Interferon-gamma is Quintessential for NOS2 and COX2 Expression in ER - Breast Tumors that Lead to Poor Outcome

A strong correlation between NOS2 and COX2 tumor expression and poor clinical outcomes in ER-breast cancer has been established. However, mechanisms of tumor induction of these enzymes are unclear. Analysis of The Cancer Genome Atlas (TCGA) revealed correlations between NOS2 and COX2 expression and Th1 cytokines. Herein, single cell RNAseq analysis of TNBC cells shows potent NOS2 and COX2 induction by IFNγ combined with IL1β or TNFα. Given that IFNγ is secreted by cytolytic lymphocytes, which improve clinical outcomes, this role of IFNγpresents a dichotomy. To explore this conundrum, tumor NOS2, COX2, and CD8 ⁺ T cells were spatially analyzed in aggressive ER-, TNBC, and HER2+ breast tumors. High expression and clustering of NOS2-expressing tumor cells occurred at the tumor/stroma interface in the presence of stroma-restricted CD8 ⁺ T cells. High expression and clustering of COX2-expressing tumor cells extended into immune desert regions in the tumor core where CD8 ⁺ T cell penetration was limited or absent. Moreover, high NOS2-expressing tumor cells were proximal to areas with increased satellitosis suggestive of cell clusters with a higher metastatic potential. Further in vitro experiments revealed that IFNγ+IL1β/TNFα increased elongation and migration of treated tumor cells. This spatial analysis of the tumor microenvironment provides important insight of distinct neighborhoods where stroma-restricted CD8 ⁺ T cells exist proximal to NOS2-expressing tumor niches that could have increased metastatic potential.

Abstract 6225: SERPINB3 promotes the aggressive basal-like/squamous subtype and correlates with poor prognosis in pancreatic ductal adenocarcinoma through metabolic reprogramming

In this study, we aimed to find genes with a key function in the development of molecular subtypes in pancreatic ductal adenocarcinoma (PDAC). Through transcriptome analysis, we discovered that the endogenous serine/cysteine proteinase inhibitor SERPINB3 (squamous cell carcinoma antigen 1, SCCA1) was distinctively upregulated in the basal-like/squamous subtype, known as an aggressive subtype, and this upregulation associated with decreased patient survival in both a test (N=123) and a validation cohort (N=84). In additional investigations of the tumor metabolome and transcriptome using PDAC patient tumors and cell lines, SERPINB3 and the basal-like/squamous subtype showed a robust relationship with upregulated levels of amino acids (e.g., hydroxyproline) whereas SERPINB3 promoted a gene signature indicative of the basal-like/squamous subtype. Additional mechanistic studies revealed that SERPINB3 and hydroxyproline promoted the migration/invasion of PDAC cells. Moreover, SERPINB3 also promoted metastasis in an orthotopic mouse model of PDAC through stromal factors that increased tumor microvessel density. To conclude, inhibiting SERPINB3 function may attenuate disease progression of the basal-like/squamous subtype in PDAC through changes to the tumor stroma and tumor metabolism.

Citation Format: Yuuki Ohara, Wei Tang, Liu Huaitian, Shouhui Yang, Peijun He, Helen Cawley, Paloma Valenzuela, Lin Zhang, Jochen Gaedcke, B. Michael Ghadimi, Matthias M. Gaida, Frank Bergmann, H. Richard Alexander, Nader Hanna, Stefan Ambs, S. Perwez Hussain. SERPINB3 promotes the aggressive basal-like/squamous subtype and correlates with poor prognosis in pancreatic ductal adenocarcinoma through metabolic reprogramming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6225.

Abstract NG06: Investigating biological mediators of social and environmental risk factors on cancer health disparities

Background: Chronic life stress is more prevalent in low socioeconomic status (SES) communities and has been shown to affect DNA methylation and the immune system. Yet, the biological processes that mediate the impact of SES on health to promote the development of chronic diseases like cancer remain poorly understood. Previous studies have shown that individuals from disadvantaged neighborhoods experience a disproportionate amount of both chemical and non-chemical stressors, in addition to epigenetic alterations such as histone modifications and aberrant DNA methylation, compared to those from advantaged neighborhoods. These alternations lead to differential epigenomic profiles between these socioeconomic groups which can be long lasting, even transgenerational. Our study aims to uncover if DNA methylation is linked to neighborhood socioeconomic deprivation and to a biology that causes changes to the immune microenvironment that would promote breast cancer development, progression, and reduced survival. We are specifically interested in this relationship among Black and White women with breast cancer, largely due to the 40% increased mortality that Black women experience compared to White women.

Methods: DNA was extracted from 426 fresh frozen breast tissue samples from 173 Black and 116 White women in the NCI-Maryland Breast Cancer Cohort, including 185 tumor samples, 137 paired adjacent normal tissue samples, and 104 normal breast tissue samples collected from reduction mammoplasty. Using zip codes, we geocoded the locations of our study participants and linked these data to Census tract-level socioeconomic deprivation from the 2000 Census using a Neighborhood Deprivation Index (NDI). We conducted a principal component analysis (PCA) to extract a single variable that represented the shared variance across the original 20 deprivation indicators. PCA loadings about 0.25 were retained in our index including % of households in poverty, % of households on public assistance, % of households with no car, % of female headed households with dependent children, % of households earning less than $30,000 per year, and the % of males and females unemployed. Higher NDI values represented greater deprivation and lower NDI values correlated with less deprivation. The NDI was analyzed either on a continuous scale, in quartiles, or was dichotomized into high and low groups based on median cutoffs. DNA methylation data was acquired using the Illumina EPIC 850K array and a differentially methylated probe (DMP) analysis was done between tumor and paired adjacent normal tissue to identify gene regions of hypo- or hyper-methylation stratified by high and low NDI status. Additionally, using a volcano plot investigating fold change differences between NDI high and NDI low methylation beta values, we identified CpG methylation probes significantly associated with high NDI status in the tumor tissue. Finally, we used a methylCIBERSORT deconvolution analysis to estimate immune cell subpopulation differences by tissue type, race, and neighborhood deprivation status.

