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The transcription factors MECOM, PAX8, SOX17 and WT1 are candidate master regulators of high-grade serous ‘ovarian’ cancer (HGSC), yet their cooperative role in the hypothesized tissue of origin, the fallopian tube secretory epithelium (FTSEC) is unknown. We generated 26 epigenome (CUT&TAG, CUT&RUN, ATAC-seq and HiC) data sets and 24 profiles of RNA-seq transcription factor knock-down followed by RNA sequencing in FTSEC and HGSC models to define binding sites and gene sets regulated by these factors incisandtrans. This revealed that MECOM, PAX8, SOX17 and WT1 are lineage-enriched, super-enhancer associated master regulators whose cooperative DNA-binding patterns and target genes are re-wired during tumor development. All four TFs were indispensable for HGSC clonogenicity and survival but only depletion of PAX8 and WT1 impaired FTSEC cell survival. These four TFs were pharmacologically inhibited by transcriptional inhibitors only in HGSCs but not in FTSECs. Collectively, our data highlights that tumor-specific epigenetic remodeling is tightly related to MECOM, PAX8, SOX17 and WT1 activity and these transcription factors are targetable in a tumor-specific manner through transcriptional inhibitors.

Applying wastewater in subsurface drip irrigation helps address water shortage in arid and semi-arid environments. Microbial contamination may result, but soil amendments such as biochar could help protect soil and water resources. To improve understanding, this study investigated spatio-temporal dynamics of fecal coliform retention in a biochar-treated soil under subsurface drip irrigation. Two dripper discharges rates of 2 and 4 l hr

Description, The CaCTS algorithm nominates cancer cell master transcription factors and guides a model of ovarian cancer regulatory circuitry., Critical developmental “master transcription factors” (MTFs) can be subverted during tumorigenesis to control oncogenic transcriptional programs. Current approaches to identifying MTFs rely on ChIP-seq data, which is unavailable for many cancers. We developed the CaCTS (Cancer Core Transcription factor Specificity) algorithm to prioritize candidate MTFs using pan-cancer RNA sequencing data. CaCTS identified candidate MTFs across 34 tumor types and 140 subtypes including predictions for cancer types/subtypes for which MTFs are unknown, including e.g. PAX8, SOX17, and MECOM as candidates in ovarian cancer (OvCa). In OvCa cells, consistent with known MTF properties, these factors are required for viability, lie proximal to superenhancers, co-occupy regulatory elements globally, co-bind loci encoding OvCa biomarkers, and are sensitive to pharmacologic inhibition of transcription. Our predictions of MTFs, especially for tumor types with limited understanding of transcriptional drivers, pave the way to therapeutic targeting of MTFs in a broad spectrum of cancers.

Triple-negative breast cancer (TNBC) has few therapeutic targets, making nonspecific chemotherapy the main treatment. Therapies enhancing cancer cell sensitivity to cytotoxic agents could significantly improve patient outcomes. A BCL2-associated agonist of cell death (BAD) pathway gene expression signature (BPGES) was derived using principal component analysis (PCA) and evaluated for associations with the TNBC phenotype and clinical outcomes. Immunohistochemistry was used to determine the relative expression levels of phospho-BAD isoforms in tumour samples. Cell survival assays evaluated the effects of BAD pathway inhibition on chemo-sensitivity. BPGES score was associated with TNBC status and overall survival (OS) in breast cancer samples of the Moffitt Total Cancer Care dataset and The Cancer Genome Atlas (TCGA). TNBC tumours were enriched for the expression of phospho-BAD isoforms. Further, the BPGES was associated with TNBC status in breast cancer cell lines of the Cancer Cell Line Encyclopedia (CCLE). Targeted inhibition of kinases known to phosphorylate BAD protein resulted in increased sensitivity to platinum agents in TNBC cell lines compared to non-TNBC cell lines. The BAD pathway is associated with triple-negative status and OS. TNBC tumours were enriched for the expression of phosphorylated BAD protein compared to non-TNBC tumours. These findings suggest that the BAD pathway it is an important determinant of TNBC clinical outcomes.

