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Principal Investigator: LISA A MAIER
Organization: NATIONAL JEWISH HEALTH
Fiscal Year: 2024
Award: $646,640
Funding agency: National Institute of Environmental Health Sciences
PROJECT SUMMARY/ABSTRACT:
The goal of this study is to define cell-specific regulatory networks and key drivers of cellular response to beryllium
(Be) that result in the granulomatous lung disease, chronic beryllium disease (CBD), at the site of organ
involvement. Relying on the complementary, unique expertise of investigative team we will define pathogenic
pathways and risk factors for CBD, its precursor (Be sensitization; BeS) and similar environmentally induced
diseases. Exposure to an inhaled Be antigen(s), in the setting of a genetically susceptible host, initiates a Th1
immune response, with antigen presentation occurring via HLA Class II on antigen presenting cell (APC) in the
context of CD4+ T cells. Subsequently, CD4+ T cells and APCs are recruited to the lung, proliferate, produce
cytokines and chemokines, and eventually form granulomas. An increased prevalence of HLA-DPB1 alleles with
a glutamic acid at amino acid position 69 (E69) is found in CBD and BeS, although this variant is found in up to
40% of Be exposed workers without BeS or CBD, suggesting that other factors or forms of genetic regulation are
important in disease pathogenesis. Growing data in other immune-mediated diseases suggests that epigenetic
mechanisms in combination with genetic susceptibility and environment may help explain disease risk. Epigenetic
modifications determine T cell and APC/macrophage differentiation and the ensuing immune response through
DNA methylation and histone modifications of key genes and thus impact health and disease. Our previous work
demonstrated DNA methylation changes associated with alterations in gene expression and disease state in
bronchoalveolar lavage (BAL) cells of CBD subjects compared to BeS and controls, including pivotal immune
response genes and networks. Single cell sequencing technologies have emerged as a key method to
characterize novel cell population and cell-specific changes in gene expression. Based on this information, our
hypothesis is that exposure to Be alters epigenetic marks, impacting gene expression and immune cell
differentiation in cell-specific manner, and ultimately risk of granulomatous lung disease. We will test this
hypothesis through three specific aims, focusing mainly on macrophages and CD4+ T cells but acknowledging
that other cell populations are important and considering them in alternative approaches and future directions. In
Aim 1 we will characterize the lung immune cell response to Be exposure using single cell ATAC-seq and CITE-
seq to measure chromatin accessibility, gene expression levels and protein epitopes at four timepoints to define
key drivers in specific cell populations. In Aim 2 we will validate the regulatory networks in uncultured lung
samples, focusing on macrophages and CD4+ Tcells, using bulk ATAC- Me and RNA-sequencing. We will
functionally validate the results from our multi-omic analysis from Aims 1 and 2 using CRSIPR-dCas9 to change
methylation, chromatin accessibility, and gene expression at loci identified as key drivers of response to Be in
cultured macrophage and T cell lines in Aim 3. Ultimately, this proposal will enhance our understanding of the
novel genes, regulatory pathways and networks, and molecular mechanisms involved in CBD etiology.
