Biology subjects

Bamford, R.

Publications and source records attributed to Bamford, R..

6 recordsLinked to original sources

bioRxiv2026

Cell-type-resolved DNA methylation profiling in the cortex reveals female-specific X chromosome differences in autism

Sex differences are a prominent feature of many neurodevelopmental conditions, particularly autism for which approximately three males are diagnosed for every female. Although epigenetic dysregulation has been implicated in autism, the extent to which autism-associated epigenetic differences vary by sex and neural cell type remains poorly understood. Using fluorescence-activated nuclei sorting (FANS), we isolated neuron-enriched (NeuN+), oligodendrocyte-enriched (SOX10+), microglia-enriched (IRF8+) and astrocyte-enriched (NeuN-/SOX10-/IRF8-) nuclei from post-mortem prefrontal cortex tissue from 24 autistic (70.8% male) and 23 non-autistic (69.6% male) donors, and performed cell-type-resolved epigenome-wide association studies (EWASs) of DNA methylation. We identified cell-type-specific autism-associated differentially methylated positions (DMPs), with microglia harbouring the largest number of associations. Modelling the interaction between sex and diagnosis revealed a striking female-specific signature concentrated on the X chromosome in microglia. At the majority of these sex-by-autism DMPs, autistic females showed lower DNA methylation compared to control females consistent with an altered X chromosome inactivation (XCI) profile. Across the X chromosome, autism-associated DNA methylation differences were significantly larger in females than males and were greater at sites annotated to genes normally subject to XCI than at genes that escape XCI. Together, these data further support the importance of microglia in autism and suggest that altered X chromosome dosage regulation may contribute to sex-dependent molecular mechanisms in autism.

genomics↗

bioRxiv2025

Modulating splicing in five prime untranslated regions to treat rare haploinsufficient disease

Rare genetic disorders collectively impact over 300 million people worldwide, yet around 95% have no specific treatments. For the many rare disorders caused by haploinsufficiency, effective therapies need to upregulate protein expression. However, therapeutic upregulation is often not straightforward. Increasing protein translation of the wildtype allele through inhibiting repressive upstream open reading frames (uORFs) has been proposed as a therapeutic approach for a few specific genes. The widespread success of steric-block antisense oligonucleotides (ASOs) for this purpose is, however, debated. Here, we explore an alternative approach, using splice-switching to exclude uORF-containing exons from the mRNA. Through a genome-wide computational screening approach, we identified 79 uORF-containing 5UTR exons in haploinsufficient monogenic disease genes as candidate exon skipping targets. We demonstrate that removing the target exon significantly increased protein translation (between 1.4-5.5 fold) in a luciferase reporter assay for four of six prioritised target 5UTR exons in neurodevelopmental disorder genes (CTCF, GRIN2B, KRIT1, and TSC1). Overall, this work supports the widespread application of 5UTR exon skipping to boost translation of clinically relevant haploinsufficient genes.

genomics↗

bioRxiv2025

Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex

The human cortex undergoes extensive epigenetic remodelling during development, although the precise temporal and cell-type-specific dynamics of DNA methylation remain incompletely understood. In this study, we profiled genome-wide DNA methylation across human cortex tissue from donors aged 6 post-conception weeks (pcw) to 108 years of age. We observed widespread, developmentally regulated, changes in DNA methylation, with pronounced shifts occurring during early- and mid-gestation that were distinct from age-associated modifications in the postnatal cortex. Using fluorescence-activated nuclei sorting (FANS), we optimized a protocol for the isolation of SATB2-positive neuronal nuclei, enabling the identification of cell-type-specific DNA methylation trajectories in developing neuronal and non-neuronal populations. Developmentally dynamic DNA methylation sites were significantly enriched near genes implicated in autism and schizophrenia, supporting a role for epigenetic dysregulation in neurodevelopmental disorders. Our findings underscore the prenatal period as a critical window of epigenomic plasticity in the central nervous system with important implications for understanding the genetic basis of neurodevelopmental phenotypes.