Results: In characterizing NDI by demographic and clinical characteristics in our cohort, we found that Black participants had significantly higher NDI levels compared to White participants (p<0.0001) in both normal and tumor tissue. When considering tumor grade and molecular breast cancer subtypes, we found that higher tumor grade was significantly associated with high NDI status (p=0.0344), and higher mean NDI levels were observed in individuals with triple negative breast cancer as compared to hormone receptor positive breast cancer. From the DMP tumor versus adjacent normal paired analysis, we observed that the high neighborhood deprivation group showed more significant methylation events than the low neighborhood deprivation group, including increased hypo- and hyper-methylation in the tumor tissue compared to the adjacent normal tissue. We also found that the location of methylation changes were similar between the NDI high and low groups, with most occurring in the gene body and intergenic regions. In tumor tissue, we identified 8 hypo-methylated CpG probes that were significantly associated with high NDI status, including decreased methylation in the gene body region of two tumor suppressor genes, LRIG1 and WWOX. As methylation in the gene body of cancer cells often correlates to decreased gene expression, our results would indicate less transcriptional activity of these tumor suppressor genes in the NDI high group, potentially resulting in an increased risk of breast cancer metastasis, worse prognosis, and higher mortality. Finally, our methylCIBERSORT analysis showed decreased neutrophils in the NDI high group, which may correlate to poor response to neoadjuvant chemotherapy and more advanced stages of breast cancer.

Significance: To date, little is known about how the epigenome translates neighborhood disadvantage into health disparities. Our findings show evidence of differential methylation expression in tumor and adjacent normal tissue for individuals experiencing high neighborhood deprivation, potentially translating to more adverse breast cancer outcomes for this group. This work gives mechanistic insight into how socioeconomic position may affect cancerous mammary gland biology by altering DNA methylation patterns and immune cell responses.

Citation Format: Brittany D. Lord, Emily Rossi, Tiffany H. Dorsey, Catherine Pichardo, William Wooten, Margaret Pichardo, Ruby Hutchison, Maeve Bailey-Whyte, Anuoluwapo Ajao, Stefan Ambs. Investigating biological mediators of social and environmental risk factors on cancer health disparities. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr NG06.

Supplementary Figure S4 from Dysregulation of miR-212 Promotes Castration Resistance through hnRNPH1-Mediated Regulation of AR and AR-V7: Implications for Racial Disparity of Prostate Cancer.. [DOI: 10.1158/1078-0432.22458242.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

<p>qRT-PCR analysis of miR-132 and miR-495 expression in microdissected prostate tumors</p>

Supplementary Figure S2 from Dysregulation of miR-212 Promotes Castration Resistance through hnRNPH1-Mediated Regulation of AR and AR-V7: Implications for Racial Disparity of Prostate Cancer.. [DOI: 10.1158/1078-0432.22458248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

<p>Suppressive subtractive hybridization and construction of race-based prostate tumor specific cDNA libraries</p>

Supplementary Figure S2 from Dysregulation of miR-212 Promotes Castration Resistance through hnRNPH1-Mediated Regulation of AR and AR-V7: Implications for Racial Disparity of Prostate Cancer.. [DOI: 10.1158/1078-0432.22458248.v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

<p>Suppressive subtractive hybridization and construction of race-based prostate tumor specific cDNA libraries</p>

Stabilization of E-cadherin adhesions by COX-2/GSK3β signaling is a targetable pathway in metastatic breast cancer

Metastatic progression of epithelial cancers can be associated with epithelial-mesenchymal transition (EMT) including transcriptional inhibition of E-cadherin (CDH1) expression. Recently, EM plasticity (EMP) and E-cadherin-mediated, cluster-based metastasis and treatment resistance have become more appreciated. However, the mechanisms that maintain E-cadherin expression in this context are less understood. Through studies of inflammatory breast cancer (IBC) and a 3D tumor cell "emboli" culture paradigm, we discovered that cyclooxygenase 2 (COX-2; PTGS2), a target gene of C/EBPδ (CEBPD), or its metabolite prostaglandin E2 (PGE2) promotes protein stability of E-cadherin, β-catenin, and p120 catenin through inhibition of GSK3β. The COX-2 inhibitor celecoxib downregulated E-cadherin complex proteins and caused cell death. Coexpression of E-cadherin and COX-2 was seen in breast cancer tissues from patients with poor outcome and, along with inhibitory GSK3β phosphorylation, in patient-derived xenografts (PDX) including triple negative breast cancer (TNBC).Celecoxib alone decreased E-cadherin protein expression within xenograft tumors, though CDH1 mRNA levels increased, and reduced circulating tumor cell (CTC) clusters. In combination with paclitaxel, celecoxib attenuated or regressed lung metastases. This study has uncovered a mechanism by which metastatic breast cancer cells can maintain E-cadherin-mediated cell-to-cell adhesions and cell survival, suggesting that some patients with COX-2+/E-cadherin+ breast cancer may benefit from targeting of the PGE2 signaling pathway.

Systemic Inflammation Indices and Association with Prostate Cancer Survival in a Diverse Patient Cohort

There is a lack of investigations assessing the performance of systemic inflammation indices as outcome predictive tools in African Americans with prostate cancer. This study aims to assess the relationships between neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), systemic immune-inflammation (SII), and systemic inflammation response index (SIRI) with survival outcomes among 680 diverse men with prostate cancer. Routine blood results were collected from self-identified African American and European American patients. We applied multivariable Cox regression modeling to examine the associations of systemic inflammation indices with overall and prostate cancer-specific survival. The median survival follow-up was 5.9 years, with 194 deaths. NLR, SII, and SIRI, but not PLR, showed associations with all-cause and prostate cancer-specific mortality when coded as dichotomized and continuous variables. NLR and SIRI were significantly associated with prostate cancer-specific mortality among all men (hazard ratio (HR) 2.56 for high vs. low NLR; HR 3.24 for high vs. low SIRI) and African American men (HR 2.96 for high vs. low NLR; HR 3.19 for high vs. low SIRI). Among European Americans, only SII showed an association with prostate cancer-specific survival. These observations suggest that inflammation indices merit further study as predictors of prostate cancer mortality.

Short term starvation potentiates the efficacy of chemotherapy in triple negative breast cancer via metabolic reprogramming

BACKGROUND

Chemotherapy (CT) is central to the treatment of triple negative breast cancer (TNBC), but drug toxicity and resistance place strong restrictions on treatment regimes. Fasting sensitizes cancer cells to a range of chemotherapeutic agents and also ameliorates CT-associated adverse effects. However, the molecular mechanism(s) by which fasting, or short-term starvation (STS), improves the efficacy of CT is poorly characterized.

