Biology subjects

Cairns, B.

Publications and source records attributed to Cairns, B..

9 recordsLinked to original sources

bioRxiv2026

SWI/SNF Alterations Define a Chromatin-Dependent Subtype of Urothelial Carcinoma

PurposeSWI/SNF (BAF) chromatin remodeling complex alterations are common in urothelial carcinoma, yet no biomarker-directed therapeutic strategies have been established for this population. We investigated whether BAF alterations delineate a biologically distinct, therapeutically actionable urothelial carcinoma subtype. Experimental DesignWe performed integrative genomic and transcriptomic analyses of 792 urothelial carcinoma tumors from the Oncology Research Information Exchange Network (ORIEN) and validated findings in the TCGA-BLCA cohort. Mechanistic studies incorporated RNA sequencing and ATAC-seq following histone deacetylase (HDAC) inhibition. Functional dependencies were assessed using patient-derived xenograft organoids and cell line models. Clinical relevance was explored in a biomarker-enriched investigator-initiated trial. ResultsApproximately half of urothelial carcinoma tumors exhibited BAF alterations, defining a previously unrecognized chromatin-altered molecular subtype characterized by activation of proliferative programs, loss of lineage identity, and altered metabolic signaling. This subtype was enriched for transcriptomic programs associated with HDAC inhibitor sensitivity and depleted of HDAC inhibitor resistance signatures. Mechanistically, HDAC inhibition induced widespread chromatin remodeling with reduced accessibility at AP-1 and TEAD-associated regions, and downregulation of E2F- and MYC-driven transcriptional networks. Functional studies confirmed enhanced HDAC inhibition sensitivity in ARID1A-mutated cell lines and a patient-derived organoid model. Early clinical observations demonstrated a durable responder treated with HDAC inhibitors and immunotherapy. ConclusionsBAF alterations define a chromatin-dependent tumor state in urothelial carcinoma that is selectively vulnerable to HDAC inhibition. Integrating genomic, epigenomic, functional, and early clinical evidence, these findings provide a rationale for biomarker-enriched clinical trials and HDAC inhibitor-based combination strategies in urothelial carcinoma.

cancer biology↗

bioRxiv2026

3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis

Sperm formation requires a radical chromatin reorganization, where nucleosomes are replaced by transition proteins (TNPs) and subsequently by protamines (PRM1 and PRM2). Although essential for fertility, the regulatory logic governing this exchange is unknown, but its presumed to be stochastic and unregulated. Using endogenously tagged PRM mouse models and stage-resolved, genome-wide profiling, we revise the order of histone-to-protamine exchange and show that the chromatin remodeling process is highly programmed. Imaging and biochemical experiments reveal a direct histone-to-PRM1 exchange, while TNPs appear after PRM1 but precede PRM2 incorporation. This temporal uncoupling of PRM1 and PRM2 incorporation coincides with dynamic, region-specific chromatin remodeling that is not governed by histone acetylation but is instructed by the three-dimensional nuclear architecture of round spermatids. Therefore, by integrating ATAC-seq, CUT&Tag, and Hi-C, we define a compartment-encoded "blueprint" that prescribes the assembly of the mature sperm epigenome and establishes a complex molecular hierarchy for the histone-to-protamine exchange.

genomics↗

bioRxiv2025

Purinergic signalling and calcium dynamics: potential drivers in the onset of coordinated intestinal motility in human fetal development

