Biology subjects

Hickey, T.

Publications and source records attributed to Hickey, T..

5 recordsLinked to original sources

bioRxiv2025

The transcription factor AP-2β defines active enhancers conferring molecular apocrine cell identity in breast cancer

The transcription factor Activating Protein 2{beta} (TFAP2B; AP-2{beta}) is a candidate marker for the molecular apocrine subtype of breast cancer, which lacks expression of the estrogen receptor alpha (ESR1; ER) but sustains a luminal breast cancer phenotype due to the presence of key luminal lineage transcription factors (GATA3, FOXA1) and activity of the androgen receptor (AR). Our objective was to better understand the expression patterns and molecular function of AP-2{beta} in breast cancer. Using multiple clinical cohorts, we show that high TFAP2B expression was associated with low proliferation in ER positive (ER+) breast cancers of ductal and lobular histology, but with enrichment for lobular tumours. High TFAP2B was also evident in high proliferation tumours lacking ER, with no specific enrichment for lobular histology. Restoring AP-2{beta} expression to highly proliferative ER+ breast cancer cell lines that lack it strongly induced apoptosis. Conversely, reducing AP-2{beta} expression in a molecular apocrine breast cancer cell line model potently inhibited proliferation and cell viability associated with downregulation of MYC oncogene expression. To identify genomic determinants of AP-2{beta} function in molecular apocrine cells in relation to other known transcriptional regulators, we performed chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) for AP-2{beta}, AR, GATA3, FOXA1, and acetylated lysine 27 in histone 3 (H3K27ac, a marker of active enhancers and promoters). When present alone, AP-2{beta} was preferentially enriched at active promotors. Enhancers bound by AR, GATA3 and FOXA1 were more active when AP-2{beta} was present and genes that define the molecular apocrine phenotype were significantly more likely to have active enhancers co-occupied by all four transcription factors. We conclude that AP-2{beta} plays a context-dependent role in breast cancer and propose that activation of enhancers defining molecular apocrine identity is a key function of AP-2{beta} in the biology of this subtype of breast cancer.

cancer biology↗

bioRxiv2024

Androgen stimulation rapidly reorganizes temporal 3D genome and epigenome states to trigger AR-mediated transcription in prostate cancer.

Androgen receptor (AR)-mediated transcription drives prostate cancer progression and remains a critical therapeutic target. AR activation by androgens triggers nuclear translocation, DNA binding at AR regulatory elements (AREs) and transcription initiation. This process involves co-factors such as FOXA1, epigenetic modifications, and 3D chromatin interactions. However, the temporal coordination of these events during AR-mediated transcription remains poorly understood. Using a time-course androgen stimulation model in prostate cancer cells, we integrated temporal multi-omics data within the MOFA+ framework to dissect AR-mediated transcriptional dynamics. Our analysis revealed that rapid AR binding at gene promoters is crucial for initiating nascent transcription of AR target genes. We identified H3K27 acetylation at flanking AREs, pre-marked by constitutive FOXA1 binding, occurs prior to AR recruitment. Additionally, androgen stimulation induced a temporal early shift in nascent transcription from MYC to AR target genes, associated with transient disruption of 3D chromatin interactions. Finally, we showed that CRISPR-mediated inhibition of AR-associated chromatin contacts suppresses distal linked target genes, demonstrating that dynamic genome architecture is functionally required for AR-driven transcription. Together these findings uncover the dynamic reorganization of 3D chromatin structure and transcription factor binding post-androgen stimulation, resulting in distinct temporal epigenomic states. This work provides new insights into the mechanisms governing AR-mediated transcriptional activation in prostate cancer and highlights the interplay between MYC and AR in regulating transcription in hormone-driven cancers.

genomics↗

bioRxiv2021

Epigenetic therapy suppresses endocrine-resistant breast tumour growth by re-wiring ER-mediated 3D chromatin interactions

