Abstract Endometrial cancer is a common gynecological malignancy with more than 410,000 new cases diagnosed worldwide in 2020. Endometrial cancer genome-wide association study (GWAS) have identified 21 robust susceptibility regions, most of which lie in non-coding regions and are presumed to act through cell type-specific regulatory elements. However, bulk tissue and cell-line models cannot fully resolve these regulatory programs. This project uses single-nucleus multi-omic (RNA+ATAC) profiling, enabling simultaneous measurement of chromatin accessibility and gene expression within the same nucleus, to generate cell type-specific enhancer-gene maps in endometrial tumors. By integrating these maps with GWAS data, we aim to identify a comprehensive set of candidate endometrial cancer risk genes. We used the 10X Multimodal GEX+ATAC single nucleus sequencing kit to map open chromatin and gene expression profiles in archival endometrial tumors available through the Australian National Endometrial Cancer Study (ANECS), a population-based case-control study of endometrial cancer with extensive clinical data. Libraries were sequenced on the NextSeq2000 platform before data processing using Cell Ranger, Seurat and Signac for cell-type-resolved enhancer-gene mapping. Exploratory enhancer-gene mapping was performed using co-accessibility and gene expression correlation analysis in Signac. Credible risk variants from 21 endometrial cancer GWAS loci were intersected with enhancers to identify candidate causal risk variants and corresponding target genes. Approximately 25,000 nuclei were successfully profiled and clustered into major endometrial cell types, including epithelial (ciliated and unciliated), fibroblast and immune cells. Initial enhancer-gene mapping using Signac co-accessibility analysis identified endometrial cancer risk variants at the 13q22.1 locus residing within epithelial cell enhancers that correlate with KLF5 expression. We have generated the first single-nucleus multimodal map of endometrial cancer, enabling direct linkage of endometrial cancer risk variants to cell type-specific regulatory elements and target genes, including KLF5, a transcription factor that regulates uterine epithelial remodeling and promotes endometrial cancer cell proliferation in experimental models. This work represents an ongoing pilot study, with further tumors and loci being analyzed to reveal cell type-specific endometrial cancer risk genes. Citation Format: Preety Bajwa, Carly Chapman, Dylan Glubb, Tracy O'Mara. Cell type-specific mapping of endometrial cancer risk genes using single-nucleus multi-omics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5921.

ABSTRACTObjectiveEndometrial cancer is one of the few cancers for which mortality is still increasing. A lack of treatment options remains a major challenge, particularly for some subtypes of the disease. GZD824, also known as olverembatinib, is a multi‐kinase inhibitor previously investigated in clinical trials for chronic myeloid leukaemia and Ph+ acute lymphoblastic leukaemia as a BCR‐ABL inhibitor. This study aimed to investigate the pre‐clinical efficacy of GZD824 for the treatment of EC.MethodsHere, we undertook pre‐clinical evaluation of GZD824 in seven endometrial cancer cell lines (HEC‐1‐A, HEC‐1‐B, MFE296, RL95‐2, Ishikawa, KLE and ARK‐1), one normal immortalised endometrium derived cell line (E6E7hTERT) and primary mesothelial and fibroblast cells isolated from normal omentum samples.ResultsGZD824 inhibited the proliferation of all endometrial cancer cell lines, which were significantly more sensitive to GZD824 compared to normal cells (p = 0.030). GZD824 significantly inhibited migration in Ishikawa (endometrioid) and ARK1 (serous) endometrial cancer cell lines and significantly inhibited invasion in the ARK1 cells. Whole transcriptome regulation following two doses (0.1 and 1 μM) of GZD824 in Ishikawa and ARK1 cells was investigated via RNA‐seq, and key components of enriched pathways were investigated at the translational level. Key pathways altered included ROR1/Wnt, GCN2‐ATF4, epithelial to mesenchymal transition (EMT) and PI3K‐AKT.ConclusionTogether, these studies support further investigation of GZD824 as a potential therapeutic agent in endometrial cancer, potentially in combination with immune checkpoint inhibitors.

