Biology subjects

Edwards, J. R.

Publications and source records attributed to Edwards, J. R..

10 recordsLinked to original sources

bioRxiv2025

HER2; p53 Co-mutated Cancers Show Increased Histone Acetylation and are Sensitive to Neratinib plus Trastuzumab Deruxtecan.

In metastatic breast cancer, HER2-activating mutations often co-occur with TP53 mutations, a combination linked to poor response to neratinib and worse prognosis. To model this clinical challenge, we bred HER2 V777L transgenic mice with two TP53 mutant alleles: TP53 R172H (the murine homolog of human TP53 R175H) and TP53fl/fl, which mimics p53 truncations common in human tumors. TP53 mutations accelerated tumor development and reduced survival in HER2-mutant mice. These co-mutant tumors were resistant to neratinib but remained sensitive to exatecan, the topoisomerase I (TOP1) inhibitor payload in trastuzumab deruxtecan (T-DXd). Mechanistically, TP53 mutant tumors exhibited upregulation of histone acetylation, hypertranscription of DNA repair factors, increased chromatin accessibility, and rendered cells more susceptible to TOP1 inhibitors via G2/M arrest and apoptosis. This vulnerability is dependent on transcriptional activity of TP53 mutations, highlighting a novel strategy to treat HER2;TP53 co-mutant breast cancers using TOP1-targeted therapies. Statement of SignificanceTP53 mutations sensitize HER2-mutant cancers to TOP1 inhibitors via chromatin accessibility and hyper-transcription, supporting combination therapy with neratinib and T-DXd in TP53/HER2 co-mutant breast cancers.

cancer biology↗

bioRxiv2025

TBRS-associated DNMT3A mutations disrupt cortical interneuron differentiation and neuronal networks

Pathogenic mutations in DNMT3A cause Tatton-Brown-Rahman Syndrome (TBRS), a disorder characterized by somatic overgrowth of multiple tissues including the brain and intellectual disability (OGID). Here, we investigated TBRS etiology using new human pluripotent stem cell models, modeling varying levels of TBRS-associated loss of DNMT3A function. We identified lineage-specific overgrowth in TBRS ventral forebrain medial ganglionic eminence (MGE)-like progenitors, due in part to increased signaling through the PIK3/AKT/mTOR pathway that could be modulated to ameliorate this phenotype. By contrast, reduced DNA methylation during MGE-like progenitor differentiation into GABAergic interneurons caused premature expression of neuronal and synaptic genes, triggering precocious neuronal maturation. As a result, TBRS GABAergic neurons exhibited sufficient hyperactivity to alter the development and structure of neuronal networks, likely contributing to the intellectual disability and autism spectrum disorder common to TBRS patients. Together, this work elucidates new roles for DNMT3A-mediated gene repression in human cortical development, identifying critical requirements for regulating GABAergic neuron production and neuronal network function. These findings also support potential relationships between pathogenic mechanisms underlying TBRS and other OGIDs, including PIK3CA-related overgrowth syndrome and Weaver Syndrome, thus providing a foundation for future studies to identify common paradigms to treat these related disorders.

neuroscience↗

bioRxiv2025

Bisphosphonates Trigger Anti-Ageing Effects Across Multiple Cell Types and Protect Against Senescence

Bisphosphonates (BPs) have been the major class of medicines used to treat disorders of excessive bone loss for over five decades. Recently it has been recognized that BPs may also have additional significant beneficial extra-skeletal effects. These include a reduction of all-cause mortality and of conditions commonly linked to ageing, such as cancer and cardiovascular disease. Here we show that bisphosphonates co-localize with lysosomal and endosomal organelles in non-skeletal cells and stimulate cell growth at low doses. In vivo spatial transcriptomic analysis revealed differentially expressed senescence markers in multiple organs of aged BP-treated mice, and a shift in cellular composition toward those of young counterparts. Similarly, a 5000-plex plasma proteome analysis from osteopenic patients before and after BP-treatment showed significant alterations in [~]400 proteins including GTPase regulators and markers of senescence, autophagy, apoptosis, and inflammatory responses. Furthermore, treatment with BPs protected against the onset of senescence in vitro. Proteome-wide target deconvolution using 2D thermal profiling revealed novel BP-binding targets (PHB2, ASAH1), and combined with RNA- and ATAC-seq of BP-treated cells and patient data, suggests downstream regulation of the MEF2A transcription factor within the heart. Collectively, these results indicate how BPs may beneficially modify the human plasma proteome, and directly impact multiple non-skeletal cell types through previously unidentified proteins, thereby influencing a range of pathways related to senescence and ageing.