METHODS

The differential responses of breast cancer or near normal cell lines to combined STS and CT were assessed by cellular viability and integrity assays (Hoechst and PI staining, MTT or H₂DCFDA staining, immunofluorescence), metabolic profiling (Seahorse analysis, metabolomics), gene expression (quantitative real-time PCR) and iRNA-mediated silencing. The clinical significance of the in vitro data was evaluated by bioinformatical integration of transcriptomic data from patient data bases: The Cancer Genome Atlas (TCGA), European Genome-phenome Archive (EGA), Gene Expression Omnibus (GEO) and a TNBC cohort. We further examined the translatability of our findings in vivo by establishing a murine syngeneic orthotopic mammary tumor-bearing model.

RESULTS

We provide mechanistic insights into how preconditioning with STS enhances the susceptibility of breast cancer cells to CT. We showed that combined STS and CT enhanced cell death and increased reactive oxygen species (ROS) levels, in association with higher levels of DNA damage and decreased mRNA levels for the NRF2 targets genes NQO1 and TXNRD1 in TNBC cells compared to near normal cells. ROS enhancement was associated with compromised mitochondrial respiration and changes in the metabolic profile, which have a significant clinical prognostic and predictive value. Furthermore, we validate the safety and efficacy of combined periodic hypocaloric diet and CT in a TNBC mouse model.

CONCLUSIONS

Our in vitro, in vivo and clinical findings provide a robust rationale for clinical trials on the therapeutic benefit of short-term caloric restriction as an adjuvant to CT in triple breast cancer treatment.

The impact of social and environmental factors on cancer biology in Black Americans

Low socioeconomic status (SES) is associated with early onset of chronic diseases and reduced life expectancy. The involvement of neighborhood-level factors in defining cancer risk and outcomes for marginalized communities has been an active area of research for decades. Yet, the biological processes that underlie the impact of SES on chronic health conditions, such as cancer, remain poorly understood. To date, limited studies have shown that chronic life stress is more prevalent in low SES communities and can affect important molecular processes implicated in tumor biology such as DNA methylation, inflammation, and immune response. Further efforts to elucidate how neighborhood-level factors function physiologically to worsen cancer outcomes for disadvantaged communities are underway. This review provides an overview of the current literature on how socioenvironmental factors within neighborhoods contribute to more aggressive tumor biology, specifically in Black U.S. women and men, including the impact of environmental pollutants, neighborhood deprivation, social isolation, structural racism, and discrimination. We also summarize commonly used methods to measure deprivation, discrimination, and structural racism at the neighborhood-level in cancer health disparities research. Finally, we offer recommendations to adopt a multi-faceted intersectional approach to reduce cancer health disparities and develop effective interventions to promote health equity.

Chronic Exposure to Nitric Oxide Induces P53 Mutations and Malignant-like Features in Human Breast Epithelial Cells

The small endogenous signaling molecule nitric oxide (NO) has been linked with chronic inflammation and cancer. The effects of NO are both concentration and temporally dependent; under some conditions, NO protects against damage caused by reactive oxygen species and activates P53 signaling. During chronic inflammation, NO causes DNA damage and inhibits repair proteins. To extend our understanding of the roles of NO during carcinogenesis, we investigated the possible effects of chronic NO exposure on MCF10A breast epithelial cells, as defined by changes in cellular morphology, chromosome/genomic stability, RNA, and protein expression, and altered cell phenotypes. Human MCF10A cells were maintained in varying doses of the NO donor DETANO for three weeks. Distinct patterns of genomic modifications in TP53 and KRAS target genes were detected in NO-treated cells when compared to background mutations. In addition, quantitative real-time PCR demonstrated an increase in the expression of cancer stem cell (CSC) marker CD44 after prolonged exposure to 300 μM DETANO. While similar changes in cell morphology were found in cells exposed to 300-500 μM DETANO, cells cultured in 100 μM DETANO exhibited enhanced motility. In addition, 100 μM NO-treated cells proliferated in serum-free media and selected clonal populations and pooled cells formed colonies in soft agar that were clustered and disorganized. These findings show that chronic exposure to NO generates altered breast epithelial cell phenotypes with malignant characteristics.

Association of Neighborhood Deprivation With Prostate Cancer and Immune Markers in African American and European American Men

Importance

Neighborhood variables may be factors in the excessive burden of prostate cancer among African American men.

Objective

To examine associations between neighborhood deprivation, circulating immune-oncology markers, and prostate cancer among African American and European American men.

Design, Setting, and Participants

A case-control study was conducted between January 1, 2005, and January 1, 2016. Participants included men with prostate cancer and age- and race-frequency-matched population controls. Participants were recruited at the Baltimore Veterans Affairs Medical Center and University of Maryland Medical Center; controls were obtained through the Maryland Motor Vehicle Administration database. National Death Index follow-up was performed through December 31, 2020, and data analysis was conducted from February 1, 2022, through October 31, 2022.

Exposures

2000 Census-tract Neighborhood Deprivation Index as a standardized score.

Main Outcomes and Measures

Primary outcomes included prostate cancer, all-cause mortality, and disease-specific mortality. Secondary outcomes included the National Comprehensive Cancer Network risk score and serum proteomes for 82 immune-oncology markers with pathway annotation.

Results

Participants included men with prostate cancer (n = 769: 405 African American, 364 European American men) and age- and race-frequency-matched population controls (n = 1023: 479 African American, 544 European American men). The median survival follow-up was 9.70 years (IQR, 5.77 years), with 219 deaths. Among 884 African American men, mean (SD) age at recruitment was 63.8 (7.6) years; mean (SD) age at recruitment among 908 European American men was 66.4 (8.1) years. In the multivariable logistic regression analysis with individual socioeconomic status adjustment, neighborhood deprivation was associated with 55% increased odds of prostate cancer among African American men (odds ratio [OR], 1.55; 95% CI, 1.33-1.81), but was not associated with the disease among European American men. Residing in the most-deprived vs least-deprived neighborhoods corresponded to 88% higher disease odds (OR, 1.88; 95% CI, 1.30-2.75) among all men and an approximate 3-fold increase among African American men (OR, 3.58; 95% CI, 1.72-7.45), but no association was noted among European American men. In Cox proportional hazard regression analyses, socioeconomic status-adjusted neighborhood deprivation was associated with an increased all-cause mortality only among African American men (hazard ratio [HR], 1.28; 95% CI, 1.08-1.53), whereas it was associated with metastatic disease and a 50% increased hazard of a prostate cancer-specific death among all men (HR, 1.50; 95% CI, 1.07-2.09). In analyses restricted to controls, neighborhood deprivation was associated with increased activity scores of serum proteome-defined chemotaxis, inflammation, and tumor immunity suppression.

