Biology subjects

Barnes, D.

Publications and source records attributed to Barnes, D..

7 recordsLinked to original sources

bioRxiv2025

Enhancement of activation-induced T cell proliferation by SIRPG in a CD47-independent manner

SIRPG, a primate-specific type 1 transmembrane protein in the Signal Regulatory Protein (SIRP) family, is predominantly expressed in T cells. It contains a short cytoplasmic domain, which does not contain any known signaling motif, and its only known ligand is CD47. Several genetic variations in SIRPG, including the V263A (rs6043409) polymorphism, linked to increased type 1 diabetes risk, highlight its potential importance. However, its expression and physiological role remain largely unclear due to its absence in rodents. Here, we demonstrate that SIRPG and GzmB exhibit near mutually exclusive expression in resting peripheral CD8+ T cells. We further show that SIRPG serves as a valuable marker for GzmK-expressing CD8+ T cells in peripheral blood and inflamed synovial fluid and that its expression in both CD4+ and CD8+ T cells is upregulated by anti-CD3 stimulation, with further enhancement by the TNF inhibitor adalimumab, but not certolizumab. While SIRPG ablation minimally affects T cell activation and IFN{gamma}/TNF production, it impairs the expression of mitosis-regulating genes like UBE2C and TOP2A, leading to reduced proliferation, and alters the expression of certain activation-induced surface molecules, including CRTAM. Notably, SIRPG-mediated proliferation and CRTAM expression are cell-autonomous and CD47-independent. Structural and functional analyses reveal that SIRPG-driven proliferation is independent of its extracellular D1 domain, not significantly affected by the V263 variant, but dependent on its cytoplasmic domain. Collectively, our findings offer novel insights into the expression, function, and mechanism of action of SIRPG in T cells.

immunology↗

bioRxiv2024

Id1, Spp1 and Pak3 are biomarkers of Smad4 and TGF-β1 dependency in conditional intestinal adenoma, organoids and colorectal cancer.

TGF-{beta} ligand activation suppresses cell growth yet can paradoxically and potently promote cancer invasion and metastasis depending on downstream pathway mutational context. Here, we evaluated the basis of this observation in conditional murine intestinal adenoma models with and without loss of Mothers against decapentaplegic homolog 4 (Smad4), with the aim of identifying TGF-{beta}-BMP-SMAD4 pathway dependent gene expression biomarkers for translational application. Conditional Lgr5-CreERT2 activation in Apcfl/flSmad4fl/flresulted in adenoma formation with recombined homozygote floxed alleles (Apc{Delta}/{Delta}Smad4{Delta}/{Delta}). The adenoma phenotype was discordant, with a reduced small intestinal adenoma burden yet development of large non-metastatic caecal adenoma with nuclear localisation of phospho-Smad2/3. Derived Apc{Delta}/{Delta}Smad4{Delta}/{Delta} adenoma organoids resisted TGF-{beta}1 dose dependent growth arrest and cell death (IC50 534pM) compared to Apc{Delta}/{Delta}Smad4+/+ (IC 24pM). TGF-{beta}1 (390pM) modified adenoma mRNA expression (bulk RNA-Seq) most significantly for Id1low and Spp1high in Apc{Delta}/{Delta}Smad4{Delta}/{Delta}. Single cell RNAseq of caecal adenoma identified expansion of Lgr5low, Pak3high and Id1low progenitor populations in Apc{Delta}/{Delta}Smad4{Delta}/{Delta}. Of the 76 Smad4 and TGF-{beta}1 dependent genes identified in adenoma organoids, 7 human equivalent genes were also significantly differentially expressed in colorectal cancer, including ID1low, SPP1high and PAK3high that also correlated with poorer survival (TCGA cohorts). Murine conditional models identified Smad4 loss of function mRNA expression biomarkers that require further evaluation as functional classifiers of colorectal cancer subtypes.

cancer biology↗

bioRxiv2022

Characterization of a KDM5 Small Molecule Inhibitor with Antiviral Activity against Hepatitis B Virus

