Biology subjects

Silcocks, M.

Publications and source records attributed to Silcocks, M..

3 recordsLinked to original sources

bioRxiv2026

Structural variation shapes regulatory and evolutionary diversity at the HLA locus

The human leukocyte antigen (HLA) region is among the most polymorphic loci in the human genome and plays a central role in immune function, yet the contribution of structural variation to its genetic and regulatory diversity remains poorly characterised. Using 460 phased, near-complete human genome assemblies from globally diverse populations, we systematically mapped structural variation and gene content across the HLA locus. We show that the HLA region contains substantially more structural variation than any other region of chromosome 6. At the HLA class II locus, all individuals could be assigned to one of 13 distinct HLA-DR-DQ structural haplotypes, whereas the HLA-A region comprised four major haplotypes, which we found to be interspersed among non-human primate lineages. These structural haplotypes exhibit marked differences in population frequency and show increasing allelic diversity over European prehistory. Integration of Iso-Seq and RNA-Seq data revealed that structural haplotypes are associated with differences in HLA gene expression, suggesting that structural variation directly influences immune gene regulation. Together, our results identify structural variation as a key and previously underappreciated contributor to HLA regulatory diversity, with broad functional and evolutionary implications for human immunity. Manuscript summaryStructural variation drives HLA haplotype diversity and gene expression differences across global human populations.

bioinformatics↗

bioRxiv2025

Host oxidative stress primes mycobacteria for rapid antibiotic resistance evolution

The rapid emergence of multidrug-resistant Mycobacterium tuberculosis (Mtb) threatens global TB control, yet the mechanisms enabling rapid evolution of drug resistance in Mtb remain poorly understood. Here we reveal that pre-existing mutations in oxidative stress response genes create permissive genomic backgrounds that accelerate high-level isoniazid resistance (INHR) without fitness costs, challenging the paradigm that resistance mutations always precede their fitness compensatory adaptations. Using M. smegmatis mc2155 (Msm) as a model, we show that brief exposure to sublethal INH (2x IC50) enriches for "low-level resistance and tolerance" (LLRT) mutants in a single step. These LLRT mutants, particularly those with ohrR loss-of-function mutations, acquire high-level resistance (> 500x IC50) at 6-fold higher rates than wildtype, primarily through otherwise-deleterious mycothiol biosynthesis mutations that become tolerable in the oxidative stress-buffered background. Crucially, we demonstrate that sublethal oxidative stress alone, mimicking host immune pressure, nearly tripled the rate of INH resistance evolution in Msm. Bayesian analysis of 1,578 clinical Mtb isolates from Vietnam confirmed that mutations in oxidative stress response genes were significantly associated with the emergence of INHR strains (p-value = 1.09x10-7). Independently, reanalysis of genome-wide CRISPRi screens revealed that the OSR network and high Bayes probability genes are functionally associated with treatment escape and survival with multiple antibiotics, including isoniazid, rifampicin, ethambutol, bedaquiline, vancomycin, clarithromycin, linezolid, and streptomycin. Our findings that host-imposed oxidative stress and inadequate drug penetration may synergistically prime Mtb populations for rapid resistance evolution suggest that targeting pre-resistance mechanisms, such as oxidative stress defenses, could help slow the emergence of antibiotic resistance in tuberculosis.

microbiology↗

bioRxiv2025

Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance

Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis (Mtb), remains a major global health concern. In this study, we harness long-read sequencing technologies and genome graph tools to construct a Mtb pangenome reference graph (PRG) from 859 high-quality, diverse, long-read assemblies. To enable accurate genotyping of SVs leveraging the PRG, we developed miniwalk, a tool that outperforms a traditional linear genome-based approach in precision for SV detection. We characterize patterns of structural variation genome-wide, revealing a virulence-associated ESX-5 deletion to be recurrent across the phylogeny, and fixed in a sub-lineage of L4. Systematic screens for additional genes that are recurrently affected by SVs implicated those related to metal homeostasis, including a copper exporter fixed in the widely distributed L1.2.1 sub-lineage. Lastly, we genotyped 41,134 isolates and found SVs putatively associated with resistance to various first and second-line drugs. These findings underscore the broader role of SVs in shaping Mtb diversity, highlighting their importance in both understanding evolution and designing strategies to combat drug-resistant TB.

genomics↗