Background and aimsIntestinal motility relies on inputs from multiple cells within a complex neuromuscular syncytium located in the gut wall. While it is known that motility is dependent on the development of motor patterns which govern coordinated contractile activity within the gut wall, knowledge regarding the onset of coordinated motor activity in humans is still lacking. This study assessed the emergence of coordinated motor patterns, and the molecular mechanisms underpinning developing motility, in the human fetal gut. MethodsHuman fetal gut samples (obtained via the MRC-Wellcome Trust Human Developmental Biology Resource-UK) were characterised by live imaging, spatiotemporal mapping, immunohistochemistry and RNAseq. ResultsHuman small intestinal samples displayed the presence of key cell types including enteric neurons, interstitial cells of Cajal, platelet-derived growth factor receptor alpha positive (PDGFR+) cells and smooth muscle at post conception week (PCW) 12. Between PCW12 and PCW16, functional assessment revealed a marked increase in the velocity (p= 0.0341) of propagating contractions. Subsequently, between PCW16 and PCW20 the number of contraction initiation sites reduced drastically (p=0.0053), enabling the emergence of long-distance propagating contractions. Expression analyses showed the development of coordinated motor activity was coincident with increased expression of various genes involved in calcium and purinergic signalling pathways. ConclusionsThese findings provide the first direct mechanistic evidence of the temporal development of coordinated contractile activity in the human fetal intestine, highlighting the role of calcium dynamics, purinergic signalling and interstitial cells in early stages of human motility development, potentially informing an improved understanding of the pathogenesis of gut motility disorders.

developmental biology↗

bioRxiv2024

SS18::SSX redistributes BAF chromatin remodelers selectively to activate and repress transcription

Synovial sarcoma (SyS) is driven by the expression of a chromosomal translocation-generated SS18::SSX fusion oncoprotein1,2. This oncoprotein fuses the SSX carboxy terminal tail that binds ubiquitylated histone H2A (H2AK119ub)3-6 to the SS18 component of both canonical (CBAF) and non-canonical (GBAF, GLTSCR1-containing) BAF-family chromatin remodeling complexes7-11, wherein SS18::SSX reprograms the epigenetic landscape. Mice that express SS18::SSX develop tumors that faithfully recapitulate human SyS histopathologically and molecularly12-14, allowing dissection of transcriptional reprogramming in vivo15,16. Here, we show that SS18::SSX redistributes GBAF complexes broadly to promoters and distal enhancers decorated by H2AK119ub, which uncharacteristically lack the transcription-silencing trimethylation of H3K27 that otherwise accompanies H2AK119ub. Fusion-GBAF instead associates with H2AK119ub and transcription-enabling H3K4 trimethylation (promoters), monomethylation (distal enhancers), and H3K27 acetylation (both). CBAF with the fusion redistributes away from typical loci, avoids H2AK119ub-bearing regions, and instead narrowly flanks transcription start sites (TSSs), co-distributed with polybromo BAF (PBAF). Accelerated tumorigenesis in our SyS mouse model followed deletion of Smarcb1 (PBAF and CBAF), Pbrm1 (PBAF-specific), and Arid1a or Arid1b (CBAF-specific). While tumors lacking Arid1a or Arid1b retained SyS character, loss of Smarcb1 or Pbrm1 resulted in tumors lacking SyS features. These findings suggest that SyS transcriptional reprogramming includes both improper GBAF localization and gene activation at H2AK119ub-bearing regulatory regions and improper gene silencing through loss of CBAF.

cancer biology↗

bioRxiv2023

Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation

Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating [~]84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.

developmental biology↗

bioRxiv2021

Maternally-inherited anti-sense piRNAs antagonize transposon expression in teleost embryos

Transposable elements threaten genome stability, and the Piwi-piRNA system has evolved to silence transposons in the germline1-6. However, it remains largely unknown what mechanisms are utilized in early vertebrate embryos prior to germline establishment and ping-pong piRNA production. To address this, we first characterized small RNAs in early zebrafish embryos and detected abundant maternally-deposited, Ziwi-associated, antisense piRNAs that map largely to evolutionarily young long terminal repeat (LTR) retrotransposons. Notably, the focal establishment of the repressive modification H3K9me2/3 coincides with these young LTR elements, is deposited independent of transcription, and is required for LTR silencing. We find piRNAs highly enriched and maintained in primordial germ cells (PGCs), which display lower LTR expression than somatic cells. To examine the consequences of piRNA loss, we used reciprocal zebrafish-medaka hybrids, which display selective activation of LTRs that lack maternally-contributed targeting piRNAs. Thus, the Piwi-piRNA system actively antagonizes transposons in the soma and PGCs during early vertebrate embryogenesis.

