chromatin accessibility
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Personalized Spatial Regulatory Networks to Decode Breast Cancer Microenvironments
PROJECT SUMMARY Triple-negative breast cancer (TNBC) is an aggressive subtype with early recurrence, high metastatic burden, and limited treatment options. While genomic alterations contribute to its progression, epigenetic plasticity and spatial organization within the tumor microenvironment (TME) play critical roles in intra-tumor heterogeneity, immune evasion, and therapy resistance, yet remain poorly understood. To address this, we will develop a cost- effective and scalable methodology that integrates spatial ATAC-seq, spatial in situ transcriptomics (Xenium), and single-nucleus (sn) Epi Multiome sequencing (snRNA-seq + snATAC-seq) from core-needle biopsies, enabling high-resolution mapping of gene regulatory networks within the intact TME. Our preliminary data from six TNBC biopsies demonstrate that spatial in situ transcriptomics and spatial ATAC-seq provide critical insights into tissue architecture but suffer from data sparsity, necessitating the integration of single-nucleus Epi Multiome data to enhance cell-type annotation and impute missing genomic features. In Aim 1, we will establish a multi- modal workflow that maximizes molecular insights from limited biopsy material by optimizing tissue-preserving and multiplexed sequencing approaches. This includes leveraging patient-specific genetic variation to deconvolute nuclei-derived data and linking it to spatial transcriptomic and spatial chromatin accessibility profiles. In Aim 2, we will develop a computational framework to integrate these multi-layered datasets, enabling spatially resolved epigenomic-transcriptomic analysis that identifies key regulatory chromatin elements and transcriptional programs associated with TNBC progression, immune infiltration, and therapy resistance. This project will generate the first comprehensive, patient-specific spatial regulatory atlas of TNBC, providing fundamental insights into how chromatin accessibility and gene expression interact within the TME. Ultimately, this work will pave the way for novel precision oncology strategies, biomarker discovery, and the development of targeted therapies that address TNBC’s spatial and molecular heterogeneity.
Sex hormone regulation of neural gene expression
Gonadal steroid hormones are the principal drivers of sex-variable biology in vertebrates. In the brain, estrogen (17β-estradiol) establishes neural sex differences in many species and modulates mood, behavior, and energy balance in adulthood. To understand the diverse effects of estradiol on the brain, we profiled the genomic binding of estrogen receptor alpha (ERα), providing the first picture of the neural actions of any gonadal hormone receptor. To relate ERα target genes to brain sex differences we assessed gene expression and chromatin accessibility in the posterior bed nucleus of the stria terminalis (BNSTp), a sexually dimorphic node in limbic circuitry that underlies sex-differential social behaviors such as aggression and parenting. In adult animals we observe that levels of ERα are predictive of the extent of sex-variable gene expression, and that these sex differences are a dynamic readout of acute hormonal state. In neonates we find that transient ERα recruitment at birth leads to persistent chromatin opening and male-biased gene expression, demonstrating a true epigenetic mechanism for brain sexual differentiation. Collectively, our findings demonstrate that sex differences in gene expression in the brain are a readout of state-dependent hormone receptor actions, rather than other factors such as sex chromosomes. We anticipate that the ERα targets we have found will contribute to established sex differences in the incidence and etiology of neurological and psychiatric disorders.
Epigenomic (re)programming of the brain and behavior by ovarian hormones
Rhythmic changes in sex hormone levels across the ovarian cycle exert powerful effects on the brain and behavior, and confer female-specific risks for neuropsychiatric conditions. In this talk, Dr. Kundakovic will discuss the role of fluctuating ovarian hormones as a critical biological factor contributing to the increased depression and anxiety risk in women. Cycling ovarian hormones drive brain and behavioral plasticity in both humans and rodents, and the talk will focus on animal studies in Dr. Kundakovic’s lab that are revealing the molecular and receptor mechanisms that underlie this female-specific brain dynamic. She will highlight the lab’s discovery of sex hormone-driven epigenetic mechanisms, namely chromatin accessibility and 3D genome changes, that dynamically regulate neuronal gene expression and brain plasticity but may also prime the (epi)genome for psychopathology. She will then describe functional studies, including hormone replacement experiments and the overexpression of an estrous cycle stage-dependent transcription factor, which provide the causal link(s) between hormone-driven chromatin dynamics and sex-specific anxiety behavior. Dr. Kundakovic will also highlight an unconventional role that chromatin dynamics may have in regulating neuronal function across the ovarian cycle, including in sex hormone-driven X chromosome plasticity and hormonally-induced epigenetic priming. In summary, these studies provide a molecular framework to understand ovarian hormone-driven brain plasticity and increased female risk for anxiety and depression, opening new avenues for sex- and gender-informed treatments for brain disorders.
Chromatin accessibility in oligodendrocyte precursors profiled by ATAC-seq: Neuroprotective effects of MgSO4 and 4-PBA alone or associated in a mouse model of encephalopathy of prematurity
FENS Forum 2024
chromatin accessibility coverage
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