Endometriosis is a common, benign condition characterized by extensive heterogeneity in lesion appearance and patient symptoms. We profiled transcriptomes of 207,949 individual cells from endometriomata (n=7), extra-ovarian endometriosis (n=19), eutopic endometrium (n=4), unaffected ovary (n=1) and endometriosis-free peritoneum (n=4) to create a cellular atlas of endometrial-type epithelial cells, endometrial-type stromal cells and microenvironmental cell populations across tissue sites. Signatures of endometrial-type epithelium and stroma differed markedly across eutopic endometrium, endometrioma, superficial extra-ovarian disease and deep infiltrating endometriosis, suggesting that extensive transcriptional reprogramming is a core component of the disease process. Endometriomas were notable for the dysregulation of pro-inflammatory pathways and upregulation of complement proteins C3 and C7. Somatic ARID1A mutation in epithelial cells was associated with upregulation of pro-angiogenic factor SOX17 and remodeling of the endothelial cell compartment. Finally, signatures of endometriosis-associated endometrial-type epithelial clusters were enriched in ovarian cancers, reinforcing the epidemiologic associations between these two diseases.

Summary The human fallopian tube harbors the cell of origin for the majority of high-grade serous “ovarian” cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We perform single-cell transcriptomic profiling of around 53,000 individual cells from 12 primary fallopian specimens to map their major cell types. We identify 10 epithelial subpopulations with diverse transcriptional programs. Based on transcriptional signatures, we reconstruct a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of advanced HGSCs identifies the “early secretory” population as a likely precursor state for the majority of HGSCs. Its signature comprises both epithelial and mesenchymal features and is enriched in mesenchymal-type HGSCs (p = 6.7 × 10−27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.

SummaryThe human fallopian tube harbors the cell-of-origin for the majority of high-grade serous ‘ovarian’ cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We performed single-cell transcriptomic profiling in 12 primary fallopian specimens from 8 patients, analyzing around 53,000 individual cells to map the major immune, fibroblastic and epithelial cell types present in this organ. We identified 10 epithelial sub-populations, characterized by diverse transcriptional programs including SOX17 (enriched in secretory epithelial cells), TTF3 and RFX3 (enriched in ciliated cells) and NR2F2 (enriched in early, partially differentiated secretory cells). Based on transcriptional signatures, we reconstructed a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of the cellular composition of advanced HGSCs based on epithelial subset signatures identified the ‘early secretory’ population as a likely precursor state for the majority of HGSCs. The signature of this rare population of cells comprised both epithelial (EPCAM, KRT) and mesenchymal (THY1, ACTA2) features, and was enriched in mesenchymal-type HGSCs (P = 6.7 × 10−27), a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia.

The five-year survival rate of ovarian cancer (OC) dramatically rises from below 40% to 90% with patients who are diagnosed early (stage I), when the disease restricts to the ovary. Thus, the ultimate goals of our research are to learn how to detect ovarian cancer at its earliest stages of development and thereby improve patient survival and to learn how the immune microenvironment contributes to the development of OC. Achieving these goals requires us to better characterize the earliest steps in ovarian carcinogenesis. The human fallopian tube harbors the cell-of-origin for most high-grade serous 'ovarian' cancers (HGSOCs), but its cellular composition, particularly the immune component, is poorly characterized. Emerging evidence from several research groups using molecular sequencing technologies of fallopian tube epithelium strongly support this hypothesis. We recently described our use of single-cell transcriptome technology (scRNA-Seq) to profile the heterogeneity of non-malignant FT and define a novel transcriptional gene regulatory network of epithelial differentiation and tumorigenesis in the human FT. Here we present an in-depth characterization of the immune cell atlas for human fallopian tubes, which has not been reported. Our unpublished analyses of our FT dataset and the publicly available HGSOC scRNA-Seq dataset demonstrate a significant difference in the immune cell landscape. There are limited macrophages and a high abundance of monocytes in non-malignant FT and adjacent normal ovaries compared to those in HGSOC tumors. This finding leads us to hypothesize that the macrophage-to-monocyte ratio and their interactions with other immune cell types in human fallopian tubes create a permissive microenvironment allowing for the development of HGSOC and can provide a biomarker for early cancer detection. To test if those myeloid cells could be a marker for early HGSOC, we performed scRNA-seq on FT from women carrying mutant alleles of BRCA1 or BRCA2 who are at high risk of HGSOC. Intriguingly, the ratio of monocytes to macrophages in the FTs from half of these high-risk individuals is more like that found in HGSOC than in normal FT. Furthermore, computational analyses on myeloid cell types and their interactions with different epithelial cells, stromal fibroblast cells, and T and NK cells revealed the extended contribution of the non-epithelial microenvironment in FT, potentially driving early HGSOC development and progression. This cellular and molecular compendium of the human fallopian tube immune landscapes in cancer-free and cancer-high-risk women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia. Citation Format: Josh Brand, Marcela Harro, Forough Abbasi, Xianzhi Lin, Matthew Siedhoff, Li Andrew, Bobbie J. Rimel, Fabiola Medeiros, Kate Lawrenson, Huy Q. Dinh. Immune landscapes and interactions in human fallopian tubes and their implications for early high-grade serous ovarian cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5148.