Conclusions and Relevance

The findings of this study suggest that deprived neighborhood residency may increase the risk of African American men for prostate cancer and a related mortality, potentially through its association with systemic immune function and inflammation.

Systemic Nos2 Depletion and Cox inhibition limits TNBC disease progression and alters lymphoid cell spatial orientation and density

Antitumor immune polarization is a key predictor of clinical outcomes to cancer therapy. An emerging concept influencing clinical outcome involves the spatial location of CD8+ T cells, within the tumor. Our earlier work demonstrated immunosuppressive effects of NOS2 and COX2 tumor expression. Here, we show that NOS2/COX2 levels influence both the polarization and spatial location of lymphoid cells including CD8+ T cells. Importantly, elevated tumor NOS2/COX2 correlated with exclusion of CD8+ T cells from the tumor epithelium. In contrast, tumors expressing low NOS2/COX2 had increased CD8+ T cell penetration into the tumor epithelium. Consistent with a causative relationship between these observations, pharmacological inhibition of COX2 with indomethacin dramatically reduced tumor growth of the 4T1 model of TNBC in both WT and Nos2- mice. This regimen led to complete tumor regression in ∼20-25% of tumor-bearing Nos2- mice, and these animals were resistant to tumor rechallenge. Th1 cytokines were elevated in the blood of treated mice and intratumoral CD4+ and CD8+ T cells were higher in mice that received indomethacin when compared to control untreated mice. Multiplex immunofluorescence imaging confirmed our phenotyping results and demonstrated that targeted Nos2/Cox2 blockade improved CD8+ T cell penetration into the 4T1 tumor core. These findings are consistent with our observations in low NOS2/COX2 expressing breast tumors proving that COX2 activity is responsible for limiting the spatial distribution of effector T cells in TNBC. Together these results suggest that clinically available NSAID's may provide a cost-effective, novel immunotherapeutic approach for treatment of aggressive tumors including triple negative breast cancer.

Pharmacometabolomics reveals urinary diacetylspermine as a biomarker of doxorubicin effectiveness in triple negative breast cancer

Triple-negative breast cancer (TNBC) patients receive chemotherapy treatment, including doxorubicin, due to the lack of targeted therapies. Drug resistance is a major cause of treatment failure in TNBC and therefore, there is a need to identify biomarkers that determine effective drug response. A pharmacometabolomics study was performed using doxorubicin sensitive and resistant TNBC patient-derived xenograft (PDX) models to detect urinary metabolic biomarkers of treatment effectiveness. Evaluation of metabolite production was assessed by directly studying tumor levels in TNBC-PDX mice and human subjects. Metabolic flux leading to biomarker production was determined using stable isotope-labeled tracers in TNBC-PDX ex vivo tissue slices. Findings were validated in 12-h urine samples from control (n = 200), ER+/PR+ (n = 200), ER+/PR+/HER2+ (n = 36), HER2+ (n = 81) and TNBC (n = 200) subjects. Diacetylspermine was identified as a urine metabolite that robustly changed in response to effective doxorubicin treatment, which persisted after the final dose. Urine diacetylspermine was produced by the tumor and correlated with tumor volume. Ex vivo tumor slices revealed that doxorubicin directly increases diacetylspermine production by increasing tumor spermidine/spermine N¹-acetyltransferase 1 expression and activity, which was corroborated by elevated polyamine flux. In breast cancer patients, tumor diacetylspermine was elevated compared to matched non-cancerous tissue and increased in HER2+ and TNBC compared to ER+ subtypes. Urine diacetylspermine was associated with breast cancer tumor volume and poor tumor grade. This study describes a pharmacometabolomics strategy for identifying cancer metabolic biomarkers that indicate drug response. Our findings characterize urine diacetylspermine as a non-invasive biomarker of doxorubicin effectiveness in TNBC.

Polygenic risk scores for prediction of breast cancer risk in women of African ancestry: a cross-ancestry approach

Polygenic risk scores (PRSs) are useful for predicting breast cancer risk, but the prediction accuracy of existing PRSs in women of African ancestry (AA) remains relatively low. We aim to develop optimal PRSs for the prediction of overall and estrogen receptor (ER) subtype-specific breast cancer risk in AA women. The AA dataset comprised 9235 cases and 10 184 controls from four genome-wide association study (GWAS) consortia and a GWAS study in Ghana. We randomly divided samples into training and validation sets. We built PRSs using individual-level AA data by a forward stepwise logistic regression and then developed joint PRSs that combined (1) the PRSs built in the AA training dataset and (2) a 313-variant PRS previously developed in women of European ancestry. PRSs were evaluated in the AA validation set. For overall breast cancer, the odds ratio per standard deviation of the joint PRS in the validation set was 1.34 [95% confidence interval (CI): 1.27-1.42] with the area under receiver operating characteristic curve (AUC) of 0.581. Compared with women with average risk (40th-60th PRS percentile), women in the top decile of the PRS had a 1.98-fold increased risk (95% CI: 1.63-2.39). For PRSs of ER-positive and ER-negative breast cancer, the AUCs were 0.608 and 0.576, respectively. Compared with existing methods, the proposed joint PRSs can improve prediction of breast cancer risk in AA women.

Whole-exome Sequencing of Nigerian Prostate Tumors from the Prostate Cancer Transatlantic Consortium (CaPTC) Reveals DNA Repair Genes Associated with African Ancestry