cell biology↗

bioRxiv2025

Active DNA demethylation is upstream of rod-photoreceptor fate determination and required for retinal development

Retinal cell fate specification from multipotent retinal progenitors is governed by dynamic changes in chromatin structure and gene expression. Methylation at cytosines in DNA (5mC) is actively regulated for proper control of gene expression and chromatin architecture. Numerous genes display active DNA demethylation across retinal development; a process that requires oxidation of 5mC to 5-hydroxymethylcytosine (5hmC) and is controlled by the ten-eleven translocation methylcytosine dioxygenase (TET) enzymes. Using an allelic series of conditional TET enzyme mutants, we determine that DNA demethylation is required upstream of NRL and NR2E3 expression for the establishment of rod-photoreceptor fate. Using histological, behavioral, transcriptomic, and base-pair resolution DNA methylation analyses, we establish that inhibition of active DNA demethylation results in global changes in gene expression and methylation patterns that prevent photoreceptor precursors from adopting a rod-photoreceptor fate, instead producing a retina in which all photoreceptors specify as cones. Our results establish the TET enzymes and DNA demethylation as critical regulators of retinal development and cell fate specification, elucidating a novel mechanism required for the specification of rod-photoreceptors.

developmental biology↗

bioRxiv2022

Breast cancer mutations HER2 V777L and PIK3CA H1047R activate the p21/CDK4/6/Cyclin D1 axis driving tumorigenesis and drug resistance.

In metastatic breast cancer, HER2 activating mutations frequently co-occur with mutations in the PIK3CA, TP53, or E-cadherin genes. Of these co-occurring mutations, HER2 and PIK3CA mutations are the most prevalent gene pair, with approximately 40% of HER2 mutated breast cancers also having activating mutations in PIK3CA. To study the effects of co-occurring HER2 and PIK3CA mutations, we bred genetically engineered mice with the HER2V777L; PIK3CAH1047Rtransgenes (HP mice) and studied the resulting breast cancers both in vivo as well as ex vivo using cancer organoids. HP breast cancers show accelerated tumor formation in vivo and increased invasion and migration in in vitro assays. HP breast cancers have resistance to the pan-HER tyrosine kinase inhibitor, neratinib, but are effectively treated by neratinib plus trastuzumab deruxtecan. Proteomic and RNA-Seq analysis of HP breast cancers showed increased gene expression of Cyclin D1 and p21WAF1/Cip1 and changes in cell cycle markers. Combining neratinib with CDK4/6 inhibitors was another effective strategy for HP breast cancers with neratinib plus palbociclib showing a statistically significant reduction in mouse HP tumors as compared to either drug alone. We validated both the neratinib plus trastuzumab deruxtecan and neratinib plus palbociclib combinations using a human breast cancer patient-derived xenograft that has very similar HER2 and PIK3CA mutations. Both of these drug combinations are being tested in phase 1 clinical trials and this study provides valuable preclinical evidence for them.

cancer biology↗

bioRxiv2020

Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM

Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXMs performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample.

bioinformatics↗

bioRxiv2020

Distinct genetic pathways define pre-leukemic and compensatory clonal hematopoiesis in Shwachman-Diamond syndrome

Shwachman-Diamond syndrome (SDS) is an inherited bone marrow failure syndrome with predisposition to developing leukemia. We found that multiple independent somatic hematopoietic clones arise early in life, most commonly harboring heterozygous mutations in EIF6 or TP53. EIF6 mutations cause functional compensation for the germline deficiency by alleviating the SDS ribosome joining defect, improving translation, and reducing p53 activation. TP53 mutations decrease checkpoint activation without affecting ribosome assembly. We link development of leukemia with acquisition of biallelic TP53 alterations. Our results define distinct pathways of clonal selection driven by germline fitness constraint and provide a mechanistic framework for clinical surveillance.

cancer biology↗

bioRxiv2018

Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity.

molecular biology↗

bioRxiv2018

A Novel in vivo Model of Anaerobic Infection: The Investigation of Clostridium perfringens in Galleria mellonella Larvae.