The 5-year survival rate of high grade serous ovarian cancer (HGSOC) has remained below 40% for decades. This rises significantly to 90% when detected early. Increasing evidence suggests that HGSOC tumors originate in the fallopian tube (FT). However, little is known about FT’s immune cell heterogeneity and how it contributes to HGSOC development. Here we show a single-cell transcriptome analysis of non-malignant FT samples, revealing high monocyte diversity that is lost in HGSOC. FT monocyte subsets display distinct inflammatory gene signatures such as IL1A, CCL3/4 and others. Trajectory inference showed potential monocyte maturation steps that started with early cytokine/chemokine secreting monocytes that gain MHCII expression and develop into macrophages or dendritic cells. We found the macrophage-to-monocyte ratio is remarkably elevated in tumors compared to adjacent normal ovary and non-cancerous FT tissues in ours and publicly available scRNA-Seq. Intriguingly, analysis of FT of patients with BRCA1/2 germline mutations revealed half of these high-risk individuals are more like those found in HGSOC tumors than in normal FT. They also showed distinct T cell phenotypes in their FTs. Our data suggested that myeloid diversity, and their interactions with T cells in the FT, might contribute to early HGSOC development. Understanding tissue-of-origins immune microenvironment has a potential contribution to early cancer detection. We anticipate this work provides evidence of how myeloid cell plasticity induces tumorigenesis and can shape different tumor microenvironments. Supported by startup grants from UW-Madison School of Medicine and Public Health and UW-Madison Cellular and Molecular Pathology Graduate Training Program travel awards

The function of critical developmental regulators can be subverted by cancer cells to control expression of oncogenic transcriptional programs. These "master transcription factors" (MTFs) are often essential for cancer cell survival and represent vulnerabilities that can be exploited therapeutically. The current approaches to identify candidate MTFs examine super-enhancer associated transcription factor-encoding genes with high connectivity in network models. This relies on chromatin immunoprecipitation-sequencing (ChIP-seq) data, which is technically challenging to obtain from primary tumors, and is currently unavailable for many cancer types and clinically relevant subtypes. In contrast, gene expression data are more widely available, especially for rare tumors and subtypes where MTFs have yet to be discovered. We have developed a predictive algorithm called CaCTS (Cancer Core Transcription factor Specificity) to identify candidate MTFs using pan-cancer RNA-sequencing data from The Cancer Genome Atlas. The algorithm identified 273 candidate MTFs across 34 tumor types and recovered known tumor MTFs. We also made novel predictions, including for cancer types and subtypes for which MTFs have not yet been characterized. Clustering based on MTF predictions reproduced anatomic groupings of tumors that share 1-2 lineage-specific candidates, but also dictated functional groupings, such as a squamous group that comprised five tumor subtypes sharing 3 common MTFs. PAX8, SOX17, and MECOM were candidate factors in high-grade serous ovarian cancer (HGSOC), an aggressive tumor type where the core regulatory circuit is currently uncharacterized. PAX8, SOX17, and MECOM are required for cell viability and lie proximal to super-enhancers in HGSOC cells. ChIP-seq revealed that these factors co-occupy HGSOC regulatory elements globally and co-bind at critical gene loci including MUC16 (CA-125). Addiction to these factors was confirmed in studies using THZ1 to inhibit transcription in HGSOC cells, suggesting early down-regulation of these genes may be responsible for cytotoxic effects of THZ1 on HGSOC models. Identification of MTFs across 34 tumor types and 140 subtypes, especially for those with limited understanding of transcriptional drivers paves the way to therapeutic targeting of MTFs in a broad spectrum of cancers.

