Biology subjects

Care, M. A.

Publications and source records attributed to Care, M. A..

6 recordsLinked to original sources

bioRxiv2023

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

Human B cell differentiation into antibody secreting plasma cells is a critical process in the adaptive immune response, whose regulation at the genetic level remains incompletely understood. To reveal the temporal sequence of transcription factor driven cellular changes we generated chromatin accessibility (ATAC-seq) and gene expression (RNA-seq) data from in vitro differentiation of human B cells into plasma cells using a published protocol for differentiation up to the plasma cell stage. Using a new computational method, cisREAD (cis-Regulatory Elements Across Differentiation), we defined a core set of cis-regulatory elements that are confidently linked to dynamic transcription factor binding and changes in gene expression across the mature B lineage. Here we describe how cisREAD identifies regulatory element communities, based on chromatin accessibility and transcription factor co-occupancy, and prioritizes those whose accessibility predicts differential gene expression through regularized regression models. Through downstream analyses of cisREAD-predicted regulation, we show how transcription factors reshape B cell epigenomes and transcriptomes in response to differentiation stimuli. Our results confirm roles for OCT2, IRF4 and PRDM1 in plasma cell differentiation, and reveal that a shift from PU.1/SPIB-driven to AP-1-driven gene regulation is a key determinant of B cell activation. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY Integration of epigenomic and transcriptomic datasets with the cisREAD method, followed by clustering and network analysis, reveals that gene regulation shifts from PU.1/SPIB to AP-1 upon B cell activation. C_FIG_DISPLAY

bioinformatics↗

bioRxiv2021

APRIL drives a co-ordinated but diverse response as a foundation for plasma cell longevity.

Antibody secreting cells (ASCs) survive in niche microenvironments, but cellular responses driven by particular niche signals are incompletely defined. The TNF superfamily member APRIL provides a niche signal that can support the transition of transitory plasmablasts into long-lived plasma cells. Here we explore how APRIL helps to establish the biological programs that promote life in the niche, by studying the initial response of primary human plasmablast to APRIL. Under conditions allowing the maturation of ex vivo or in vitro generated plasmablasts, we find that APRIL drives activation of ERK, p38 and JNK. This is accompanied by a classical NF{kappa}B response. Under these conditions induction of AKT phosphorylation is also observed with similar kinetics, paralleled by FOXO1 phosphorylation and nuclear exclusion. Time course gene expression data resolve the downstream co-ordinated transcriptional response. The APRIL-signal propagates via immediate early genes and classical NF{kappa}B responsive targets to converge onto modules of MYC- and OCT2-regulated gene expression linked to cell growth, as well as leading to enhanced expression of ICAM1 and SQSTM1 associated with adhesion and metabolic/stress responses. Thus, APRIL drives a combination of multiple transcriptional programs that co-ordinate cell growth, stress response and adhesion in human ASCs, providing a broad foundation to support plasma cell longevity.

immunology↗

bioRxiv2019

A dichotomy in association of core transcription factors and gene regulation during the activated B-cell to plasmablast transition.

The activated B-cell (ABC) to plasmablast transition is the cusp of antibody secreting cell (ASC) differentiation but is incompletely defined. We apply expression time-courses, parsimonious gene correlation network analysis, and ChIP-seq to explore this in human cells. The transition initiates with input signal loss leading within hours from cell growth dominant programs to enhanced proliferation, accompanied from 24h by ER-stress response, secretory optimization and upregulation of ASC features. Clustering of genomic occupancy for ASC transcription factors (TFs) IRF4, BLIMP1 and XBP1 with CTCF and histone marks defines distinct patterns for each factor in plasmablasts. Integrating TF-associated clusters and modular gene expression identifies a dichotomy: XBP1 and IRF4 significantly link to gene modules induced in plasmablasts, but not to modules of repressed genes, while BLIMP1 links to modules of ABC genes repressed in plasmablasts but is not significantly associated with modules induced in plasmablasts. Pharmacological inhibition of the G9A (EHMT2) histone-methytransferase, a BLIMP1 co-factor that catalyzes repressive H3K9me2 marks, leaves functional ASC differentiation intact but de-represses ABC-state genes. Thus, in human plasmablasts IRF4 and XBP1 emerge as the dominant association with ASC gene expression, while BLIMP1 links to repressed modules with particular focus in repression of the B-cell activation state.