In this study, we used whole-exome sequencing of a cohort of 45 advanced-stage, treatment-naïve Nigerian (NG) primary prostate cancer tumors and 11 unmatched nontumor tissues to compare genomic mutations with African American (AA) and European American (EA) The Cancer Genome Atlas (TCGA) prostate cancer. NG samples were collected from six sites in central and southwest Nigeria. After whole-exome sequencing, samples were processed using GATK best practices. BRCA1 (100%), BARD1 (45%), BRCA2 (27%), and PMS2(18%) had germline alterations in at least two NG nontumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%), and PMS2 (16%)] similar to NG samples. Of the most frequently mutated genes, BRCA1 showed a statistically (P ≤ 0.05) higher germline mutation frequency in men of African ancestry (MAA) and increasing variant frequency with increased African ancestry. Disaggregating gene-level mutation frequencies by variants revealed both ancestry-linked and NG-specific germline variant patterns. Driven by rs799917 (T>C), BRCA1 showed an increasing mutation frequency as African ancestry increased. BRCA2_rs11571831 was present only in MAA, and BRCA2_rs766173 was elevated in NG men. A total of 133 somatic variants were present in 26 prostate cancer-associated genes within the NG tumor cohort. BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%), and PMS2 (11%) showed mutation frequencies >10%. Compared with TCGA cohorts, NG tumors showed statistically significant elevated frequencies of BRCA2, APC, and BRCA1. The NG cohort variant pattern shared similarities (cosign similarities ≥0.734) with Catalogue of Somatic Mutations in Cancer signatures 5 and 6, and mutated genes showed significant (q < 0.001) gene ontology (GO) and functional enrichment in mismatch repair and non-homologous repair deficiency pathways. Here, we showed that mutations in DNA damage response genes were higher in NG prostate cancer samples and that a portion of those mutations correlate with African ancestry. Moreover, we identified variants of unknown significance that may contribute to population-specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the NG prostate cancer exome to date and highlight the need to increase diversity of study populations.

Significance

MAA have higher rates of prostate cancer incidence and mortality, however, are severely underrepresented in genomic studies. This is the first study utilizing whole-exome sequencing in NG men to identify West African ancestry-linked variant patterns that impact DNA damage repair pathways.

Creatine riboside is a cancer cell-derived metabolite associated with arginine auxotrophy

The metabolic dependencies of cancer cells have substantial potential to be exploited to improve the diagnosis and treatment of cancer. Creatine riboside (CR) is identified as a urinary metabolite associated with risk and prognosis in lung and liver cancer. However, the source of high CR levels in patients with cancer as well as their implications for the treatment of these aggressive cancers remain unclear. By integrating multiomics data on lung and liver cancer, we have shown that CR is a cancer cell–derived metabolite. Global metabolomics and gene expression analysis of human tumors and matched liquid biopsies, together with functional studies, revealed that dysregulation of the mitochondrial urea cycle and a nucleotide imbalance were associated with high CR levels and indicators of a poor prognosis. This metabolic phenotype was associated with reduced immune infiltration and supported rapid cancer cell proliferation that drove aggressive tumor growth. CR^hi cancer cells were auxotrophic for arginine, revealing a metabolic vulnerability that may be exploited therapeutically. This highlights the potential of CR not only as a poor-prognosis biomarker but also as a companion biomarker to inform the administration of arginine-targeted therapies in precision medicine strategies to improve survival for patients with cancer.

Validation of a multi-ancestry polygenic risk score and age-specific risks of prostate cancer: A meta-analysis within diverse populations

Background

We recently developed a multi-ancestry polygenic risk score (PRS) that effectively stratifies prostate cancer risk across populations. In this study, we validated the performance of the PRS in the multi-ancestry Million Veteran Program and additional independent studies.

Methods

Within each ancestry population, the association of PRS with prostate cancer risk was evaluated separately in each case-control study and then combined in a fixed-effects inverse-variance-weighted meta-analysis. We further assessed the effect modification by age and estimated the age-specific absolute risk of prostate cancer for each ancestry population.

Results

The PRS was evaluated in 31,925 cases and 490,507 controls, including men from European (22,049 cases, 414,249 controls), African (8794 cases, 55,657 controls), and Hispanic (1082 cases, 20,601 controls) populations. Comparing men in the top decile (90-100% of the PRS) to the average 40-60% PRS category, the prostate cancer odds ratio (OR) was 3.8-fold in European ancestry men (95% CI = 3.62-3.96), 2.8-fold in African ancestry men (95% CI = 2.59-3.03), and 3.2-fold in Hispanic men (95% CI = 2.64-3.92). The PRS did not discriminate risk of aggressive versus nonaggressive prostate cancer. However, the OR diminished with advancing age (European ancestry men in the top decile: ≤55 years, OR = 7.11; 55-60 years, OR = 4.26; >70 years, OR = 2.79). Men in the top PRS decile reached 5% absolute prostate cancer risk ~10 years younger than men in the 40-60% PRS category.

Conclusions

Our findings validate the multi-ancestry PRS as an effective prostate cancer risk stratification tool across populations. A clinical study of PRS is warranted to determine whether the PRS could be used for risk-stratified screening and early detection.

Funding

This work was supported by the National Cancer Institute at the National Institutes of Health (grant numbers U19 CA214253 to C.A.H., U01 CA257328 to C.A.H., U19 CA148537 to C.A.H., R01 CA165862 to C.A.H., K99 CA246063 to B.F.D, and T32CA229110 to F.C), the Prostate Cancer Foundation (grants 21YOUN11 to B.F.D. and 20CHAS03 to C.A.H.), the Achievement Rewards for College Scientists Foundation Los Angeles Founder Chapter to B.F.D, and the Million Veteran Program-MVP017. This research has been conducted using the UK Biobank Resource under application number 42195. This research is based on data from the Million Veteran Program, Office of Research and Development, and the Veterans Health Administration. This publication does not represent the views of the Department of Veteran Affairs or the United States Government.

Abstract 1507: Tumor only analysis of whole exome sequencing from a multi-institutional Nigerian prostate cancer cohort reveals DNA repair genes associated with African ancestry

