) and c-Myc (P<0.001 for all tests) were highest in TNBCs. Expression of Cyclin E positively correlated with phospho-RPA32 (Spearman correlation r=0.37, P<0.001) and {gamma}-H2AX (Spearman correlation r=0.63, P<0.001). Combined, these data indicate that replication stress is predominantly observed in TNBCs, and is associated with expression levels of Cyclin E. These results indicate that Cyclin E overexpression may be used as a biomarker for patient selection in the clinical evaluation of drugs that target the DNA replication stress response.

cancer biology↗