Biology subjects

Kerem, B.

Publications and source records attributed to Kerem, B..

4 recordsLinked to original sources

bioRxiv2025

Nucleotide insufficiency induced by p53 deficiency leads to replication stress driving genomic instability

P53 prevents DNA damage by inducing repair processes, cell cycle arrest or apoptosis. P53 loss leads to replication stress and genomic instability, yet the mechanisms underlying these effects and their contribution to catastrophic genomic events such as chromothripsis remain poorly understood. Using patient-derived fibroblasts with germline p53 variants, that spontaneously undergo chromothripsis, and p53-downregulated fibroblasts, we discovered that p53 loss leads to aberrant transcriptional upregulation, increasing nucleotide consumption while simultaneously decreasing nucleotide biosynthesis. This imbalance in production and consumption results in insufficient nucleotide pools, leading to replication stress and genomic instability, which are rescued by nucleoside supplementation or transcription normalization. The replication stress triggers telomere dysfunction, micronuclei formation, and ultimately chromothripsis. Emerging dominant chromothriptic clones exhibit normal DNA replication, telomere stabilization, and ecDNA, highlighting critical features for clonal selection. Hence, p53 coordinates transcription and nucleotide pools, crucial for maintaining genomic stability and preventing early cancer development.

cancer biology↗

bioRxiv2021

Antisense oligonucleotide-based drug development for Cystic Fibrosis patients carrying the 3849+10kb C-to-T splicing mutation

Antisense oligonucleotide (ASO)-based drugs for splicing modulation were recently been approved for various genetic diseases with unmet need. Here we aimed to develop an ASO-based splicing modulation therapy for Cystic Fibrosis (CF) patients carrying the 3849+10kb C-to-T splicing mutation in the CFTR gene. We have screened, in FRT cells expressing this mutation, ~30 ASOs chemically modified with 2'-O-Methyl on a phosphrothioate backbone, targeted to prevent the recognition and inclusion of a cryptic exon generated due to the mutation. The screening identified five ASO candidates able to promote CFTR correct splicing and rescue channel activity. Further analyses in well differentiated primary human nasal and bronchial epithelial cells (HNEs, HBEs), derived from patients carrying at least one 3849+10kb C-to-T allele, led to the identification of a highly potent lead ASO. The ASO was efficiently delivered by free uptake into patients HNEs and HBEs and completely restored CFTR function to wild type levels in cells from a homozygous patient and led to 43{+/-}8% of wild type levels in cells from various heterozygous patients. Optimized efficiency was further obtained with 2-Methoxy Ethyl chemical modification. The results demonstrate the therapeutic potential and clinical benefit of ASO-based splicing modulation for genetic diseases caused by splicing mutations.

genetics↗

bioRxiv2020

Topoisomerase 1 dependent R-loop deficiency as a mechanism underlying oncogene-induced replication stress and genomic instability

DNA replication is a complex process that is tightly regulated to ensure faithful genome duplication, and its perturbation leads to DNA damage and genomic instability. Replication stress is commonly associated with slow and stalled replication forks. Recently, accelerated replication has emerged as a non-canonical form of replication stress. However, the molecular basis underlying fork acceleration is largely unknown. Here we show that increased topoisomerase 1 (TOP1) expression induces aberrant replication fork acceleration and DNA damage by decreasing RNA-DNA hybrids (R-loops). Degradation of R-loops by overexpression of RNaseH1 also accelerates replication and generates DNA damage. Furthermore, upregulation of TOP1 by activation of the mutated HRAS oncogene leads to fork acceleration and DNA damage in pre-senescent cells. In these cells, restoration of TOP1 expression level or mild replication inhibition rescues the perturbed replication and reduces DNA damage. These findings highlight the importance of TOP1 equilibrium in the regulation of R-loop homeostasis to ensure faithful DNA replication and genome integrity.

cell biology↗

bioRxiv2019

Replication Timing and Transcription Identifies a Novel Fragility Signature Under Replication Stress

Common fragile sties (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Therefore, the molecular mechanism underlying CFS instability remains unclear. Here, we explored the transcriptional profile and temporal order of DNA replication (replication timing, RT) of cells under replication stress conditions. We show that the RT of only a small portion of the genome is affected by replication stress, and that CFSs are enriched for delayed RT. We identified a signature for chromosomal fragility, comprised of replication stress-induced delay in RT of early/mid S-phase replicating regions within actively transcribed large genes. This fragility signature enabled precise mapping of the core fragility region. Furthermore, the signature enabled the identification of novel fragile sites that were not detected cytogenetically, highlighting the improved sensitivity of our approach for identifying fragile sites. Altogether, this study reveals a link between altered DNA replication and transcription of large genes underlying the mechanism of CFS expression. Thus, investigating the RT and transcriptional changes in cancer may contribute to the understanding of mechanisms promoting genomic instability in cancer.

genetics↗