immunology↗

bioRxiv2019

JARID2 facilitates transcriptional reprogramming in glioblastoma in response to standard treatment

BackgroundGlioblastoma (GBM) is a fatal and incurable brain cancer with a dismal prognosis. In order to impact on this disease, we need to understand how infiltrating, non resectable tumour cells resist chemoradiation and facilitate disease recurrence. To this end, we generated or acquired bulk tumour RNA sequencing data from 45 paired primary and locally recurrent GBM tumours (split into original and validation cohorts) from patients that received standard treatment. We also generated DNA methylation profiles for 9 pairs and sequenced RNA from single cells isolated from a patient derived GBM spheroid model at different timepoints following in vitro chemoradiation.\n\nResultsWe have identified a set of genes with Jumonji and AT-Rich Interacting Domain 2 (JARID2) binding sites in their promoters that are universally dysregulated in post-standard treatment recurrent GBMs compared to the primary tumour. The direction of dysregulation is patient-dependent and not associated with differential promoter DNA methylation. Our in vitro experiments suggest that this dysregulation occurs dynamically following treatment as opposed to resulting from selection of cells with specific expression profiles.\n\nConclusionJARID2 is an accessory protein to a chromatin remodeling complex, responsible for histone modifications observed during cell state transitions in both normal brain and GBM. We propose that JARID2 facilitates GBM recurrence following treatment by indirect transcriptional reprogramming of surviving cells in whichever manner is needed to reproduce the phenotypic heterogeneity required for tumour regrowth in vivo. The mechanism of this reprogramming may present a therapeutic vulnerability for more effective treatment of GBM.

cancer biology↗

bioRxiv2018

Growth-factor like gene regulation is separable from survival and maturation in antibody secreting cells

Recurrent mutational activation of the MAP kinase pathway in plasma cell myeloma implicates growth factor-like signaling responses in the biology of antibody secreting cells (ASCs). Physiological ASCs survive in niche microenvironments, but how niche signals are propagated and integrated is poorly understood. Here we dissect such a response in human ASCs using an in vitro model. Applying time course expression data and parsimonious gene correlation networking analysis (PGCNA), we map expression changes that occur during the maturation of proliferating plasmablast to quiescent plasma cell under survival conditions including the potential niche signal TGFB3. This analysis demonstrates a convergent pattern of differentiation, linking UPR/ER stress to secretory optimization, co-ordinated with cell cycle exit. TGFB3 supports ASC survival while having a limited effect on gene expression including up-regulation of CXCR4. This is associated with a significant shift in response to SDF1 in ASCs with amplified ERK1/2 activation, growth factor-like immediate early gene regulation and EGR1 protein expression. Similarly, ASCs responding to survival conditions initially induce partially overlapping sets of immediate early genes, without sustaining the response. Thus, in human ASCs growth factor-like gene regulation is transiently imposed by niche signals but is not sustained during subsequent survival and maturation.

immunology↗

bioRxiv2018

Defining common principles of gene co-expression refines molecular stratification in cancer

Cancers converge onto shared patterns that arise from constraints placed by the biology of the originating cell lineage and microenvironment on recurrent programs driven by oncogenic events. This structure should be transferable to molecular stratification. We exploit expression data resources and a parsimonious and computationally efficient network analysis method to define consistent expression modules in colon and breast cancer. Comparison between cancer types identifies principles of gene co-expression: cancer hallmarks, functional and structural gene batteries, copy number variation and biology of originating lineage. Mapping outcome data at gene and module level onto these networks generates a detailed interactive resource. Testing the utility of the resulting modules in TCGA data defines specific associations of module expression with mutation state, identifying striking associations such as mast cell gene expression and mutation pattern in breast cancer. These analyses provide evidence for a generalizable framework to enhance molecular stratification in cancer.

bioinformatics↗