Men of African ancestry (MAA) have the highest global incidence and mortality of prostate cancer (PCa); however, the biology underlying this harsh disease presentation remains poorly understand, largely due to Africans and people within the African diaspora being under-represented in genomics research. MAA are younger at diagnosis, have higher tumor volume at diagnosis and have higher tumor aggression compared to European American men. Additionally, genomic profiling continues to show that PCa etiology and phenotype are influenced by higher amounts of African ancestry and that West African ancestry is associated with unique genomic alterations. Herein we utilize whole exome sequencing of a unique cohort of 45 advanced stage, treatment naïve Nigerian primary PCa tumors and 11 unmatched non-tumor tissue to compare genomic variants with African (AA) and European (EA) American TCGA PCa tumors. Nigerian samples were collected from 6 sites in central and southwest Nigeria. After whole exome sequencing, samples were processed using GATK best practices. Four genes [BRCA1 (100%), BARD1 (45%), BRCA2 (27%) and PMS2 (18%)] had germline variants in at least two Nigerian non-tumor samples. Across 111 germline variants, the AA cohort reflected a pattern [BRCA1 (68%), BARD1 (34%), BRCA2 (28%) and PMS2 (16%)] similar to Nigerian samples. Of the most frequently mutated genes, BRCA1 showed a statistically (p ≤ 0.05) higher mutation frequency in MAA. Disaggregating gene level mutation frequencies by variant revealed both ancestry linked and Nigerian specific germline variant patterns. Driven by rs799917, BRCA1 showed increasing mutation frequency as African admixture increased. BRCA2_rs11571831 was only present in MAA and BRCA2_rs766173 was increased in Nigerian men. 133 somatic variants were present in 26 PCa associated genes within the Nigerian tumor cohort. Nine genes [BRCA2 (27%), APC (20%), ATM (20%), BRCA1 (13%), DNAJC6 (13%), EGFR (13%), MAD1L1 (13%), MLH1 (11%) and PMS2 (11%)] showed mutation frequencies above 10%. Compared to TCGA cohorts, BRCA2, APC and BRCA1 showed statistically significant increases in Nigerian tumors. The Nigerian cohort variant pattern shared similarities (cosign similarities ≥ 0.734) with COSMIC signatures 5 and 6 and mutated genes showed significant (q &lt; 0.001) GO and functional enrichment in mismatch repair and non-homologous repair deficiency (HRD) pathways. Here, we show that variants in DDR genes are increased in Nigerian PCa and that a portion of those variants correlate with increased African ancestry. Moreover, we identify variants of unknown significance that may contribute to population specific routes of tumorigenesis and treatment. These results present the most comprehensive characterization of the Nigerian PCa exome to date and further highlight the need to increase study population diversity.

Citation Format: Jason A. White, Ernest Kaninjing, Kayode A. Adeniji, Paul Jibrin, John O. Obafunwa, Chidiebere N. Ogo, Mohammed Faruk, Solomon Rotimi, Ademola Popoola, Omolara A. Fatiregun, Olabode P. Oluwole, Balasubramanyam Karanam, Wei Tang, Stefan Ambs, Folake T. Odedina, Damali N. Martin, Clayton Yates. Tumor only analysis of whole exome sequencing from a multi-institutional Nigerian prostate cancer cohort reveals DNA repair genes associated with African ancestry [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 1507.

Abstract 1167: Genomic comparison between African American men & European American men with prostate cancer

Compared to European American men (EAM), African American men (AAM) have 2-3 times higher prostate cancer (PCa) mortality rates. AAM diagnose with more aggressive PCa at an earlier age & clinically advanced disease compared to EAM. Studies suggested that tumor biology & cellular heterogeneity/gene profile, have a potential contribution to racial differences, which remain even when controlled for access to care and stage at presentation. Moreover, men of African ancestry from the Caribbean & South America experience incidence & mortality rates similar to AAM, suggesting a possible ancestral basis for some of these expected outcomes. Additionally, the association of the genomic findings with patient ancestry and with other characteristics such as tumor biology & transcriptomic alterations remains poorly understood. Here we hypothesize that African ancestry drives aggressive prostate cancer and leads to genetic alterations with upregulation of unique Immune-inflammatory signature in AAM of African descent. To assess our hypothesis, we performed genome-wide sequencing (WES & RNA Seq), for a total of (n= 72) patients obtained from treatment-naive PCa who self-reported their race. Out of those 72 samples, 47 samples RNA Seq match with WES. To verify the self-reported race, we used ADMIXTURE to generate a quantitative estimate of each individual ancestral composition. Most of our cohorts who self-reported as AAM, their ancestry assigned to African Ancestry (Ancestry proportion &gt; 70%) with either Bantu subpopulation in Sub-Saharan area and/or Yoruba (Nigeria) subpopulation. Descriptive statistical analyses of the study population were conducted and stratified by race & pathology stage. Our results showed that AA men are diagnosed with PCa at a younger age and higher pathology stage. We ran differential gene expression (DGEs) using EdgR/DESeq2 and enriched pathways based on the patient's ancestry/race using GSEA & EdgR gene ontology function. Our DGEs analyses revealed that gene sets such as activation of the innate immune system and immune-inflammation pathway, as well as interleukin signaling, are positively enriched (p-value 0.05), while gene sets such as RNA Polymerase II transcription and metabolisms signaling are negatively enriched (p-value 0.05) in AAM. Moreover, our WES analysis showed that patients with high African Ancestry associated with AR-related mutation such as FOXA1, PTEN, TP53, EPHB2 with SPOP mutation (18% in AAM vs 8% in EAM) on top of these mutations. Interestingly, when we stratified patients based on PD-L1 expression, AAM with high PD-L1 (Immunogenic) has higher CD8+ T cells/PD-1+ expression than AAM patients with low PD-L1 (Non-Immunogenic). WES analysis showed that AAM with high PD-L1 express SPOP mutation. Our study's findings could lead to new therapeutic strategies using anti-inflammatory drugs and immune modulators to decrease the disease burden among men at high risk for PCa.

Citation Format: Isra A. Elhussin, Jason White, Tiffany Dorsey, Moray J. Campbell, Melissa B. Davis, Stefan Ambs, Isaac Kim, Clayton Yates. Genomic comparison between African American men & European American men with prostate cancer [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 1167.

Abstract LB162: Human herpesvirus 8 infection is associated with prostate cancer among IFNL4-ΔG carriers

Background: Chronic inflammation as seen with chronic infections, has been proposed as a risk factor for prostate cancer. Numerous studies failed to identify a specific microbial agent associated with prostate cancer risk. We have previously reported that human herpesvirus 8 (HHV-8) is associated with increased prostate cancer risk in Tobago; a population that is 97% of African ancestry. This association was not found in several studies of US men, who were predominately of European American ancestry. It is unclear if the discrepancies between US and Tobago men are due to differences in HHV-8 seroprevalence rates or ancestry-related genetics. Previous studies have reported that the dinucleotide germline variant, rs368234815-ΔG, in the IFNL4 gene encoding interferon λ4 is more prevalent among individuals of African ancestry and impairs viral clearance. In this study, we investigated whether the association of HHV-8 with prostate cancer is IFNL4-ΔG-dependent.