ABSTRACTImportant research progress into the mechanisms of Clostridium perfringens associated diseases (CPAD) has been slowed by the lack of a reliable infection model. Wax moth larvae (Galleria mellonella) have emerged as a viable alternative to traditional mammalian organisms since they are economic, survive at 37{degrees}C and require no specialist equipment. This study aims to establish whether G. mellonella larvae can be developed as a viable model for the study of CPAD and their suitability for studying novel treatment strategies. In addition, the study demonstrates a novel time-lapse approach to data collection. Mortality and morbidity rates of larvae challenged with 105 CFU of C. perfringens isolates from various sources were observed over 72h and dose response data obtained using inoculum sizes of 10 - 105 CFU. Phenoloxidase enzyme activity was investigated as a marker for immune response and tissue burden by histopathological techniques. Results show that C. perfringens is pathogenic towards G. mellonella although potency varies between isolates. Infection activates the melanisation pathway resulting in melanin deposition but no increase in enzyme activity was observed. Efficacy of antibiotic therapy (penicillin G, bacitracin, neomycin and tetracycline) administered parenterally loosely correlates with that of in vitro analysis. The findings suggest G. mellonella can be a useful in vivo model of infection when investigating CPAD. Although they are unlikely to replace traditional mammals they may be useful as a pre-screening assay for virulence of C.perfringens strains or as a simple, cheap and rapid in vivo assay in the development and pre-clinical development of novel therapeutics.\n\nHighlightsO_LINovel in vivo model for the study of Clostridium perfringens infection.\nC_LIO_LINovel time-lapse approach to data collection.\nC_LIO_LIFirst report of the use of G. mellonella model for characterizing virulence in C. perfringens strains.\nC_LIO_LIAntibiotic therapy in the model that loosely correlates with in vitro testing.\nC_LI

microbiology↗

bioRxiv2018

Integrative analysis of 5-methyl- and 5-hydroxymethylcytosine indicates a role for 5-hydroxymethylcytosine as a repressive epigenetic mark

Since the discovery of 5-hydroxymethylcytosine (5hmC) as a prominent DNA base modification found in mammalian genomes, an emergent question has been what role this mark plays in gene regulation. 5hmC is hypothesized to function as an intermediate in the demethylation of 5-methylcytosine (5mC) and also in reactivation of silenced regulatory elements, including promoters and enhancers. Further, weak positive correlations have been observed between gene body 5hmC and gene expression. We previously demonstrated that ME-Class, which uses a high-resolution model of whole-genome bisulfite sequencing data, is an effective tool to understand relationships between 5mC and expression. In this work, we present ME-Class2, a machine-learning based tool to perform integrative 5mCG, 5hmCG and expression analysis. Using ME-Class2 we analyze whole-genome single-base resolution 5mC and 5hmC datasets from 20 primary tissue and cell samples to uncover relationships between 5hmC and expression. The addition of 5hmC improves model performance for tissues with high-levels of 5hmC such as the brain. Our analysis further indicates that conversion of 5mC to 5hmC within 2kb of the transcription start site associates with distinct functions depending on the summed level of 5mC + 5hmC. Unchanged levels of 5mC + 5hmC (i.e. conversion from 5mC to stable 5hmC) associate with repression. Meanwhile, decreases in 5mC + 5hmC (i.e. 5hmC-mediated demethylation) associate with gene activation. As more large-scale, genome-wide, differential DNA methylation studies become available, tools such as ME-Class2 will prove invaluable to interpret epigenomic data and guide mechanistic studies into the function of 5hmC.

bioinformatics↗