Biology subjects

Czarnecki, J.

Publications and source records attributed to Czarnecki, J..

4 recordsLinked to original sources

bioRxiv2026

Global signatures of Ribonucleotide Excision Repair deficiency and its therapeutic vulnerabilities

Cancer therapies increasingly exploit DNA repair deficiencies, yet many clinically actionable repair-deficient states remain undetectable because they lack robust biomarkers and are not identifiable through gene-based diagnostics. Here, we show that deficiency of ribonucleotide excision repair (RER), a pathway that removes misincorporated ribonucleotides from genomic DNA, generates a distinct genome-wide mutational phenotype comprising characteristic insertion-deletion, substitution, and structural variation signatures. Using these features, we developed RERDetect, a whole-genome classifier that identifies RER-deficient tumors across diverse cancer types. Application of RERDetect to more than 11,000 primary and metastatic cancers revealed a recurrent subset of tumors with evidence of RER deficiency, the majority lacking detectable genetic alterations in RNASEH2 genes. We identified promoter hypermethylation of RNASEH2C as a recurrent mechanism of pathway inactivation. RER-deficient cells exhibited distinct vulnerabilities, including sensitivity to EXO1 and FANCM inhibition. These findings establish RER deficiency as a previously unrecognized and therapeutically actionable DNA repair-deficient state in cancer, demonstrating the power of mutational scars to identify clinically relevant tumor phenotypes that evade conventional genomic diagnostics.

genomics↗

bioRxiv2026

Mutational and functional heterogeneity of homology-directed repair deficiency and clinical implications

Homology-directed repair deficiency (HRd) encompasses mutations in multiple genes yet is treated clinically as a single entity. Here, through parallel analyses of isogenic knockouts of multiple HR pathway genes, integrating multi-omic analyses with genome-wide CRISPR-Cas9-dependency and resistance screens, we show that HRd is not a single entity but exists along a molecular and functional continuum. BRCA1, BRCA2, PALB2, RAD51C, and RAD51D mutants shared many HRd-associated mutational signatures, while RAD51B, BRIP1, CDK12 exhibited distinct genomic patterns. Functional heterogeneity was equally apparent: synthetic lethal interactions including CIP2A and a novel dependency on PRDX1 were penetrant across most HRd genotypes, whereas FANCM dependency was linked to HRd subtypes characterized by tandem duplications. PARPi resistance screens in distinct HRd contexts uncovered BRIP1 and RECQL5 as new BRCA2-specific resistance genes. HRd is thus a complex continuum, underscoring why modernizing the molecular taxonomy utilizing all genomic features available per patient is crucial to informing precision interventions.

genomics↗

bioRxiv2026

Anopheles resistance to deltamethrin can be caused by the increased abundance of an enteric Aeromonas taxon

The enteric bacteriome of Anopheles mosquito vector has been linked with its vectorial competence, however, its influence on insecticide resistance is poorly understood. We found that the depletion of the bacterial microbiome in susceptible Anopheles strains, resulting from antibiotic treatment, led to greater than 50% insecticide deltamethrin tolerance compared to untreated mosquitoes. Simultaneous inhibition of cytochrome P450 activity reverted the antibiotic-induced tolerance phenotype, indicating that the antibiotic-induced deltamethrin tolerance is P450-dependent. We found that the antibiotic treatment, while suppressing most enteric bacterial taxa, allowed proliferation of a particular antibiotic-tolerant Aeromonas taxon, most closely related to Aeromonas hydrophila. Increasing the abundance of this taxon in mosquitoes not treated with antibiotics phenocopied the tolerance phenotype, converting deltamethrin-susceptible Anopheles to deltamethrin-tolerant mosquitoes. Collectively, these results highlight a mechanistic interplay in Anopheles mosquitoes between antibiotic-induced enteric dysbiosis and cytochrome P450-mediated detoxification that promotes insecticide tolerance. This effect could influence mosquito vectorial capacity, especially in Africa, where auto-medication with antibiotics is highly prevalent.

microbiology↗

bioRxiv2025

Replication coordination marks the domestication of large extrachromosomal replicons in bacteria

Bacterial genomes often include extrachromosomal replicons (ERs), ranging from small plasmids to nearly chromosome-sized elements, that foster genome plasticity and adaptation. Despite their prevalence, the mechanisms underlying ER domestication and their long-term adaptation within bacterial hosts remain largely unexplored. By analyzing over 40,000 complete bacterial genomes, we identified two main ER categories: small ERs with diverse GC content and large ERs ([≥]10% the size of the main chromosome) that closely match the GC content of the chromosome. Across multiple phyla, marker frequency analyses showed that large ERs maintain a 1:1 copy number with the chromosome. Another key finding of this study is that large ERs terminate replication in synchrony with the chromosome. Hi-C contact maps revealed consistent ori-ori interactions between chromosomes and ERs. In large ERs, inter-replichore and ter-ter interactions, along with the recruitment of key chromosomal segregation motifs, suggest the co-option of chromosome-associated replication and segregation machineries. Together, our findings indicate that as ERs become larger, they become increasingly reliant on chromosome-driven processes for stable inheritance, potentially explaining why they do not exceed the size of the chromosome.

microbiology↗