Determining the function of non-coding regulatory variants in cancer is a key challenge transcriptional biology. We investigated genetic (germline and somatic) determinants of regulatory mechanisms in renal cell carcinoma (RCC) using H3K27ac ChIP-seq data in 10 matched tumor/normal samples and RNA-seq data from 496/66 tumor/normal samples from The Cancer Genome Atlas (TCGA). Unsupervised clustering of H3K27ac activity cleanly separated tumor from normal individuals, highlighting extensive epigenetic reprogramming during transformation. We developed a novel method to test each chromatin feature for evidence of an allele-specific quantitative trait locus (asQTL) and evaluate tumor/normal differences in allele-specificity (d-asQTLs) while modelling local structural variation and read overdispersion. At an FDR of 5%, we identified 1,356 unique asQTL chromatin peaks in normal tissues; 2,868 in tumors; and 1,054 d-asQTLs (primarily imbalanced in tumor). The d-asQTL peaks were significantly enriched for RCC genome-wide association study (GWAS) heritability (32x, P=1.8×10−3), more so than any other functional feature including all H3K27ac peaks (12x), super-enhancers (5x), and asQTL genes (4x). Intersection of asQTLs with RCC GWAS loci identified putative functional features for 6/17 known loci including tumor-specific activity at SCARB1, a cholesterol metabolism mediator, which has recently been implicated in RCC progression. We validated the asQTL variant through CRISPR interference (CRISPRi) and demonstrated a concomitant allelic effect on the overlapping enhancer and on downstream SCARB1 expression. Knockdowns of master transcription factors (TFs) involved in the hypoxia pathway altered the expression of SCARB1 in a kidney cancer cell line, consistent with a variant-TF interaction. Genome-wide, d-asQTLs were significantly enriched for tumor-specific binding of hypoxic transcription factors, implicating a more general mechanism for polygenic germline-somatic interaction.

Clear cell ovarian and kidney cancers are rare but aggressive cancers characterized by resistance to traditional chemotherapies. The transcriptional drivers of these tumors are poorly understood, but the histologic similarities suggest that a subset of common factors may drive differentiation of the clear cell phenotype, agnostic of anatomic origin. Master transcription factors (MTFs) are the essential transcriptional regulators that create interconnected auto-regulatory circuits critical for tumor cell survival. Candidate MTFs can be identified due to their characteristic high level, tissue-specific expression, functional essentiality in tumor models, and participation in interconnected core regulatory transcriptional circuits. We collated 5 high grade serous ovarian cancer, 5 clear cell ovarian cancer, 5 papillary renal cell cancer and 11 clear cell renal cell cancer primary tissue and 27 cell line data sets for clear cell ovarian and kidney cancers, and non-clear cell tumors of the same organs. We integrated gene expression, super-enhancer landscapes and global maps of open chromatin to identify candidate MTFs specific to clear cell tumors. This identified known Hepatocyte nuclear factor-1-beta (HNF1B), commonly over-expressed in >90% of clear cell cancers and other novel candidates, including RARA, which encodes retinoic acid receptor alpha. Clear cell kidney and ovarian cancer cell lines are often co-dependent on sustained expression of HNF1B and RARA for survival, suggesting perturbed retinoic acid signaling represents a novel therapeutic target for clear cell tumors. Transcriptional inhibitors provide a novel therapeutic target for many cancers that may otherwise be chemoresistant. Clear cell lines are particularly sensitive to general transcriptional inhibitors in in-vitro models; functional analyses are ongoing to determine the role of RARA, HNF1B and other factors in explaining these responses. Citation Format: Marla Elizabeth Scott, Robbin Nameki, Forough Abbasi, Marcos Abraao de Souza Fonseca, Rosario (Ivetth) Corona de la Fuente, Kate Lawrenson. Core regulatory circuits of clear cell ovarian and kidney cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2433.