Methods: We investigated the association of HHV-8 seropositivity with prostate cancer in 728 IFNL4-ΔG-genotyped cases and 813 genotyped population-based control men from the NCI-Maryland Prostate Cancer Case-Control study. Associations between HHV-8 and prostate cancer were assessed in multivariable unconditional logistic regression models. We calculated adjusted odds ratios (OR) and stratified the analysis into men harboring the IFNL4-ΔG-variant and non-carriers (ΔG/ΔG or ΔG/TT vs. TT/TT).

Results: HHV-8 seropositivity was higher in cases than controls (OR 1.76; 95%CI: 1.20 - 2.59). The association of HHV-8 seropositivity with prostate cancer was restricted to carriers of the ΔG allele (OR 2.19: 95%CI: 1.38 - 3.48). HHV-8 seropositivity did not associate with prostate cancer among TT/TT genotype carriers (OR 1.03: 95%CI: 0.51 - 2.11). Further stratification by race/ethnicity showed that HHV-8 is associated with prostate cancer exclusively among carriers of the ΔG allele in both European American (OR 2.59; 95%CI: 1.20 - 5.56) and African American men (OR 1.96; 95%CI: 1.08 - 3.56).

Conclusions: HHV-8 seropositivity is associated with increased odds of prostate cancer in men harboring the IFNL4 rs368234815-ΔG variant.

Impact: The study establishes IFNL4-ΔG as a candidate prostate cancer risk factor in men with an HHV-8 infection. This gene-environment association of IFNL4-ΔG with prostate cancer should be further evaluated using prospective study designs.

Citation Format: Frank J. Jenkins, Tsion Z. Minas, Wei Tang, Tiffany H. Dorsey, Stefan Ambs. Human herpesvirus 8 infection is associated with prostate cancer among IFNL4-ΔG carriers [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 LB162.

Abstract 1445: Influence of neighborhood deprivation on the DNA epigenome in cancerous breast tissue from African American and European American women

Low socioeconomic status (SES) associates with early onset of chronic diseases and reduced life-expectancy. This relationship is only partly explained by unhealthy behavioral habits and inadequate access to health care. Chronic life stress is more prevalent in low SES communities and has been shown to affect DNA methylation and the immune system. Yet, the biological processes that mediate the impact of SES on health to promote the development of chronic diseases like cancer remain poorly understood. Our study aims to uncover whether DNA methylation is linked to neighborhood socioeconomic deprivation and to a biology that causes inflammation and changes to the immune environment, thereby promoting breast cancer progression and affecting response to therapy. These differences have been characterized in 181 breast tumors (108 African American (AA), 73 European American (EA)). We geocoded the addresses of our participants and linked these data to a Census-level neighborhood deprivation index (NDI). Statistically significant associations between NDI, race and methylation beta values were determined using linear regression followed by Benjamini-Hochbergcorrection. Of the 18 CpG sites that differed between individuals with low and high neighborhood deprivation, 3 were hypermethylated in women with high neighborhood deprivation. We also used methylCIBERSORT to estimate immune subpopulation differences by race group, breast cancer subtype, and ND. For AA women with aggressive triple negative breast cancer, neighborhood deprivation was significantly positively correlated with absolute immune cell scores (p=0.011), including a higher absolute score for endothelial cell expression (p=0.006) and eosinophils (p=0.049). Our findings give insight into how socioeconomic position and neighborhood deprivation may affect cancerous mammary gland biology by altering DNA methylation patterns.

Citation Format: Brittany D. Lord, Emily Rossi, Tiffany Dorsey, Maeve Kiely, Ruby Hutchinson, Stefan Ambs. Influence of neighborhood deprivation on the DNA epigenome in cancerous breast tissue from African American and European American women [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 1445.

Abstract P1-06-03: Promotion of E-cadherin-mediated tumor cell adhesion by COX-2/GSK3β signaling is a targetable mechanism of metastatic breast cancer

Purpose: Metastatic progression and treatment resistance of breast cancer has been associated with epithelial-mesenchymal transition (EMT), including downregulation of E-cadherin (CDH1) gene expression, which can be initiated by inflammatory signaling such as by COX-2 (PTGS2). However, E-cadherin expression is maintained in many advanced breast cancers, including inflammatory BC (IBC), where it plays an essential role in forming tumor cell emboli within the cancer parenchyma and dermal lymph vasculature and which predict poor outcomes. Thus, the study of IBC offers an opportunity to understand the mechanisms of IBC and other aggressive BCs that lead to E-cadherin-associated cluster-based metastasis, which has recently received heightened recognition. Here, we have investigated the mechanisms that sustain E-cadherin expression in metastatic breast cancer to identify new targeted treatment options. Study Design and Methods: In vitro emboli formation assays and gene/protein expression studies with IBC (SUM149, IBC-3) and non-IBC (SUM159, MCF-7) cell lines along with gene silencing, overexpression, and pharmacological interventions. Analysis of experimental (SUM149) and spontaneous (orthotopic patient-derived xenograft, PDX) lung metastases and of circulating tumor cells (CTCs) in xenograft models treated with celecoxib (Cxb) and/or paclitaxel by imaging cytometry, immunohistochemistry, and/or Western analysis. Results: By analyzing the transcription factor C/EBPδ (CEBPD) and cells derived from inflammatory breast cancer (IBC), an aggressive breast cancer subtype that often presents with E-cadherin-dependent tumor cell emboli, we discovered that COX-2, unexpectedly, sustained E-cadherin protein expression without changing its mRNA levels. Using an in vitro tumor cell emboli culture paradigm (3D), we found that COX-2 or its metabolite PGE2 increased AKT activity and the inhibitory phosphorylation on GSK3β that prevents degradation of p120 catenin (CTNND1), a stabilizer of E-cadherin adhesion complexes. Conversely, the COX-2 inhibitor celecoxib downregulated E-cadherin specifically at the protein level and caused cell death in 3D. Co-expression of E-cadherin and COX-2 was seen in breast cancer patients with poor outcomes and, along with inhibitory GSK3β phosphorylation, in patient-derived xenografts (PDX) of metastatic triple-negative breast cancers (TNBC). Celecoxib alone decreased E-cadherin protein expression within xenograft primary tumors, reduced circulating tumor cells (CTCs) and clusters, and sensitized lung metastases to paclitaxel treatment. Conclusions: Our study uncovered a novel function of COX-2/PGE2 in promoting E-cadherin protein expression and cell-cell adhesions that are relevant for tumor cell cluster-based metastasis. Indeed, COX-2 inhibition reduced CTC clusters in a xenograft model, and sentized established metastases to chemotherapy. These results suggest that patients with COX-2+/E-cadherin+ metastastic BC, including IBC, may specifically benefit from targeting the PGE2 pathway in cobniation therapy approaches.

