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Analysis of Single Nuclear Chromatin Accessibility Demonstrates Unique Myeloid Populations Differentially Influence Prognosis in Human Pancreatic Ductal Adenocarcinoma [snMultiome]

ABSTRACT: Background: A better understanding of the pancreatic adenocarcinoma (PDAC) immune microenvironment is critical to improving outcomes. Myeloid cells are of particular importance for PDAC progression. Circulating monocytes are recruited and hijacked by the tumor to become immune suppressive tumor-associated macrophages. Meanwhile, tissue resident macrophages are innately anti-inflammatory and pro-fibrotic. Open chromatin and transcription factor activity provide source and function data for myeloid cells. Thus, we explore single nuclear assay for transposase accessible chromatin (ATAC) sequencing (snATAC-Seq), a method to analyze open gene promoters and transcription factor binding, as an important means for discerning the myeloid composition in human PDAC tumors. Methods: Frozen pancreatic tissues (benign or PDAC) were digested into single nuclei suspensions. snATAC-Seq and sn-Multiome (ATAC + RNA) libraries were prepared using 10X Chromium technology and sequenced by an Illumina sequencer. Signac was used for preliminary analysis, clustering, and differentially accessible chromatin region identification. snMultiome data was used to validate cell annotations for the snATAC-Seq data. Results: Unique populations comprised the benign and tumor samples. Myeloid cell transcription factor activities were higher in tumor samples than benign pancreatic samples, enabling us to further stratify myeloid populations in PDAC tumors. GO enrichment analysis showed myeloid cells can activate immune response in tumors. Subcluster analysis revealed eight distinct myeloid populations. GO enrichment demonstrated unique functions of different myeloid populations, including IL-1b signaling (recruited monocytes) and intracellular protein transport (dendritic cells). Conclusions: These data suggest snATAC-Seq as a method for retrospective analysis of frozen human pancreatic tissues to identify myeloid populations. Understanding the source specific potential function of myeloid cells is important for patient prognosis in PDAC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE241895 | GEO | 2024/02/15

REPOSITORIES: GEO

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Project description:Background: A better understanding of the pancreatic adenocarcinoma (PDAC) immune microenvironment is critical to improving outcomes. Myeloid cells are of particular importance for PDAC progression. Circulating monocytes are recruited and hijacked by the tumor to become immune suppressive tumor-associated macrophages. Meanwhile, tissue resident macrophages are innately anti-inflammatory and pro-fibrotic. Open chromatin and transcription factor activity provide source and function data for myeloid cells. Thus, we explore single nuclear assay for transposase accessible chromatin (ATAC) sequencing (snATAC-Seq), a method to analyze open gene promoters and transcription factor binding, as an important means for discerning the myeloid composition in human PDAC tumors. Methods: Frozen pancreatic tissues (benign or PDAC) were digested into single nuclei suspensions. snATAC-Seq and sn-Multiome (ATAC + RNA) libraries were prepared using 10X Chromium technology and sequenced by an Illumina sequencer. Signac was used for preliminary analysis, clustering, and differentially accessible chromatin region identification. snMultiome data was used to validate cell annotations for the snATAC-Seq data. Results: Unique populations comprised the benign and tumor samples. Myeloid cell transcription factor activities were higher in tumor samples than benign pancreatic samples, enabling us to further stratify myeloid populations in PDAC tumors. GO enrichment analysis showed myeloid cells can activate immune response in tumors. Subcluster analysis revealed eight distinct myeloid populations. GO enrichment demonstrated unique functions of different myeloid populations, including IL-1b signaling (recruited monocytes) and intracellular protein transport (dendritic cells). Conclusions: These data suggest snATAC-Seq as a method for retrospective analysis of frozen human pancreatic tissues to identify myeloid populations. Understanding the source specific potential function of myeloid cells is important for patient prognosis in PDAC.

Project description:Immunotherapeutics represent highly promising agents with the potential to improve patient outcomes in a variety of cancer types. Unfortunately, single-agent immunotherapy has achieved limited clinical benefit to date in patients suffering from pancreatic ductal adenocarcinoma (PDAC). This may be due to the presence of a uniquely immunosuppressive tumor microenvironment (TME) present in PDACs, which creates a barrier to effective immune surveillance. Critical obstacles to immunotherapy in PDAC tumors include the dense desmoplastic stroma that acts as a barrier to T-cell infiltration and the high numbers of tumor-associated immunosuppressive cells. We have identified hyperactivated focal adhesion kinase (FAK) activity in neoplastic PDAC cells as a significant regulator of the fibrotic and immunosuppressive TME. We found that FAK activity was elevated in human PDAC tissues and correlates with high levels of fibrosis and poor CD8+ cytotoxic T-cell infiltration. Single-agent FAK inhibition (VS-4718) dramatically limited tumor progression, resulting in a doubling of survival in the p48-Cre/LSL-KrasG12D/p53Flox/+ (KPC) mouse model of human PDAC. This alteration in tumor progression was associated with dramatically reduced tumor fibrosis, decreased numbers of tumor-infiltrating immature myeloid cells and immunosuppressive macrophages. We postulated that these desirable effects of FAK inhibition on the TME might render PDAC tumors more sensitive to immunotherapy. Accordingly, we found that VS-4718 rendered the previously unresponsive KPC mouse model responsive to anti-PD1 and anti-CTLA4 antagonists leading to a nearly tripling of survival times. These data suggest that FAK inhibition increases immune surveillance by overcoming the fibrotic and immunosuppressive PDAC TME thus rendering tumors more responsive to immunotherapy. We treated KP orthotopic tumor-bearing mice with vehicle and FAK inhibitor (FAKi) for 14 days, then extracted total RNA from tumor tissues.

Dataset Information

Analysis of Single Nuclear Chromatin Accessibility Demonstrates Unique Myeloid Populations Differentially Influence Prognosis in Human Pancreatic Ductal Adenocarcinoma [snMultiome]

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