Objectives: Thyroid dysfunction, particularly hypothyroidism, has been associated with endometrial cancer in observational studies; however, these findings may be confounded by obesity, an endometrial cancer risk factor. To clarify these associations, we performed Mendelian randomisation analysis, a genetic approach that mitigates confounding and reverse causation analyses. Methods: We accessed European-ancestry GWAS summary statistics for endometrial cancer (12,270 cases; 46,126 controls), endometrioid (8758 cases), and non-endometrioid (1230 cases) subtypes. Thyroid dysfunction phenotype and BMI GWAS data were predominantly from individuals of European descent. We used these datasets to conduct univariable and multivariable Mendelian randomisation analyses incorporating body mass index (BMI). Results: Our main finding was a causal association between hypothyroidism and decreased risk of endometrial cancer (OR = 0.93; 95% CI 0.89–0.97; p = 3.96 × 10−4). Subtype analysis revealed a decreased risk of the most common histological subtype, endometrioid endometrial cancer, and a similar protective association for Hashimoto’s thyroiditis, an autoimmune disease and common cause of hypothyroidism. Sensitivity analyses confirmed the robustness of the associations. Further analyses revealed that while BMI was causally associated with hypothyroidism risk, both BMI and hypothyroidism independently influenced endometrial cancer risk. Conclusions: Our study has identified hypothyroidism as a protective factor for endometrial cancer, challenging previous observational associations and highlighting potential confounding by obesity. Further investigation into immune mechanisms, particularly those linked to Hashimoto’s thyroiditis, may provide insights into the biological pathways underlying endometrial cancer development.

The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERα) for proliferation, but little is known about its transcriptional regulation in these tumors. We generate epigenomics, transcriptomics, and Hi-C datastreams in healthy and tumor endometrial tissues, identifying robust ERα reprogramming and profound alterations in 3D genome organization that lead to a gain of tumor-specific enhancer activity during EC development. Integration with endometrial cancer risk single-nucleotide polymorphisms and whole-genome sequencing data from primary tumors and metastatic samples reveals a striking enrichment of risk variants and non-coding somatic mutations at tumor-enriched ERα sites. Through machine learning-based predictions and interaction proteomics analyses, we identify an enhancer mutation which alters 3D genome conformation, impairing recruitment of the transcriptional repressor EHMT2/G9a/KMT1C, thereby alleviating transcriptional repression of ESR1 in EC. In summary, we identify a complex genomic-epigenomic interplay in EC development and progression, altering 3D genome organization to enhance expression of the critical driver ERα.

Genome-wide association studies have suggested numerous colorectal cancer (CRC) susceptibility genes, but their causality and therapeutic potential remain unclear. To prioritise causal associations between gene expression/splicing and CRC risk (52,775 cases; 45,940 controls), we perform a transcriptome-wide association study (TWAS) across six tissues with Mendelian randomisation and colocalisation, integrating sex- and anatomical subsite-specific analyses. Here we reveal 37 genes with robust causal links to CRC risk, ten of which have not previously been reported by TWAS. Most likely causal genes with evidence of cancer cell dependency show elevated expression linked to risk, suggesting therapeutic potential. Notably, SEMA4D, encoding a protein targeted by an investigational CRC therapy, emerges as a key risk gene. We also identify a female-specific association with CRC risk for CCM2 expression and subsite-specific associations, including LAMC1 with rectal cancer risk. These findings offer valuable insights into CRC molecular mechanisms and support promising therapeutic avenues.

Background:Obesity is a major risk factor for endometrial cancer, but it is unknown whether it impacts the association between genetic risk and endometrial cancer. We incorporated polygenic risk score and epidemiological risk factors in the prediction of and investigated associations of BMI and polygenic risk score with endometrial cancer risk. Methods:We generated polygenic risk score for endometrial cancer in 129,829 unrelated female participants of European ancestry (including 956 incident cases with endometrial cancer) in the UK Biobank and predicted endometrial cancer using endometrial cancer polygenic risk score and established epidemiological risk factors, including BMI. We evaluated the performance of endometrial cancer prediction models by odds ratios and area under the receiver operating characteristic curves (AUCs) to using logistic regression. Individual and joint associations of BMI and polygenic risk score with endometrial cancer were assessed using Cox proportional hazards models. Results:An integrated model incorporating both polygenic risk score and epidemiological risk factors achieved a modest, but statistically significant, improvement in predicting endometrial cancer status compared with the model that included epidemiologic risk factors alone (AUC = 0.74 versus 0.73; P = 3.98 × 10-5). Obese participants (BMI ≥ 30 kg/m2) in the top polygenic risk tertile had the highest endometrial cancer risk. We observed independent effects of genetic risk and BMI on endometrial cancer risk. Conclusion:Integrating polygenic risk score with epidemiological risk factors may offer insights into population stratification for endometrial cancer susceptibility. Higher endometrial cancer polygenic risk is associated with endometrial cancer, irrespective of BMI.

