Biology subjects

Raschle, M.

Publications and source records attributed to Raschle, M..

4 recordsLinked to original sources

bioRxiv2025

Mitotic BLM functions are required to maintain genomic stability

The BLM helicase is a critical genome maintenance protein involved in diverse cellular processes including DNA replication, repair, transcription, and chromosome segregation. During mitosis, it cooperates with the PICH helicase and topoisomerases to resolve ultrafine DNA bridges (UFBs) - non-chromatinized DNA structures that link sister chromatids - through a mechanism that is not yet fully understood. Here we tagged endogenous BLM and PICH with fluorescent proteins and BLM with an auxin-inducible degron to generate a cell model system that enables temporal tracking of UFB dynamics in the presence or absence of BLM. Time-resolved lattice light sheet microscopy established the dynamic localization patterns of BLM and PICH throughout the cell cycle. While BLM cycles between PML bodies and DNA repair foci in interphase, it dissociates from chromatin at the mitotic entry, and re-associates during anaphase to UFBs as well as to CENP-B-positive mitotic foci. Acute BLM depletion during mitosis increased the fraction of unresolved UFBs, micronuclei containing acentric fragments, binucleation, and resulted in subtle genomic abnormalities detected by single-cell whole genome sequencing. These findings highlight a mitosis-specific role for BLM in UFB resolution and underscore its function in preserving genomic stability. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=87 SRC="FIGDIR/small/659902v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@92d8b2org.highwire.dtl.DTLVardef@d0a915org.highwire.dtl.DTLVardef@10cac60org.highwire.dtl.DTLVardef@108da58_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Explainable Machine Learning Identifies Dosage Compensation Factors in Aneuploid Human Cancer Cells

Aneuploidy, a hallmark of cancer, leads to widespread changes in chromosome copy number, altering the abundance of hundreds or thousands of proteins. How-ever, evidence suggests that levels of proteins encoded on affected chromosomes are often buffered toward their abundances observed in diploid cells. Despite its preval-ence, the molecular mechanisms driving this protein dosage compensation remain largely unknown. It is unclear whether all proteins are buffered to a similar degree, what factors determine buffering, and whether dosage compensation varies across different cell lines or tumor types. Moreover, its potential adaptive advantage and therapeutic relevance remain unexplored. Here, we established a novel approach to quantify protein dosage buffering in a gene copy number-dependent manner, show-ing that dosage compensation is widespread but variable in cancer cell lines and in vivo tumor samples. By developing multifactorial machine learning models, we identify mean gene dependency, protein complex participation, haploinsufficiency, and mRNA decay as key predictors of buffering. We also show that dosage com-pensation can affect oncogenic potential and that higher buffering correlates with reduced proteotoxic stress and increased drug resistance. These findings highlight protein dosage compensation as a crucial regulatory mechanism and a potential therapeutic target in aneuploid cancers.

cancer biology↗

bioRxiv2024

Proteogenomic analysis reveals adaptive strategies to alleviate the consequences of aneuploidy in cancer

Aneuploidy is prevalent in cancer and associates with fitness advantage and poor patient prognosis. Yet, experimentally induced aneuploidy initially leads to adverse effects and impaired proliferation, suggesting that cancer cells must adapt to aneuploidy. We performed in vitro evolution of cells with extra chromosomes and obtained cell lines with improved proliferation and gene expression changes congruent with changes in aneuploid cancers. Integrated analysis of cancer multi-omics data and model cells revealed increased expression of DNA replicative and repair factors, reduced genomic instability, and reduced lysosomal degradation. We identified E2F4 and FOXM1 as transcription factors required for adaptation to aneuploidy in vitro and in cancers and validated this finding. The adaptation to aneuploidy also coincided with specific copy number aberrations that correlate with poor patient prognosis. Chromosomal engineering mimicking these aberrations improved aneuploid cell proliferation, while loss of previously present extra chromosome impaired it. The identified common adaptation strategies suggest replication stress, genomic instability, and lysosomal stress as common liabilities of aneuploid cancers.

genetics↗

bioRxiv2018

The CMG helicase bypasses DNA protein cross-links to facilitate their repair

Covalent and non-covalent nucleoprotein complexes impede replication fork progression and thereby threaten genome integrity. Using Xenopus laevis egg extracts, we previously showed that when a replication fork encounters a covalent DNA-protein cross-link (DPC) on the leading strand template, the DPC is degraded to a short peptide, allowing its bypass by translesion synthesis polymerases. Strikingly, we show here that when DPC proteolysis is blocked, the replicative DNA helicase (CMG), which travels on the leading strand template, still bypasses the intact DPC. The DNA helicase RTEL1 facilitates bypass, apparently by translocating along the lagging strand template and generating single-stranded DNA downstream of the DPC. Remarkably, RTEL1 is required for efficient DPC proteolysis, suggesting that CMG bypass of a DPC normally precedes its proteolysis. RTEL1 also promotes fork progression past non-covalent protein-DNA complexes. Our data suggest a unified model for the replisomes response to nucleoprotein barriers.

biochemistry↗