Biology subjects

Noordermeer, S. M.

Publications and source records attributed to Noordermeer, S. M..

7 recordsLinked to original sources

bioRxiv2026

S6K1 and S6K2 regulate homologous recombination DNA repair through control of BRCA1 protein stability

Recent studies have suggested that S6 kinase 1 (S6K1) contributes to DNA repair (DR). However, the specific pathways and mechanisms involved in this regulation remain unclear. Moreover, it has not been investigated whether S6K2, a functional homologue of S6K1, also contributes to DR. In this study, we investigated the function of both S6K1 and S6K2 (S6K1/2) proteins in DR and demonstrate that both are important for efficient Homologous Recombination-mediated repair (HR). Double knockout of S6K1/2 prevented the formation of BRCA1 and RAD51 foci and increases sensitivity to DNA-damaging agents such as PARP1 inhibitors, cisplatin, and X-ray irradiation. In addition, double knockout of S6K1/2 increased markers of genomic instability, while single knockout had little effect on HR markers and genome stability, which suggests that one kinase can compensate for the loss of the other. Mechanistically, we show that S6K1/2 regulate BRCA1 protein stability, limiting its degradation by the proteasome. Finally, pharmacological inhibition of S6K1/2 sensitised HR-proficient breast cancer cells to Olaparib. Our findings clarify the role of S6K1/2 proteins in HR and suggest that targeting these kinases may be a therapeutic strategy to enhance PARP inhibitor efficacy in HR-proficient tumours.

molecular biology↗

bioRxiv2026

DNA end-resection is stimulated by an interaction between BRCA1 exon 11 and TOPBP1

Approximately 60% of the tumour suppressor protein BRCA1 is encoded by a single exon. Many tumours carry mutations in this exon, often resulting in exon skipping and thus a protein of a severely reduced size. Although none of the well-described protein domains of BRCA1 are encoded by this exon 11, the isoform lacking this part shows a hypomorphic activity in homologous recombination. To better understand the function of this large exon, we performed proteomic analyses to identify interaction partners via this part of the protein. Here, we report a DNA damage-and phospho-dependent interaction of TOPBP1 to the protein region of BRCA1 encoded by exon 11. Mechanistically, this interaction is required for BRCA1s role in end-resection during homologous recombination. In contrast, the interaction is not required for TOPBP1s role in ATR activation. Our data provide novel mechanistic insight into the function of this poorly characterized part of the BRCA1 protein.

molecular biology↗

bioRxiv2024

Finding novel vulnerabilities of hypomorphic BRCA1 alleles

With the recent rise in CRISPR/Cas9-mediated genome-wide synthetic lethality screens, many new synthetic lethal targets have been identified for diseases with underlying genetic causes such as tumours with BRCA1 mutations. Such screens often use full deficiency of a protein to identify novel vulnerabilities. However, patient-derived mutations not only result in loss of the protein but often also concern missense mutations with hypomorphic phenotypes. Here we study the genetic vulnerabilities of two previously described hypomorphic BRCA1 missense mutations and compare these to a BRCA1-depleted setting to study whether this affects screening for synthetic lethal interactions. Our research showed that BRCA1I26A mutated cells have very similar vulnerabilities to BRCA1 wildtype cells, confirming its low tumorigenic effect. In contrast, the BRCA1R1699Q mutation induced a more similar phenotype to BRCA1-deficient cells. For this mutation, we also unveiled a unique vulnerability to the loss of NDE1. Specifically in BRCA1R1699Q mutated cells, and not BRCA1-proficient or -deficient cells, NDE1 loss leads to increased genomic instability. Altogether our findings highlight the importance to differentiate between patient-derived mutations when assessing novel treatment targets.

cancer biology↗

bioRxiv2023

Chemo-phosphoproteomic profiling with ATR inhibitors berzosertib and gartisertib uncovers new biomarkers and DNA damage response regulators