AbstractNumerous potential susceptibility genes have been identified for colorectal cancer (CRC). However, it remains unclear which genes have a causal role in CRC risk, whether these genes are associated with specific types of CRC, and if they have potential for therapeutic targeting. We performed a multi-tissue transcriptome-wide association study (TWAS) across six relevant normal tissues (n=187-670) and applied a causal framework (involving Mendelian randomisation and genetic colocalisation) to prioritise causal associations between gene expression or splicing events and CRC risk (52,775 cases; 45,940 controls), incorporating sex- and anatomical subsite-specific analyses. We identified 35 genes with robust evidence for a potential causal role in CRC, including ten genes not previously identified by TWAS. Among these genes,SEMA4Demerged as a significant discovery; it is not located at any established CRC genome-wide association study (GWAS) risk locus and its encoded protein is targeted by an antibody currently being clinically studied for CRC treatment. Several genes showed increased expression associated with CRC risk and evidence of CRC cell dependency in CRISPR screen analyses, highlighting their potential as targets for therapeutic inhibition. A female-specific association with CRC risk was observed forCCM2expression, which is involved in progesterone signalling pathways. Subsite-specific associations were also found, including a link between rectal cancer risk and expression ofLAMC1, which encodes a target for a clinically approved drug. Additionally, we performed a focused analysis of established drug targets to further identify potential therapies for CRC, revealingPDCD1, the product of which (PD-1) is targeted by a clinically approved CRC immunotherapy. In summary, our comprehensive analysis provides valuable insights into the molecular underpinnings of CRC and supports promising avenues for therapeutic intervention.

Known risk loci for endometrial cancer explain approximately one third of familial endometrial cancer. However, the association of germline copy number variants (CNVs) with endometrial cancer risk remains relatively unknown. We conducted a genome-wide analysis of rare CNVs overlapping gene regions in 4115 endometrial cancer cases and 17,818 controls to identify functionally relevant variants associated with disease. We identified a 1.22-fold greater number of CNVs in DNA samples from cases compared to DNA samples from controls (p = 4.4 × 10–63). Under three models of putative CNV impact (deletion, duplication, and loss of function), genome-wide association studies identified 141 candidate gene loci associated (p < 0.01) with endometrial cancer risk. Pathway analysis of the candidate loci revealed an enrichment of genes involved in the 16p11.2 proximal deletion syndrome, driven by a large recurrent deletion (chr16:29,595,483-30,159,693) identified in 0.15

Abstract Obesity is more strongly associated with endometrial cancer risk than any other cancer type. However, the extent to which genetic susceptibility influences the risk of endometrial cancer independent of obesity remains unknown. Thus, this study aimed to evaluate the predictive performance of polygenic risk score (PRS), body mass index (BMI) and other factors in determining endometrial cancer risk, as well as to explore joint effects on endometrial cancer. PRS was generated using 1.1 million HapMap3 variants from the largest published endometrial cancer genome-wide association study. An endometrial cancer prediction model was constructed using established endometrial cancer risk factors (age, BMI, number of live births, ever taken oral contraceptive pill, age of menarche, and predicted age of menopause). Additionally, an integrated prediction model was constructed, combining the endometrial cancer PRS with established risk factors. The ability of models to predict endometrial cancer status was assessed in unrelated participants of European ancestry from the UK Biobank cohort, encompassing 1,867 participants with endometrial cancer (860 incident cases) and 133,322 cancer-free controls. The integrated model including PRS and risk factors had a modest yet statistically significant improvement in prediction of endometrial cancer status, compared with the model using risk factors alone (AUC 0.752 versus 0.741; P = 1.28 × 10−7). When examining incident cases, participants in the middle and top tertiles of the PRS distribution had a 1.96- (95% CI 1.39-2.77; P = 1.28 × 10−4) and 3.03-fold (95% CI 2.01-4.58; P = 1.60 × 10−8) elevated risk of developing endometrial cancer, respectively, in contrast to those in the lowest tertile. As expected, elevated BMI was associated with increased endometrial cancer risk. Compared to participants with a normal BMI, overweight participants (25kg/m2 ≤ BMI < 30kg/m2) had a 1.58-fold increased hazard ratio (HR; 95% CI 1.32-1.90; P = 8.43 × 10−7), while obese participants (BMI ≥ 30kg/m2) a 3.23-fold increased HR (95% CI 2.71-3.85; P < 2.00 × 10−16). Notably, we observed multiplying effects of BMI and PRS on endometrial cancer risk, with obese participants in the top tertile of the PRS distribution having a 7.53-fold increased HR (95% CI 3.78-14.99; P = 9.41 × 10−9). In summary, these findings indicate that higher PRS was associated with endometrial cancer risk, irrespective of BMI. Moreover, the integration of PRS with established risk factors may aid in better stratifying the general population for their susceptibility to endometrial cancer. Citation Format: Tracy A. O'Mara, Xuemin Wang, Laure Dossus, Marc J. Gunter, Emma J. Crosbie, Dylan M. Glubb. Highlighting the combined effects of BMI and polygenic risk score on endometrial cancer risk [abstract]. In: Proceedings of the AACR Special Conference on Endometrial Cancer: Transforming Care through Science; 2023 Nov 16-18; Boston, Massachusetts. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(5_Suppl):Abstract nr PR001.