Three-dimensional (3D) epigenome remodelling is an important mechanism of gene deregulation in cancer. However, its potential as a target to overcome therapy resistance remains largely unaddressed. Here we show that FDA-approved epigenetic therapy Decitabine (5-Aza-mC) suppresses tumour growth in preclinical metastatic ER+ breast tumour xenograft models. Decitabine-induced genome-wide DNA hypomethylation results in large-scale 3D epigenome deregulation, including de-compaction of higher order chromatin structure and loss of topologically associated domain boundary insulation. Significant DNA hypomethylation at ER-enhancer elements was associated with gain in ER binding, creation of ectopic 3D enhancer-promoter interactions and concordant activation of ER-mediated transcription pathways. Importantly long-term withdrawal of epigenetic therapy partially restores methylation at ER-enhancer elements, resulting in loss of ectopic 3D enhancer-promoter interactions and associated gene repression. Our study illustrates how epigenetic therapy has potential to target ER+ endocrine-resistant breast cancer by DNA methylation-dependent rewiring of 3D chromatin interactions associated with suppression of tumour growth.

molecular biology↗

bioRxiv2019

MicroRNA-194 promotes lineage plasticity in advanced prostate cancer

MicroRNA-194 (miR-194) promotes prostate cancer metastasis, but the precise molecular mechanisms by which it achieves this are unknown. Here, by integrating Argonaute high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (Ago-HITS-CLIP) with RNA sequencing and exon-intron split analysis, we defined a 163-gene miR-194 \"targetome\" in prostate cancer. These target genes were predominantly down-regulated through canonical 3UTR recognition sites and were enriched within pathways involved in cytoskeletal organisation and cell movement. In clinical prostate cancer samples, miR-194 activity was inversely correlated with the androgen receptor (AR) signalling axis. At a mechanistic level, this inverse correlation was explained by down-regulation of miR-194 expression by AR. Accordingly, miR-194 expression and activity was significantly elevated in neuroendocrine prostate cancer (NEPC), an aggressive AR-independent disease subtype. MiR-194 enhanced the transdifferentiation of prostate adenocarcinoma cells to a neuroendocrine-like state, at least in part by targeting FOXA1, a transcription factor with a key role in maintaining the prostate epithelial lineage. Importantly, a miR-194 inhibitor effectively inhibited the growth of cell lines and patient-derived organoids with neuroendocrine features. Overall, our study reveals a novel post-transcriptional mechanism regulating the plasticity of prostate cancer cells and provides a rationale for targeting miR-194 in this NEPC.

cancer biology↗

bioRxiv2019

A real-time PCR for the differentiation of typhoidal and non-typhoidal Salmonella

Rapid and accurate differentiation of Salmonella spp. causing enteric fever from non-typhoidal Salmonella is essential for clinical management of cases, laboratory risk management and implementation of public health measures. Current methods used for confirmation of identification including biochemistry and serotyping as well as whole genome sequencing analyses, takes several days. Here we report the development and evaluation of a real-time PCR assay that can be performed directly on crude DNA extracts from bacterial colonies, for the rapid identification of typhoidal and non-typhoidal Salmonella. This novel two-hour assay identifies the genus Salmonella by detecting the ttr gene, encoding tetrathionate reductase, and defines typhoidal Salmonella by the detection of S. Typhi and Paratyphi-specific gene combinations. PCR assay performance was determined using 211 clinical cultures of Salmonella (114 non-typhoidal and 97 Typhoidal strains) and 7 clinical non-Salmonella cultures. In addition, the specificity of the assay was evaluated in silico using a diverse in-house collection of 1882 Salmonella whole genome sequences. The real-time PCR results for 218 isolates and the genomic analysis of the 1882 isolates produced 100% sensitivity and 100% specificity (based on a 7 gene profile) for identifying typhoidal Salmonella compared to the Salmonella whole genome sequening identification methods currently used at Public Health England. This paper describes a robust real-time PCR assay for the rapid, accurate identification of typhoidal and non-typhoidal Salmonella which will be invaluable for the urgent screening of isolates from symptomatic individuals, the safe processing of isolates in laboratories and for assisting the management of public health risks.

microbiology↗