developmental biology↗

bioRxiv2021

A system for CBAF reconstitution reveals roles for BAF47 domains and BCL7 in nucleosome ejection

Canonical BAF (CBAF) is an essential 12-protein chromatin-remodeling complex that slides and/or ejects nucleosomes using the alternative catalytic ATP-dependent DNA translocases BRG1 or BRM. Currently, the regulation of BRG1/BRM activity and nucleosome ejection remain incompletely understood. To address this, we developed a system for full CBAF reconstitution and purification, and created a novel nucleosome ejection assay. ARID1A and DPF2 were dispensable for assembly and chromatin remodeling activity, contrasting with prior work. The actin-related protein BAF53A and {beta}-actin components interacted and enhanced DNA translocation, and were required for BCL7A incorporation, which potentiated ejection. BAF47 also regulated ejection, utilizing two stimulatory domains and an autoinhibitory domain. Finally, we provide evidence for direct nucleosome ejection at low nucleosome density on closed circular arrays. Taken together, we provide powerful new tools for CBAF mechanistic investigation and reveal new roles for several CBAF components.

biochemistry↗

bioRxiv2020

Germ plasm localisation dynamics mark distinct phases of transcriptional and post-transcriptional regulation control in primordial germ cells

In many animal models, primordial germ cell (PGC) development depends on maternally-deposited germ plasm to avoid somatic cell fate. Here, we show that PGCs respond to regulatory information from the germ plasm in two distinct phases and mechanisms in zebrafish. We show that PGCs commence zygotic genome activation together with the rest of the embryo with no demonstrable differences in transcriptional and chromatin accessibility levels. Thus, cytoplasmic germ plasm determinants only affect post-transcriptional stabilisation of RNAs to diverge transcriptome from somatic cells, which, unexpectedly, also activate germ cell-specific genes. Perinuclear relocalisation of germ plasm is coupled to dramatic divergence in chromatin opening and transcriptome from somatic cells characterised by PGC-specific chromatin topology. Furthermore, we reveal Tdrd7, regulator of germ plasm localisation, as crucial determinant of germ fate acquisition.

developmental biology↗

bioRxiv2018

Genome-Wide Reconstitution of Chromatin Transactions: RSC Preferentially disrupts H2A.Z-Containing Nucleosomes

Chromatin transactions are typically studied in vivo, or in vitro using artificial chromatin lacking the epigenetic complexity of the natural material. Attempting to bridge the gap between these approaches, we established a system for isolating the yeast genome as a library of mono-nucleosomes harboring the natural epigenetic signature, suitable for biochemical manipulation. Combined with deep sequencing, this library was used to investigate the intrinsic stability of individual nucleosomes, and - as proof of principle - the nucleosome preference of the chromatin remodeling complex, RSC. Our data indicate that the natural stability of nucleosomes differs greatly, with nucleosomes on tRNA genes and on promoters of protein-coding genes standing out as intrinsically unstable. Interestingly, RSC shows a distinct preference for nucleosomes derived from regions with a high density of histone variant H2A.Z, and this preference is indeed markedly diminished using nucleosomes from cells lacking H2A.Z. Importantly, the preference for H2A.Z remodeling/nucleosome ejection can also be reconstituted with recombinant nucleosome arrays. Together, our data indicate that, despite being separated from their genomic context, individual nucleosomes can retain their original identity as promoter- or TSS-nucleosomes. Besides shedding new light on nucleosome stability and the chromatin remodeler RSC, the simple experimental system outlined here should be generally applicable to the study of chromatin transactions.

biochemistry↗