The ATR kinase protects cells against DNA damage and replication stress and represents a promising anti-cancer drug target. The ATR inhibitors (ATRi) berzosertib and gartisertib are in clinical trials for treatment of advanced solid tumours as monotherapy or in combination with genotoxic agents. However, the pharmacodynamic ATR biomarker phospho-CHK1 has shown limited sensitivity in for quantitative assessment of ATR activity in clinical trials. Therefore, better biomarkers are needed, and with this in mind we carried out quantitative phospho-proteomic screening for ATR biomarkers that are highly sensitive to berzosertib and gartisertib. Screening identified novel ATR-dependent targets in three broad classes: i) targets whose phosphorylation is highly sensitive to ATRi; ii) novel targets with known genome maintenance roles; iii) novel targets whose cellular roles are unclear, including SCAF1. We show that SCAF1 interacts with RNAPII in a phospho-dependent manner and suppresses homologous recombination in cells lacking the BRCA1 tumour suppressor. Taken together these data reveal potential new ATR biomarkers and new genome maintenance factors.

biochemistry↗

bioRxiv2023

EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells

Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevated EXO1 expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.

molecular biology↗

bioRxiv2021

Two redundant ubiquitin-dependent pathways of BRCA1 localization to DNA damage sites

The tumor suppressor BRCA1 accumulates at sites of DNA damage in a ubiquitin-dependent manner. In this work, we revisit the role of the ubiquitin-binding protein RAP80 in BRCA1 recruitment to damaged chromatin. We found that RAP80, or the phosphopeptide-binding residues in the BRCA1 BRCT domains, act redundantly with the BRCA1 RING domain to promote BRCA1 recruitment to DNA double-strand break sites. We show that that RNF8 E3 ubiquitin ligase acts upstream of both the RAP80- and RING-dependent activities whereas RNF168 acts uniquely upstream of the RING domain. The function of the RING domain in BRCA1 recruitment is not solely linked to its role in mediating an interaction with BARD1 since RING mutations that do not impact BARD1 interaction, such as the E2-binding deficient Ile26Ala (I26A) mutation, produce a BRCA1 protein unable to accumulate at DNA damage sites in the absence of RAP80. Cells that combine the BRCA1 I26A mutation and mutations that disable the RAP80-BRCA1 interaction are deficient in RAD51 filament formation and are hypersensitive to poly (ADP-ribose) polymerase inhibition. Our results suggest that in the absence of RAP80, the BRCA1 E3 ligase activity is necessary for the recognition of unmethylated histone H4 Lys20 and histone H2A Lys13/Lys15 ubiquitylation by BARD1 although we cannot rule out the possibility that the RING- E2 complex itself may facilitate ubiquitylated nucleosome recognition in other ways. Finally, given that tumors expressing RING-less BRCA1 isoforms readily acquire resistance to therapy, this work suggests that targeting RAP80, or its interaction with BRCA1, could represent a novel strategy for restoring sensitivity of such tumors to DNA damaging agents.

molecular biology↗

bioRxiv2021

CIP2A is a prime synthetic-lethal target for BRCA-mutated cancers

BRCA1/2-mutated cancer cells must adapt to the genome instability caused by their deficiency in homologous recombination. Identifying and targeting these adaptive mechanisms may provide new therapeutic strategies. Here we present the results of genome-scale CRISPR/Cas9-based synthetic lethality screens in isogenic pairs of BRCA1- and BRCA2-deficient cells that identified the gene encoding CIP2A as essential in a wide range of BRCA1- and BRCA2-mutated cells. Unlike PARP inhibition, CIP2A-deficiency does not cause accumulation of replication-associated DNA lesions that require homologous recombination for their repair. CIP2A is cytoplasmic in interphase but, in mitosis, accumulates at DNA lesions as part of a complex with TOPBP1, a multifunctional genome stability factor. In BRCA-deficient cells, the CIP2A-TOPBP1 complex prevents lethal mis-segregation of acentric chromosomes that arises from impaired DNA synthesis. Finally, physical disruption of the CIP2A-TOPBP1 complex is highly deleterious in BRCA-deficient cells and tumors, indicating that targeting this mitotic chromosome stability process represents an attractive synthetic-lethal therapeutic strategy for BRCA1- and BRCA2-mutated cancers.

cancer biology↗