PDF file - 46K, KDR regions containing dense clusters of transcription factor binding motifs identified by Cluster-Buster.

PDF file - 29K, VEGFR-2 levels and disease stage. Panel A shows the log2-transformed VEGFR-2 levels from NSCLC samples of different disease stages. In panel B, Group 1 is composed of stages I and II; Group 2 is composed of stages III and IV. The result of a t-test examining the differences between the two groups is shown.

PDF file - 948K, Analysis of LD between KDR SNPs in the NSCLC cohort. The values in the squares show significant r2 values.

Alternative splicing contributes to cancer development. Indeed, splicing analysis of cancer genome-wide association study (GWAS) risk variants has revealed likely causal variants. To systematically assess GWAS variants for splicing effects, we developed a prioritization workflow using a combination of splicing prediction tools, alternative transcript isoforms, and splicing quantitative trait locus (sQTL) annotations. Application of this workflow to candidate causal variants from 16 endometrial cancer GWAS risk loci highlighted single-nucleotide polymorphisms (SNPs) that were predicted to upregulate alternative transcripts. For two variants, sQTL data supported the predicted impact on splicing. At the 17q11.2 locus, the protective allele for rs7502834 was associated with increased splicing of an exon in a NF1 alternative transcript encoding a truncated protein in adipose tissue and is consistent with an endometrial cancer transcriptome-wide association study (TWAS) finding in adipose tissue. Notably, NF1 haploinsufficiency is protective for obesity, a well-established risk factor for endometrial cancer. At the 17q21.32 locus, the rs2278868 risk allele was predicted to upregulate a SKAP1 transcript that is subject to nonsense-mediated decay, concordant with a corresponding sQTL in lymphocytes. This is consistent with a TWAS finding that indicates decreased SKAP1 expression in blood increases endometrial cancer risk. As SKAP1 is involved in T cell immune responses, decreased SKAP1 expression may impact endometrial tumor immunosurveillance. In summary, our analysis has identified potentially causal endometrial cancer GWAS risk variants with plausible biological mechanisms and provides a splicing annotation workflow to aid interpretation of other GWAS datasets.

PDF file - 30K, MVD and tumor histology. Panel A shows the log2-transformed MVD percentage of NSCLC samples from different tumor histologies (SCC = squamous cell carcinoma; AC = adenocarcinoma; LCC = large cell carcinoma; NOS = not otherwise specified). In panel B, Group 1 is composed of squamous cell carcinomas and NSCLCs not otherwise specified/mixed; Group 2 is composed of adenocarcinomas and large cell carcinomas. The result of a t-test examining the differences between the two groups is shown.

PDF file - 26K, Correlation of VEGFR-2 and KDR mRNA levels.

PDF file - 60K, KDR conserved regions determined using comparative genomics analysis in the UCSC Genome Browser.

Study schematic for patients genotyped in this study.

PDF file - 31K, Correlation of VEGFR-2 and MVD levels.