Chronic hepatitis B (CHB) is a global health care challenge and a major cause of liver disease. To find new therapeutic avenues with a potential to functionally cure chronic Hepatitis B virus (HBV) infection, we performed a focused screen of epigenetic modifiers to identify replication inhibitors. From this work we identified isonicotinic acid inhibitors of the histone lysine demethylase 5 (KDM5) with potent anti-HBV activity. To enhance the cellular permeability and liver accumulation of the most potent KDM5 inhibitor identified (GS-080) an ester prodrug was developed (GS-5801) that resulted in improved bioavailability and liver exposure as well as an increased H3K4me3:H3 ratio on chromatin. GS-5801 treatment of HBV-infected primary human hepatocytes inhibited HBV replication and antigen levels. Evaluation of GS-5801 antiviral activity in a humanized mouse model of HBV infection, however, did not result in antiviral efficacy, despite achieving pharmacodynamic levels of H3K4me3:H3 predicted to be efficacious from the in vitro model. Here we discuss potential reasons for the disconnect between in vitro and in vivo efficacy, which highlight the translational difficulties of epigenetic targets for viral diseases.

pharmacology and toxicology↗

bioRxiv2019

Genome-wide association study identifies 32 novel breast cancer susceptibility loci from overall and subtype-specific analyses

Breast cancer susceptibility variants frequently show heterogeneity in associations by tumor subtype. To identify novel loci, we performed a genome-wide association study (GWAS) including 133,384 breast cancer cases and 113,789 controls, plus 18,908 BRCA1 mutation carriers (9,414 with breast cancer) of European ancestry, using both standard and novel methodologies that account for underlying tumor heterogeneity by estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status and tumor grade. We identified 32 novel susceptibility loci (P<5.0x10-8), 15 of which showed evidence for associations with at least one tumor feature (false discovery rate <0.05). Five loci showed associations (P<0.05) in opposite directions between luminal- and non-luminal subtypes. In-silico analyses showed these five loci contained cell-specific enhancers that differed between normal luminal and basal mammary cells. The genetic correlations between five intrinsic-like subtypes ranged from 0.35 to 0.80. The proportion of genome-wide chip heritability explained by all known susceptibility loci was 37.6% for triple-negative and 54.2% for luminal A-like disease. These findings provide an improved understanding of genetic predisposition to breast cancer subtypes and will inform the development of subtype-specific polygenic risk scores.

genetics↗

bioRxiv2019

Chromatin interactome mapping at 139 independent breast cancer risk signals

Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression. We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 independent breast cancer risk signals, and explore the functional mechanism underlying altered risk at the 12q24 risk region. Our results demonstrate the power of combining genetics, computational genomics and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.

molecular biology↗

bioRxiv2019

Fine-mapping of 150 breast cancer risk regions identifies 178 high confidence target genes

Genome-wide association studies have identified breast cancer risk variants in over 150 genomic regions, but the mechanisms underlying risk remain largely unknown. These regions were explored by combining association analysis with in silico genomic feature annotations. We defined 205 independent risk-associated signals with the set of credible causal variants (CCVs) in each one. In parallel, we used a Bayesian approach (PAINTOR) that combines genetic association, linkage disequilibrium, and enriched genomic features to determine variants with high posterior probabilities (HPPs) of being causal. Potentially causal variants were significantly over-represented in active gene regulatory regions and transcription factor binding sites. We applied our INQUSIT pipeline for prioritizing genes as targets of potentially causal variants, using gene expression (eQTL), chromatin interaction and functional annotations. Known cancer drivers, transcription factors and genes in the developmental, apoptosis, immune system and DNA integrity checkpoint gene ontology pathways, were over-represented among the 178 highest confidence target genes.

genetics↗

bioRxiv2018

Shared heritability and functional enrichment across six solid cancers

Quantifying the genetic correlation between cancers can provide important insights into the mechanisms driving cancer etiology. Using genome-wide association study summary statistics across six cancer types based on a total of 296,215 cases and 301,319 controls of European ancestry, we estimate the pair-wise genetic correlations between breast, colorectal, head/neck, lung, ovary and prostate cancer, and between cancers and 38 other diseases. We observed statistically significant genetic correlations between lung and head/neck cancer (rg=0.57, p=4.6x10-8), breast and ovarian cancer (rg=0.24, p=7x10-5), breast and lung cancer (rg=0.18, p=1.5x10-6) and breast and colorectal cancer (rg=0.15, p=1.1x10-4). We also found that multiple cancers are genetically correlated with non-cancer traits including smoking, psychiatric diseases and metabolic characteristics. Functional enrichment analysis revealed a significant excess contribution of conserved and regulatory regions to cancer heritability. Our comprehensive analysis of cross-cancer heritability suggests that solid tumors arising across tissues share in part a common germline genetic basis.

genomics↗