Terms: <ATAC><Alleles><Allelomorphs><Amino Acids><Antigen Presentation><Antigen-Presenting Cells><Antigenic Determinants><Antigens><Berylliosis><Beryllium><Beryllium Disease><Beryllium granuloma><Binding Determinants><Biological Markers><Bronchioalveolar Lavage><Bronchoalveolar Lavage><Bronchopulmonary Lavage><CD4 Cells><CD4 Positive T Lymphocytes><CD4 T cells><CD4 helper T cell><CD4 lymphocyte><CD4+ T-Lymphocyte><CD4-Positive Lymphocytes><CITE sequencing><CITE-seq><CITEseq><COVID-19><CV-19><Causality><Cell Body><Cell Culture Techniques><Cell Differentiation><Cell Differentiation process><Cell Line><CellLine><Cells><Cellular Indexing of Transcriptomes and Epitopes by Sequencing><Chemotactic Cytokines><Chromatin><Chronic berylliosis><Chronic beryllium disease><Chronic beryllium lung><Chronic beryllium lung disease><Chronic beryllium poisoning><Coronavirus Infectious Disease 2019><DNA Methylation><DNA analysis><Data><Development><Disease><Disorder><Drug Targeting><Environment><Environmental Exposure><Epigenetic><Epigenetic Change><Epigenetic Mechanism><Epigenetic Process><Epitopes><Etiology><Exposure to><Fibrotic lesions in lung><Flow Cytofluorometries><Flow Cytofluorometry><Flow Cytometry><Flow Microfluorimetry><Flow Microfluorometry><Future><Gene Expression><Genes><Genetic><Genetic Polymorphism><Genetic Predisposition><Genetic Predisposition to Disease><Genetic Susceptibility><Genetic propensity><Genomic approach><Glutamic Acid><Goals><Granuloma><Granulomatous><Granulomatous Lesion><HLA-DP1B><HLA-DPB1><HLA-DPB1 gene><HLADPB1><Health><Hereditary><Heritability><Homologous Chemotactic Cytokines><Hour><Immune><Immune Response Genes><Immune response><Immunes><Immunological response><Inflammation><Inhalation><Inhaling><Inherited><Inherited Predisposition><Inherited Susceptibility><Innate Immune Response><Intercrines><Investigation><Ir Gene><L-Glutamic Acid><LPTN><Life><Lung><Lung Lavage><Lung Parenchyma><Lung Respiratory System><Lung Tissue><Lung Tissue Fibrosis><Lung scar><Lung tissue scar><Macrophage><Measures><Mediating><Methods><Methylation><Modification><Molecular><Mφ><Organ><Pathogenesis><Pathogenicity><Pathway interactions><Persons><Population><Position><Positioning Attribute><Predisposition><Prevalence><Proliferating><Proteins><Pulmonary Fibrosis><Pulmonary Scar><Pulmonary Tissue fibrosis><RNA Seq><RNA sequencing><RNAseq><Regulation><Regulatory Pathway><Respiratory Epithelium><Risk><Risk Factors><SCM-1><SCM-1a><SCM1><SCYC1><SIS cytokines><Sampling><Scarring at the lung><Scarring in the lung><Single cell seq><Site><Strains Cell Lines><Structure of parenchyma of lung><Structure of respiratory epithelium><Susceptibility><System><T-Cells><T-Lymphocyte><T4 Cells><T4 Lymphocytes><Technology><Testing><Time><Transcription Regulation><Transcriptional Control><Transcriptional Regulation><Validation><Variant><Variation><Work><XCL1><XCL1 gene><accessory cell><airway epithelium><aminoacid><analyze DNA><asthmatic airway><beryllium poisoning><bio-markers><biologic marker><biomarker><biomarker identification><bronchopulmonary lavage therapy><causation><cell culture><cell cultures><cellular differentiation><cellular indexing of transcriptomes and epitopes by single cell sequencing><chemoattractant cytokine><chemokine><coronavirus disease 2019><coronavirus disease-19><coronavirus infectious disease-19><cultured cell line><cytokine><developmental><disease causation><disease risk><disorder risk><epigenetically><epigenome><fibrosis in the lung><fibrotic lung><flow cytophotometry><genetic etiology><genetic mechanism of disease><genetic vulnerability><genetically predisposed><genomic effort><genomic strategy><global gene expression><global transcription profile><granulomatous lung disease><granulomatous lung disorder><histone modification><host response><identification of biomarkers><identification of new biomarkers><immune system response><immunogen><immunoresponse><lung fibrosis><marker identification><member><multiomics><multiple omics><neo-antigen><neo-epitopes><neoantigens><neoepitopes><novel><panomics><pathway><peripheral blood><polymorphism><pulmonary><recruit><respiratory tract epithelium><response><scATAC sequencing><scATAC-seq><single cell ATAC-seq><single cell ATAC-sequencing><single cell Assay for Transposase Accessible Chromatin sequencing><single cell next generation sequencing><single cell sequencing><single cell sequencing assay for transposase accessible chromatin><single-cell Assay for Transposase-Accessible Chromatin with sequencing><single-cell assay for transposase-accessible chromatin using sequencing><single-cell assay for transposase-accessible chromatin-seq><targeted drug therapy><targeted drug treatments><targeted therapeutic><targeted therapeutic agents><targeted therapy><targeted treatment><thymus derived lymphocyte><transcriptome><transcriptome sequencing><transcriptomic sequencing><validations>