genomics↗

bioRxiv2024

An atlas of expressed transcripts in the prenatal and postnatal human cortex

Alternative splicing is a post-transcriptional mechanism that increases the diversity of expressed transcripts and plays an important role in regulating gene expression in the developing central nervous system. We used long-read transcriptome sequencing to characterise the structure and abundance of full-length transcripts in the human cortex from donors aged 6 weeks post-conception to 83 years old. We identified thousands of novel transcripts, with dramatic differences in the diversity of expressed transcripts between prenatal and postnatal cortex. A large proportion of these previously uncharacterised transcripts have high coding potential, with corresponding peptides detected in proteomic data. Novel putative coding sequences are highly conserved and overlap de novo mutations in genes linked with neurodevelopmental disorders in individuals with relevant clinical phenotypes. Our findings underscore the potential of novel coding sequences to harbor clinically relevant variants, offering new insights into the genetic architecture of human disease. Our cortical transcript annotations are available as a resource to the research community via an online database.

genomics↗

bioRxiv2023

Regulation of astrocyte metabolism by mitochondrial translocator protein 18kDa

The mitochondrial translocator protein 18kDa (TSPO) has been linked to a variety of functions from steroidogenesis to regulation of cellular metabolism and is an attractive therapeutic target for chronic CNS inflammation. Studies in the periphery using Leydig cells and hepatocytes, as well as work in microglia, indicate that the function of TSPO may vary between cells depending on their specialised roles. Astrocytes are critical for providing trophic and metabolic support in the brain as part of their role in maintaining brain homeostasis. Recent work has highlighted that TSPO expression increases in astrocytes under inflamed conditions and may drive astrocyte reactivity. However, relatively little is known about the role TSPO plays in regulating astrocyte metabolism and whether this protein is involved in immunometabolic processes in these cells. Using TSPO-deficient (TSPO-/-) mouse primary astrocytes in vitro (MPAs) and a human astrocytoma cell line (U373 cells), we performed metabolic flux analyses. We found that loss of TSPO reduced basal astrocyte respiration and increased the bioenergetic response to glucose reintroduction following glucopenia, while increasing fatty acid oxidation (FAO). Lactate production was significantly reduced in TSPO-/- astrocytes. Co-immunoprecipitation studies in U373 cells revealed that TSPO forms a complex with carnitine palmitoyltransferase 1a, which presents a mechanism wherein TSPO may regulate FAO in astrocytes. Compared to TSPO+/+ cells, inflammation induced by 3h lipopolysaccharide (LPS) stimulation of TSPO-/- MPAs revealed attenuated tumour necrosis factor release, which was enhanced in TSPO-/- MPAs at 24h LPS stimulation. Together these data suggest that while TSPO acts as a regulator of metabolic flexibility in astrocytes, loss of TSPO does not appear to modulate the metabolic response of astrocytes to inflammation, at least in response to the stimulus/time course used in this study.

neuroscience↗

bioRxiv2022

The Vaccinia virus chondroitin sulfate binding protein drives host membrane curvature to facilitate fusion

Virus binding serves to define virus tropism and species specificity1. Virus binding proteins are classically considered as facilitators of cell surface attachment prior to receptor engagement and virus internalization. For efficient entry vaccinia virus (VACV) - the prototypic poxvirus - relies on four binding proteins and an eleven-protein entry fusion complex (EFC)2. We recently demonstrated that VACV binding and fusion proteins are organized into distinct functional domains, with localization of EFC proteins to virion tips directly influencing membrane fusion activity3. However, the relationship between virus binding protein distribution, virion binding orientation and subsequent membrane fusion remain unexplored. Here, we show that virus binding proteins guide side-on virion binding and promote curvature of the host membrane towards EFC-containing virion tips to facilitate virus fusion. Using a cell-derived membrane-bleb model system together with super-resolution and electron microscopy we found that side-bound VACV virions induce membrane invagination in the presence of low pH. Repression or deletion of individual binding proteins revealed that three of four contribute to binding orientation, amongst which the chondroitin sulphate binding protein, D8, is required for host membrane bending. Consistent with low-pH dependent macropinocytic entry of vaccinia virus4,5, loss of D8 prevents virion-associated macropinosome membrane bending, disrupts fusion pore formation and infection kinetics. Our results extend the role of viral binding proteins from mere attachment factors to active participants in successful viral membrane fusion and further illustrate the influence of virus protein architecture on successful infection.

microbiology↗