Biology subjects

Chen, B.-R.

Publications and source records attributed to Chen, B.-R..

6 recordsLinked to original sources

bioRxiv2026

Centromeric α-satellite DNA is a hotspot of genotoxic damage, incomplete repair, and cytoplasmic mislocalization

Centromeric -satellite DNA constitutes a highly repetitive and structurally specialized component of the human genome, yet the mechanisms underlying its damage susceptibility and repair fidelity under genotoxic stress remain undefined. Here, we demonstrate that genotoxic stress preferentially targets active centromeres, generating DNA double-strand breaks (DSBs) within -satellite arrays. Using bleomycin as a defined genotoxic perturbation, we identify dynamic alterations in centromeric repeat content, manifesting as net copy number losses and gains across multiple chromosome-specific -satellite arrays following damage. Similar centromere-associated damage signatures are observed in fibroblasts from patients with limited cutaneous systemic sclerosis, indicating that these features extend beyond experimental systems. Centromeric DSBs engage ATM-dependent DNA damage signaling and are repaired predominantly through RAD51-associated homologous recombination; however, repair fails to fully restore centromeric integrity. This incomplete repair is associated with defects in kinetochore organization, chromosome missegregation, and the formation of micronuclei containing centromeric DNA. Notably, [~]30% of these structures retain CENP-B but lacks detectable CENP-A, indicating disruption of centromere chromatin organization. Centromeric chromatin is frequently mislocalized to the cytoplasm following nuclear envelope perturbation, where immunofluorescence analysis reveals proximity to MHC class II (HLA-DRB1). Together, these findings establish centromeric -satellite DNA as a vulnerability hotspot under genotoxic stress, with implications for chromosome instability and chromatin antigen exposure in fibrosis-associated autoimmunity.

genetics↗

bioRxiv2025

Centromere instability links genome damage to immune activation in systemic sclerosis

Systemic sclerosis (SSc) is a fibrotic autoimmune disease in which genomic sources of instability and their immunological consequences remain poorly defined. We show that bleomycin, a widely used SSc fibrosis model, induces DNA double-strand breaks (DSBs) at active centromeres. Similar centromeric damage signatures were observed in fibroblasts from patients with limited cutaneous SSc, consistent with prior observations. Quantification of -satellite repeat content revealed dynamic changes in repeat abundance, consistent with deletions and insertions and incomplete restoration following damage. These breaks are repaired primarily ATM-dependent, RAD51-associated homologous recombination, but repair remains incomplete. Incomplete repair is associated with altered kinetochore assembly, chromosome missegregation, and increased formation of micronuclei and cytoplasmic chromatin enriched in centromere proteins. These fragments escape via nuclear envelope rupture and show spatial colocalization with MHC class II molecules. Together, these findings establish bleomycin-induced centromere damage as a tractable model to study active-centromere instability, its incomplete repair, and the resulting chromatin mislocalization in fibroblasts, with features relevant to systemic sclerosis.

genetics↗

bioRxiv2024

Senataxin and DNA-PKcs Redundantly Promote Non-Homologous End Joining Repair of DNA Double Strand Breaks During V(D)J Recombination

Non-homologous end joining (NHEJ) is required for repairing DNA double strand breaks (DSBs) generated by the RAG endonuclease during lymphocyte antigen receptor gene assembly by V(D)J recombination. The Ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) kinases regulate functionally redundant pathways required for NHEJ. Here we report that loss of the senataxin helicase leads to a significant defect in RAG DSB repair upon inactivation of DNA-PKcs. The NHEJ function of senataxin is redundant with the RECQL5 helicase and the HLTF translocase and is epistatic with ATM. Co-inactivation of ATM, RECQL5 and HLTF results in an NHEJ defect similar to that from the combined deficiency of DNA-PKcs and senataxin or losing senataxin, RECQL5 and HLTF. These data suggest that ATM and DNA-PKcs regulate the functions of senataxin and RECQL5/HLTF, respectively to provide redundant support for NHEJ.

cell biology↗

bioRxiv2021

DNA-PK Promotes DNA End Resection at DNA Double Strand Breaks in G0 cells

DNA double-strand break (DSB) repair by homologous recombination is confined to the S and G2 phases of the cell cycle partly due to 53BP1 antagonizing DNA end resection in G1 phase and non-cycling quiescent (G0) cells where DSBs are predominately repaired by non-homologous end joining (NHEJ). Unexpectedly, we uncovered extensive MRE11- and CtIP-dependent DNA end resection at DSBs in G0 mammalian cells. A whole genome CRISPR/Cas9 screen revealed the DNA-dependent kinase (DNA-PK) complex as a key factor in promoting DNA end resection in G0 cells. In agreement, depletion of FBXL12, which promotes ubiquitylation and removal of the KU70/KU80 subunits of DNA-PK from DSBs, promotes even more extensive resection in G0 cells. In contrast, a requirement for DNA-PK in promoting DNA end resection in proliferating cells at the G1 or G2 phase of the cell cycle was not observed. Our findings establish that DNA-PK uniquely promotes DNA end resection in G0, but not in G1 or G2 phase cells, and has important implications for DNA DSB repair in quiescent cells.

molecular biology↗

bioRxiv2021

LIN37-DREAM Prevents DNA End Resection and Homologous Recombination at DNA Double Strand Breaks in Quiescent Cells

DNA double strand break (DSB) repair by homologous recombination (HR) is thought to be restricted to the S- and G2- phases of the cell cycle in part due to 53BP1 antagonizing DNA end resection in G1-phase and non-cycling quiescent (G0) cells. Here, we show that LIN37, a component of the DREAM transcriptional repressor, functions in a 53BP1-independent manner to prevent DNA end resection and HR in G0 cells. Loss of LIN37 leads to expression of HR proteins, including BRCA1, BRCA2, PALB2 and RAD51, and DNA end resection in G0 cells even in the presence of 53BP1. In contrast to 53BP1-deficiency, DNA end resection in LIN37-deficient G0 cells depends on BRCA1 and leads to RAD51 filament formation and HR. LIN37 is not required to protect DNA ends in cycling cells at G1-phase. Thus, LIN37 regulates a novel 53BP1-independent cell phase-specific DNA end protection pathway that functions uniquely in quiescent cells.

cell biology↗

bioRxiv2019

Acute Myeloid Leukemia Driven by the CALM-AF10 Fusion Gene is Dependent on BMI1

A subset of acute myeloid and lymphoid leukemia cases harbor a t(10;11)(p13;q14) translocation resulting in the CALM-AF10 fusion gene. Standard chemotherapeutic strategies are often ineffective in treating patients with CALM-AF10 fusions. Hence, there is an urgent need to identify molecular pathways dysregulated in CALM-AF10-positive leukemias which may lay the foundation for novel targeted therapies. Here we demonstrate that the Polycomb Repressive Complex 1 gene BMI1 is consistently overexpressed in adult and pediatric CALM-AF10-positive leukemias. We demonstrate that genetic Bmi1 depletion abrogates CALM-AF10-mediated transformation of murine hematopoietic stem and progenitor cells (HSPCs). Furthermore, CALM-AF10-positive murine and human AML cells are profoundly sensitive to the small-molecule BMI1 inhibitor PTC209 as well as to PTC596, a compound in clinical development that has been shown to result in downstream degradation of BMI1 protein. PTC-596 significantly prolongs survival of mice injected with a human CALM-AF10 cell line in a xenograft assay. In summary, these results validate BMI1 as a bonafide candidate for therapeutic targeting in AML with CALM-AF10 rearrangements.

cancer biology↗