Chromatin accessibility landscape of human updates triple-negative breast cancer cell lines reveals variation by patient donor ancestry

African American (AA) women have an excessive risk of developing triple-negative breast cancer (TNBC). We employed Assay for Transposase-Accessible Chromatin using sequencing to characterize differences in chromatin accessibility between nine commonly used TNBC cell lines de?rived from patients of European and African ancestry. Principal component and chromosome mapping analyses of accessibility peaks with the most variance revealed separation of chromatin profiles by patient group. Motif enrichment and footprinting analyses of disparate open chromatin regions revealed differences in transcription factor activity, identifying 79 with ancestry-associated binding patterns (FDR < 0.01). AA TNBC cell lines ex?hibited increased accessibility for 62 transcription factors associated with epithelial-to-mesenchymal transition, cancer stemness/chemotherapeutic resistance, proliferation, and aberrant p53 regulation, as well as KAISO, which has been previously linked to aggressive tumor characteristics in AA patients with cancer. Differential Assay for Transposase-Accessible Chromatin signal analysis identified 1,596 genes located within promoters of differentially open chromatin regions in AA-derived TNBC, identifying DNA methyltransferase 1 as the top upregulated gene associated with African ancestry. Pathway analyses with these genes revealed enrichment in several pathways, including hypoxia. Culturing cells under hypoxia showed ancestry-specific stress responses that led to the identification of a core set of AA-associated transcription factors, which included members of the Kruppel-like factor and Sp subfamilies, as well as KAISO, and identified ZDHHCI, a gene previously implicated in immunity and STING activation, as the top upregulated AA-specific gene under hypoxia. Together, these data reveal a differential chromatin landscape in TNBC associated with donor ancestry. The open chromatin structure of AA TNBC may contribute to a more lethal disease.</p

Human-CMV short sequence homology in GVHD tissue specific peptide and gene distribution from GTEx analysis (n = 18).

<p>GVHD incidence denotes the specific organs affected in each patient; Peptides, lists the number of unique peptide-HLA complexes matched between human and CMV peptide library; the column, <i>Genes</i> lists the source genes for the aforementioned peptides; <i>GVHD tissue specific peptides</i> lists the number of peptides which bind HLA with an IC50 <500nM, and are expressed in tissues affected by GVHD; <i>GVHD tissue gene expression</i> denotes the number of genes expressed at an RPKM >10 corresponding to the GVHD tissue specific peptides. Note: *- All patients with an asterisk following their numeric representation experienced CMV reactivation prior to GVHD (except Patients 67 and 71, <i>de novo</i> CMV infected) and patients without an asterisk experienced GVHD prior to CMV reactivation. **- human peptides may have overlapping areas of homology yielding a higher number of matches. Immunogenic CMV genes in this context refer to the genes associated with HCMV ORF-specific CD8+ T memory cell responses measured in frequency among CMV seropositive patients previously [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178763#pone.0178763.ref036" target="_blank">36</a>].</p

CMV+GVHD cross reactivity potential.

<p>Patient-specific peak CMV peptide matches intersecting peak alloreactive peptides (IC50<500 nM) as a cross-reactivity potential stratified by donor type contained within each DRP alloreactive peptide library.</p

GVHD tissue-specific immunogenic CMV peptide matches, CMV reactivation before GVHD patients.

<p>Patient-specific process of cross comparison along with the source genes, IC50 values to indicate inverse binding affinity and GVHD organ specific tissue involvement. *Note: Twelve patients with CMV reactivation/infection before GVHD onset exhibited previously identified immunogenic CMV peptide matches with gene expression specific to the tissues affected by GVHD (above); The filter of immunogenicity provides a connection to T cell reactivity shown <i>in vitro</i> to the listed CMV genes in a separate patient population [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0178763#pone.0178763.ref036" target="_blank">36</a>]; Patient 79 with muscle/fascia GVHD showed no muscle-specific previously <i>known immunogenic</i> CMV peptide matches but still had three relevant CMV peptide matches expressed in the skeletal muscle (not shown); Tissues in parentheses were also affected by GVHD but without immunogenic matches/expression by patient; Patients 67 and 71 experienced <i>de novo</i> CMV infection; All 13 patients exhibited multiple CMV peptide matches with unknown immunogenicity.</p

CMV- Human match analysis per DRP (IC50 <500 nM) by donor type according to continuous amino acid sequence homology (one standard deviation from the mean value).

<p>CMV- Human match analysis per DRP (IC50 <500 nM) by donor type according to continuous amino acid sequence homology (one standard deviation from the mean value).</p

Bioinformatic pipeline of the alloreactive peptide library comparison with the CMV proteome.

<p>A determination of the potential for Pro-GVHD DRP cross-reactivity upon CMV reactivation correlated with GVHD-tissue specific distribution of peptides & immunogenicity.</p

HCMV cross-reactivity potential of 77 SCT DRP from whole exome sequencing data using sliding window match analysis.

<p>HCMV cross-reactivity potential of 77 SCT DRP from whole exome sequencing data using sliding window match analysis.</p

Matrix depicting the T cell clonal interaction with mHA-HLA.

<p>Matrix depicting the T cell clonal interaction with mHA-HLA.</p

Matrix depicting T cell clonal cross-reactivity between CMVp-HLA and mHA-HLA.

<p>*-indicates response of the alloreactive T cell clone to a viral pathogen peptide,bound to the same HLA as the mHA and vice versa. For example, TC₁ recognizes, mHA₁ HLA + CMVp₂HLA, TC_1CMV recognizes, mHA₁ HLA + CMVp₁ HLA, and so on.</p