Lay, E. | bioRxiv Science

bioRxiv2024

YAP engages RIF1 to dampen replication stress in squamous cell carcinoma.

Squamous cell carcinoma cells experience high levels of replication stress due to oncogene-induced cell cycle deregulation. How such cells sustain rapid proliferation despite replication stress is still not fully understood. Here, we discovered, using rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) analysis, that the squamous cell carcinoma oncoprotein YAP engages with RIF1, a key regulator of DNA replication and DNA damage repair under replication stress. RIF1 is highly expressed in human squamous cell carcinoma cell lines and tissues and upregulated during tumour progression. Depletion of RIF1 in squamous cell carcinoma cells exacerbates their endogenous replication stress. Mechanistically, we show that YAP interacts with RIF1 specifically at broken replication forks, and that YAP depletion impairs DNA damage repair under replication stress. Our results thus demonstrate that YAPs oncogenic functions in squamous cancers involve both transcriptional and non-transcriptional mechanisms, the latter through interaction with RIF1 to dampen replication stress.

cancer biology↗

bioRxiv2021

HAM-ART: An optimised culture-free Hi-C metagenomics pipeline for tracking antimicrobial resistance genes in complex microbial communities.

Shotgun metagenomics is a powerful tool to identify antimicrobial resistance (AMR) genes in microbiomes but has the limitation that extrachromosomal DNA, such as plasmids, cannot be linked with the host bacterial chromosome. Here we present a laboratory and bioinformatics pipeline HAM-ART (Hi-C Assisted Metagenomics for Antimicrobial Resistance Tracking) optimised for the generation of metagenome-assembled genomes including both chromosomal and extrachromosomal AMR genes. We demonstrate the performance of the pipeline in a study comparing 100 pig faecal microbiomes from low- and high-antimicrobial use pig farms (organic and conventional farms). We found significant differences in the distribution of AMR genes between low- and high-antimicrobial use farms including a plasmid-borne lincosamide resistance gene exclusive to high-antimicrobial use farms in three species of Lactobacilli. Author SummaryAntimicrobial resistance (AMR) is one of the biggest global health threats humanity is facing. Understanding the emergence and spread of AMR between different bacterial species is crucial for the development of effective countermeasures. In this paper we describe a user-friendly, affordable and comprehensive (laboratory and bioinformatics) workflow that is able to identify, associate and track AMR genes in bacteria. We demonstrate the efficiency and reliability of the method by comparing 50 faecal microbiomes from pig farms with high-antibiotic use (conventional farms), and 50 faecal microbiomes from pig farms with low-antibiotic use (organic farms). Our method provides a novel approach to resistance gene tracking, that also leads to the generation of high quality metagenomic assembled genomes that includes genes on mobile genetic elements, such as plasmids, that would not otherwise be included in these assembled genomes.

bioinformatics↗