The human fallopian tube harbors the cell-of-origin for the majority of high-grade serous ‘ovarian’ cancers (HGSCs), but its cellular composition, particularly the epithelial component, is poorly characterized. We performed single-cell transcriptomic profiling in 12 primary fallopian specimens from 8 patients, analyzing around 53,000 individual cells to map the major immune, fibroblastic and epithelial cell types present in this organ. We identified 10 epithelial sub-populations, characterized by diverse transcriptional programs including SOX17 (enriched in secretory epithelial cells), TTF3 and RFX3 (enriched in ciliated cells) and NR2F2 (enriched in early, partially differentiated secretory cells). Based on transcriptional signatures, we reconstructed a trajectory whereby secretory cells differentiate into ciliated cells via a RUNX3high intermediate. Computational deconvolution of the cellular composition of advanced HGSCs based on epithelial subset signatures identified the ‘early secretory’ population as a likely precursor state for the majority of HGSCs. The signature of this rare population of cells comprised both epithelial (EPCAM, KRT) and mesenchymal (THY1, ACTA2) features, and was enriched in mesenchymal-type HGSCs, a group known to have particularly poor prognoses. This cellular and molecular compendium of the human fallopian tube in cancer-free women is expected to advance our understanding of the earliest stages of fallopian epithelial neoplasia. Further computational analyses on fibroblast and immune cells together with tumor single-cell data reveals extended contribution of non-epithelial microenvironment and cell-cell interactions and communications in fallopian tube that potentially drive HGSC progression. Citation Format: Huy Q. Dinh, Xianzhi Lin, Forough Abbasi, Robbin Nameki, Marcela Haro, Claire Olingy, Heidi Chang, Lourdes Hernandez, Simon Gayther, Kelly N. Wright, Paul-Joseph Aspuria, Beth Karlan, Rosario I. Corona, Andrew Li, B.J. Rimel, Matthew Siedhoff, Fabiola Medeiros, Kate Lawrenson. Single-cell transcriptomics identifies gene expression networks driving differentiation and tumorigenesis in the human fallopian tube [abstract]. In: Proceedings of the AACR Virtual Special Conference on the Evolving Tumor Microenvironment in Cancer Progression: Mechanisms and Emerging Therapeutic Opportunities; in association with the Tumor Microenvironment (TME) Working Group; 2021 Jan 11-12. Philadelphia (PA): AACR; Cancer Res 2021;81(5 Suppl):Abstract nr PO023.

Summary: Fallopian tube secretory epithelial cells (FTSECs) are likely the main precursor cell type of high-grade serous ovarian cancers (HGSOCs), but these tumors may also arise from ovarian surface epithelial cells (OSECs). We profiled global landscapes of gene expression and active chromatin to characterize molecular similarities between OSECs (n = 114), FTSECs (n = 74), and HGSOCs (n = 394). A one-class machine learning algorithm predicts that most HGSOCs derive from FTSECs, with particularly high FTSEC scores in mesenchymal-type HGSOCs (padj < 8 × 10−4). However, a subset of HGSOCs likely derive from OSECs, particularly HGSOCs of the proliferative type (padj < 2 × 10−4), suggesting a dualistic model for HGSOC origins. Super-enhancer (SE) landscapes were also more similar between FTSECs and HGSOCs than between OSECs and HGSOCs (p < 2.2 × 10−16). The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs. : Lawrenson et al. profile gene expression and active chromatin in ∼200 ovarian and fallopian epithelial isolates and implement machine learning to demonstrate that most high-grade serous ovarian cancers (HGSOCs) derive from fallopian tube epithelial cells, but a subset may originate from ovarian epithelia. SOX18 induces mesenchymal features to drive early neoplasia in fallopian tube precursors. Keywords: high-grade serous ovarian cancer, ovarian surface epithelial cell, fallopian tube secretory epithelial cell, super enhancers, transcription factors, SOX18, single-cell RNA-seq, RNA-seq, machine learning, one-class logistic regression models, dual origins

