Biology subjects

Woolley, C.

Publications and source records attributed to Woolley, C..

3 recordsLinked to original sources

bioRxiv2026

Genetic context drives evolution of divergent antibiotic survival phenotypes in Staphylococcus epidermidis

Effective treatment of infections is a global challenge, complicated by bacterias capacity to endure antibiotics. Survival under drug pressure is often driven by interactions between genetic factors rather than single genes. To investigate the genomics underlying antibiotic survival, we analysed Staphylococcus epidermidis isolates from clinical infections and carriage using high-throughput phenotyping, population genomics, and directed evolution. We observed widespread multidrug resistance, with strong links between specific genomic elements and resistance. All isolates harbouring mecA were resistant to oxacillin, though minimum inhibitory concentrations varied significantly, suggesting modulation by additional genetic factors. Directed evolution revealed potentiating mutations that enhanced oxacillin resistance in mecA+ strains. In mecA-isolates, however, evolution of mutations in the same genes conferred increased survival to oxacillin through antibiotic tolerance. These findings show that antibiotic resistance and tolerance can be genetically connected yet phenotypically distinct, and suggest a complex epistatic genetic landscape that shapes antibiotic survival phenotypes in S. epidermidis.

microbiology↗

bioRxiv2026

DNA methylation signatures of mismatch repair-deficient colorectal cancer

BackgroundColorectal cancer (CRC) is a molecularly heterogeneous disease shaped by both genetic and epigenetic alterations. Approximately 15% of CRCs display widespread CpG island hypermethylation, known as the CpG Island Methylator Phenotype (CIMP). CIMP-high (CIMP-H) tumours frequently exhibit MLH1 promoter hypermethylation, leading to mismatch repair deficiency (MMRd) and microsatellite instability (MSI). However, DNA methylation patterns associated with MSI, independent of CIMP and MLH1 silencing, and the influence of clinical variables such as anatomical location and patient age on the CRC methylome remain poorly characterised. MethodsWe performed epigenome-wide DNA methylation profiling of 259 primary CRC tissue samples using the Illumina EPICv2 array, comparing differential methylation between MSI and microsatellite stable (MSS) CRC, adjusting for tumour purity, MLH1 promoter methylation, CIMP status, and anatomical location, to account for known confounders. We further evaluated the independent effects of anatomical location and patient age on global methylation patterns. ResultsEpigenome-wide differential methylation between MSS and MSI CRC was dominated by MLH1 promoter hypermethylation. After adjusting for MLH1 hypermethylation and CIMP status, we identified a distinct set of 656 CpG sites associated with MMRd independent of MLH1 silencing. These included hypermethylation at LRP6, GSK3{beta}, and CDK12, implicating altered WNT signalling and transcriptional regulation pathways. Comparison of MSI subgroups revealed the co-occurrence of MLH1 hypermethylation with promoter hypermethylation at TXNRD1. Anatomical location showed a strong independent effect on methylation patterns, while we observed only modest effects of patient age on the CRC methylome after adjustment for confounders. ConclusionsWe identified a distinct methylation profile distinguishing MSS and MSI CRC, including MLH1-independent markers of MMRd, as well as novel differentially methylated loci within MSI subgroups. We further showed that anatomical location has a strong independent impact on the CRC methylome. Together, these findings refine the molecular characterisation of CRC and highlight potential epigenetic markers that could inform patient stratification and precision oncology.

cancer biology↗

bioRxiv2019

A CRISPR Knockout Screen Identifies Foxf1 as a Suppressor of Colorectal Cancer Metastasis That Acts Through Reduced mTOR Signalling

IntroductionA greater understanding of molecular mechanisms underlying metastasis is necessary for development of new strategies to prevent and treat cancer.\n\nMethodsWe performed a genome-wide CRISPR/Cas9 knockout screen in MC38 colorectal cancer (CRC) cells transplanted orthotopically into mice to identify genes that promote metastasis. We undertook focussed molecular analyses to identify mechanisms underlying metastasis.\n\nResultsThe screen identified several gene knockouts over-represented in lung metastases, including Dptor (mTOR signalling) and Foxf1 (gastrointestinal tumour predisposition). We validate that loss of Foxf1 promotes metastasis, increased Foxf1 expression restrained cellular migration in-vitro and human CRC metastases express lower Foxf1 than paired primary tumours. Analysis of gene expression changes downstream of Foxf1 identified increased mTOR signalling as a possible mechanism of metastasis caused by Foxf1 loss, consistent with Dptor identification. We confirmed this mechanism demonstrating that mTOR inhibitor sirolimus reduced lung metastasis burden in xenografts.\n\nConclusionMesenchymal Foxf1 plays a major role in intestinal development. We have shown for the first time, through an unbiased genetic screen, that reduced epithelial Foxf1 results in raised mTOR signalling and metastasis.\n\nAuthorship statementLennard Lee-study concept and design, acquisition of data, analysis, interpretation of data, drafting of the manuscript, statistical analysis and obtained funding. Connor Woolley-acquisition of data, analysis and interpretation of data. Thomas Starkey-acquisition of data, analysis, interpretation of data, drafting of the manuscript. Luke Freeman-Mills-interpretation of data. Andrew Bassett-technical and material support. Fanny Fanchini-technical support. Lai Mun Wang-acquisition of data and study supervision. Annabelle Lewis-study supervision. Roland Arnold-analysis, interpretation of data, statistical analysis. Ian Tomlinson-study supervision and critical revision of the manuscript.\n\nConflict of InterestThe authors whose names are listed above declare that they have no conflict of interest.

cancer biology↗