Citation Format: Kuppusamy Balamurugan, Saadiya Sehareen, Savitri Krishnamurthy, Shikha Sharan, Wei Tang, Naoto Ueno, Stefan Ambs, Dipak Poria, Esta Sterneck. Promotion of E-cadherin-mediated tumor cell adhesion by COX-2/GSK3β signaling is a targetable mechanism of metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-06-03.

Abstract PR-11: Blood levels of TNFRSF9 and PTN predict lethal prostate cancer among African American men

OBJECTIVE: Differentiating men who have lethal forms of prostate cancer from those with a more slow-growing disease remains a major challenge in clinical oncology. Risk stratification strategies are particularly needed for men of African descent who disproportionately bear the prostate cancer burden. Methods: Using a high throughput proximal extension assay, we simultaneously measured 82 immune-oncological proteins in the blood of 819 prostate cancer patients at diagnosis of whom 394 were African American (AA) and 425 were European American (EA). These patients were followed up for a median of 8.6 years since their diagnosis during which 57 died of prostate cancer while 202 died of all causes. To identify an immune-oncology protein signature predictive of lethal prostate cancer, we applied a cross-validated, regularized Cox regression model. Included in this model were the 82 immune-oncology proteins and 6 covariates of clinical significance (age, education, BMI, smoking history, aspirin use, and diabetes). Results: We did not identify a robust predictive signature of lethal prostate cancer for EA patients. However, for AA patients a signature primarily driven by tumor necrosis factor receptor superfamily member 9 (TNFRSF9) and pleiotrophin (PTN) (both positively associated with the risk of lethal disease) and regular aspirin use (negatively associated with risk) were the top predictors (P &lt; 0.05) based on two selection criteria: the feature frequency and the weight of the features' contribution to the prediction. These features combined predicted prostate cancer-specific mortality with an accuracy of 83.7% (SE=3.8%). The two proteins alone, TNFRSF9 and PTN, predicted prostate cancer-specific mortality with an accuracy of 78.2% (SE=4.2%). AA prostate cancer patients with high levels (&gt; median) of both TNFRSF9 and PTN in their blood at diagnosis had the worst prostate cancer-specific survival. By 10 years, 33% of cases with high levels of both TNFRSF9 and PTN died of prostate cancer compared to only 5% of cases with low levels of both or either of these proteins. Conclusions: Our study describes novel blood markers of lethal prostate cancer that can be used for risk stratification of AA patients at the time of diagnosis. AA patients with high levels of both TNFRSF9 and PTN in their sera had the highest risk of dying from prostate cancer. These markers may also be applicable to African prostate cancer patients since the blood-based immunome of Ghanaian and AA men are similar, as shown by our data.

Citation Format: Tsion Zewdu Minas, Julián Candia, Tiffany H. Dorsey, Francine Baker, Wei Tang, Maeve Kiely, Cheryl J. Smith, Symone V. Jordan, Obadi M. Obadi, Anuoluwapo Ajao, Christopher A. Loffredo, Clayton Yates, Michael B. Cook, Stefan Ambs. Blood levels of TNFRSF9 and PTN predict lethal prostate cancer among African American men [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-11.

Abstract PR-08: Diabetes affects metabolism, redox signaling, DNA repair capacity and mutational burden in breast cancer

Comorbidities disproportionately affect underserved populations. Diabetes can increase cancer risk and decreases breast cancer survival. Diabetes-associated breast cancer risk impacts African American women more than European Americans. The goal of this study was to understand how diabetes may shape breast tumor biology. We performed an RNA and whole-exome sequencing (WES) analysis, together with global metabolomics, of matched breast tumors from patients with or without diabetes, with the majority being of African American descent. Additionally, as an experimental model, we generated mammary xenografts following orthotopic injection of breast cancer cells (MDA-MB-231, MDA-MB-468, and HS578T) into the mammary fat pad of diabetic mice (NOD.Cg-Rag1 tm1Mom Ins2 Akita Il2rg tm1Wjl/SzJ). After 4-6 weeks we collected the tumors and performed RNAseq and metabolome analysis. Analyzing the metabolome profile of both human breast tumors and xenografts, we observed a distinct metabolite pattern in diabetic breast tumors and diabetic mice. The key observation was the enrichment of food and microbial-derived metabolites under diabetes, indicating that diabetes may promote the accumulation of these metabolites in breast tumors. Next, we analyzed the RNAseq data from the same tumors and xenografts. Here, we applied Gene Set Enrichment Analysis (GSEA) with the transcriptomic data to find specific pathways activated under diabetic conditions. GSEA indicated the enrichment of gene signatures related to mesenchymal and stem cell-like phenotypes both in the patient tumor and xenografts under diabetes. Additionally, we discovered an enrichment of the reactive oxygen species (ROS) pathway in diabetic tumors and xenografts. Consistent with this observation, treating breast cancer cells (MDA-MB-231 and HS578T) with high glucose (25mM) increased superoxide radical production in these cells. Since higher ROS levels could cause DNA damage, we examined DNA damage in breast cancer cells cultured under high glucose. Here we observed an increase in DNA damage under high glucose as indicated by robust nuclear γH2AX and 53BP1 immunostaining. An additional KEGG analysis indicated the inhibition of various DNA repair pathways (e.g. base-excision, nucleotide excision, and mismatch repair) in breast tumors and xenografts. Corroborating this finding with our WES data, we observed a significant enrichment of several mutational signatures (SBS5, SBS15, and SBS30 DNA repair deficiency signatures) in breast tumors of diabetic patients, suggesting that diabetes may interfere with DNA repair pathways in breast tumors. Taken together, this study suggests that diabetes promotes a mesenchymal and stem cell-like phenotype in human breast tumors with higher oxidative stress & DNA damage and a decreased DNA repair capacity. Our data further indicate that breast tumors from diabetic patients may have an increased susceptibility to DNA damage response inhibitors like PARP inhibitors.

Citation Format: Gatikrushna Panigrahi, Tiffany Dorsey, Wei Tang, Julian Candia, Amy Zhang, Stefan Ambs. Diabetes affects metabolism, redox signaling, DNA repair capacity and mutational burden in breast cancer [abstract]. In: Proceedings of the AACR Virtual Conference: 14th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2021 Oct 6-8. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr PR-08.