Ovarian cancer is a rare but highly lethal gynecologic malignancy, causing around 14,000 deaths annually in the US. The current standard of care for ovarian cancer includes a combination of surgical cytoreduction and platinum-based chemotherapy. Despite these aggressive treatments, most patients suffer from fatal relapses that indicate an urgent need for novel targeted therapies. Master Transcription Factors (MTFs) are transcriptional regulators responsible for cellular identity, and are associated with cell type specific regions of active chromatin termed super-enhancers (SEs). In cancer, MTFs are drivers of tumor development across a variety of organs, and MTF interfering therapies are one of the most successful therapies available today. To further identify tumor-specific MTFs, we have developed the ‘Cancer Core Transcription factor Specificity (CaCTS)' algorithm and prioritized MTFs from a pan-cancer cohort of 10,000 tumors profiled by RNA-sequencing. Results demonstrated that many tumor MTFs derived from CaCTS were specific to its normal tissue-type, validating the algorithm's ability to identify factors involved in cellular identity. On the other hand, a set of highly expressed TFs were frequently observed in multiple cancer types, indicating two distinct classes of MTFs: lineage-specific MTFs and pan-cancer MTFs. In High-Grade Serous Ovarian Cancer (HGSOC), CaCTS prioritized 21 TFs with lineage specific MTF traits. All 21 candidate MTFs were highly expressed in primary HGSOC specimens and aligned with HGSOC SEs identified via H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq). As expected, WT1 and PAX8 were identified, transcription factors previously implicated to be essential in HGSOC lineage specificity. Our algorithm also identified ZNF217, a novel candidate MTF in HGSOC. ZNF217 plays a key role in breast cancer, a tumor type that shares many epidemiological, hormonal and genetic risk factors with HGSOC. Mining of a publicly available gene knockout experiment in 13 HGSOC cell lines revealed ZNF217 to have similar levels of gene essentiality as PAX8. We are currently examining the role of ZNF217 as a MTF in HGSOC by determining its target genes, binding partners, and cellular consequences of siRNA-mediated knockdown. We expect ZNF217 to occupy SEs that drive expression of genes critical for cell identity, co-occupy SEs with other candidate MTFs, and depletion of ZNF217 to result in loss of cell state. Understanding the mechanisms of transcriptional control in HGSOC will ultimately help to identify clinically relevant drivers which can serve as novel therapeutic targets for this devastating disease. Citation Format: Robbin Nameki, Marcos A. S. Fonseca, Jessica Reddy, Kevin C. Vavra, Felipe Segato, Rosario I. Corona, Ji-Heui Seo, Annie Liu, Forough Abbasi, Xianzhi Lin, Beth Y. Karlan, Matthew L. Freedman, Simon A. Gayther, Houtan Noushmehr, Kate Lawrenson. PAN-CANCER TRANSCRIPTION FACTOR ANALYSES IDENTIFY ZNF217 AS A NOVEL DRIVER IN HGSOC [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-042.

Determining the function of non-coding regulatory variants in cancer remains a key challenge. We investigated genetic (germline and somatic) determinants of regulatory mechanisms in renal cell carcinoma (RCC) using H3K27ac ChIP-seq data in 10 matched tumor/normal samples and RNA-seq data from 496/66 tumor/normal samples from The Cancer Genome Atlas (TCGA). Unsupervised clustering of H3K27ac activity cleanly separated tumor from normal individuals, highlighting extensive epigenetic reprogramming during transformation. We developed a novel method to test each chromatin feature for allele-specific activity (asQTL) and evaluate tumor/normal differences in allele-specificity (d-asQTLs) while modelling local structural variation and read overdispersion. At an FDR of 5%, we identified 1,356 unique asQTL chromatin peaks in normal tissues; 2,868 in tumors; and 1,054 d-asQTLs (primarily imbalanced in tumor). The d-asQTL peaks were significantly enriched for RCC GWAS heritability (32x, P=1.8x10-3), more so than any other functional feature including all H3K27ac peaks (12x), super-enhancers (5x), and regions near asQTL genes (4x). Intersection of asQTLs with RCC genome-wide association study (GWAS) data identified putative functional features for 6/17 known loci including tumor-specific activity at SCARB1, which has recently been implicated as a prognostic biomarker in RCC. d-asQTLs were significantly enriched for tumor-specific binding of transcription factors in the hypoxia pathway, implicating a general mechanism for polygenic germline-somatic interaction. Citation Format: Alexander Gusev, Sandor Spisak, Forough Abbasi, Andre Fay, Hallie Carol, Ji-Heui Seo, Toni Choueiri, Kate Lawrenson, Matthew Freedman. Widespread germline-somatic regulatory differences in renal cell carcinoma prioritize risk mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr SY25-02.