Abstract C024: Lifestyle-associated advanced glycation end products are elevated in ER+ positive breast cancer patients, alter response to therapy, and can be targeted by lifestyle intervention

Lifestyle factors associated with personal behavior can alter tumor-associated biologic pathways and thereby increase cancer risk, growth and disease recurrence. Advanced glycation end products (AGEs) are reactive metabolites produced endogenously as a byproduct of normal metabolism. A Western lifestyle consisting of high-fat, high-sugar and processed foods as well as little exercise can lead to a significant increase in AGE accumulation in the body and is also associated with driving cancer disparity. Increased AGE accumulation promotes disease phenotypes through modification of the genome, protein crosslinking and dysfunction, and aberrant cell signaling. We evaluated AGE levels in biospecimens from ER+ and ER- breast cancer patients, examined their role in therapy resistance, and assessed the ability of a lifestyle intervention to reduce circulating AGE levels in ER+ breast cancer survivors. A correlation between ER status and AGE levels was observed in tumor and serum samples. AGE treatment of ER+ breast cancer cells impacted pathways associated with ER regulation. We observed a significant increase in phosphorylation of ERalpha following AGE treatment when compared to untreated control with no change in total ERalpha levels. We also observed a significant increase in both AKT and ERK phosphorylation in ER+ cell lines in response to AGE treatment in a time-dependent manner. Inhibition of AKT with Ly294002 and inhibition of ERK with the MEK inhibitor U0126 significantly reduced ERalpha phosphorylation in the presence of AGE. Significantly, ER+ cells treated with AGEs no longer responded to hormonal therapy with tamoxifen. In a proof-of-concept study we examined the ability of a defined exercise and dietary intervention (i.e., cardiac rehabilitation) to reduce circulatory AGE levels in ER+ breast cancer survivors. A significant increase in average very active minutes and average calories burned was observed as a result of the intervention. This was accompanied by a significant reduction in dietary-AGE intake and also showed significant reductions in circulating AGE levels when fasting serum samples were analyzed by ELISA. An analysis of IL6 and CRP levels by ELISA in the same AGE assessed samples revealed no significant differences at any time point. There is a potential prognostic and therapeutic role for lifestyle-derived AGEs in cancer disparity. Given the potential benefits of lifestyle intervention on cancer incidence and mortality, opportunities exist for the development of community health and nutritional programs aimed at reducing AGE exposure in order to improve cancer prevention and treatment outcomes. Lifestyle interventions that lower AGE levels may then be utilized to reduce breast cancer incidence and improve prognosis in cancer disparity populations.

Citation Format: Katherine R. Walter, Ford E. Ford, Mathew J. Gregoski, Rita M. Kramer, Kendrea D. Knight, Laura Spruill, Lourdes M. Nogueira, Bradley A. Krisanits, Marian H. Taylor, Amanda C. La Rue, Michael B. Lilly, Stefan Ambs, King Chan, Tonya F. Turner, Heidi Varner, Shweta Singh, Jaime Uribarri, Elizabeth Garrett-Mayer, Kent E. Armeson, Ebony J. Hilton, Mark Clair, Victoria J. Findlay, Lindsay L. Peterson, Gayenell Magwood, David P. Turner. Lifestyle-associated advanced glycation end products are elevated in ER+ positive breast cancer patients, alter response to therapy, and can be targeted by lifestyle intervention [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr C024.

Abstract B051: IFNL4-deltaG allele is associated with an interferon signature in tumors and survival of African-American men with prostate cancer

Purpose: Men of African ancestry experience an excessive prostate cancer mortality that could be related to an aggressive tumor biology. We previously described an immune-inflammation signature in prostate tumors of African-American patients. Here, we further deconstructed this signature and investigated its relationships with tumor biology, survival, and a common germline variant in the interferon λ4 (IFNL4) gene.

Experimental Design: We analyzed gene expression in prostate tissue datasets and performed IFNL4 genotype and survival analyses. We also overexpressed IFNL4 in human prostate cancer cells.

Results: We found that a distinct interferon signature that is analogous to the previously described “Interferon-related DNA Damage Resistance Signature” (IRDS) occurs in prostate tumors. Evaluation of two independent patient cohorts revealed that IRDS is detected about twice as often in prostate tumors of African-American than European-American men. Furthermore, analysis in The Cancer Genome Atlas (TCGA) showed an association of increased IRDS in prostate tumors with decreased disease-free survival. To explain these observations, we assessed whether IRDS is associated with an IFNL4 germline variant (rs368234815-ΔG) that controls production of IFN-λ4 protein, a type-III interferon, and is most common in individuals of African ancestry. We show that the IFNL4 rs368234815-ΔG allele was significantly associated with IRDS in prostate tumors and overall survival of African-American patients. Moreover, IFNL4 overexpression induced IRDS-like signatures in three human prostate cancer cell lines.

Conclusions: Tumor interferon signaling has recently been shown to modulate response and resistance to immune checkpoint blockade. Here, we describe a distinct and biologically relevant interferon signature, IRDS, in prostate tumors that has a high prevalence in African-American patients. Our observations indicate that IRDS and IFNL4 rs368234815-ΔG may have a function in the tumor biology and survival of African-American patients, and influence immune therapy outcomes, which should be examined in future studies.

Citation Format: Wei Tang, Tiffany Wallace, Ming Yi, Cristina Magi-Galluzzi, Tiffany Dorsey, Olusegun Onabajo, Adeola Obajemu, Symone Jordan, Christopher Loffredo, Robert Stephens, Robert Silverman, George Stark, Eric Klein, Ludmila Prokunina-Olsson, Stefan Ambs. IFNL4-deltaG allele is associated with an interferon signature in tumors and survival of African-American men with prostate cancer [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr B051.

Abstract PR12: Using whole exome sequencing of archived FFPE tissue to characterize the mutational landscape of prostate cancer in Nigerian men

Compared to other ancestral groups, men of African ancestry (MAA) have the highest incidence and mortality of prostate cancer (PCa), with African men having the highest. Multiple studies have demonstrated that genetic/biologic differences in African American (AA) tumor biology contribute to PCa development and aggressiveness; furthermore, building evidence suggests that the observed differences are population specific and form unique paths to cancer aggressiveness. Despite this, MAA continue to be underrepresented in PCa studies. This lack of adequate representation greatly diminishes the ability to identify clinical interventions to address this disparate disease. In this study, we used whole-exome sequencing of 148 Nigerian PCa FFPE samples (75 Tumor, 62 BPH, and 11 non-matched Normal) to determine the mutational landscape of PCa. Samples were collected from 6 sites in central and southwest Nigeria and quality screened. Samples passing QC were sequenced (Illumina HiSeq 4000 PE150) and read files were processed using the Tumor Only Somatic Mutation pipeline developed by the CCR Collaborative Bioinformatics Resource (CCBR). In addition to the CCBR pipeline, Exomiser was used to prioritize non-silent variants according to variant frequency, pathogenicity, quality, and model organism phenotype data. 246 genes showed significant (p ≥ 0.05) tumor mutation and high prioritization (Exomiser score ≥ 0.75). These genes included BCR, KMD1A, MSH6, TLR4, and BMPR1B with mutation rates of 17%, 13%, 12%, 11%, and 8%, respectively. These rates were higher than process matched controls and TCGA tumor samples. Mutation signature analysis showed enrichments in 4 Cosmic signatures. 38.6% of Tumor samples contained signatures similar (cosine similarity [cs] = 0.912) to Signature 1, 29.3% were similar (cs = 0.849) to Signature 4, 14.6% were similar (cs = 0.743) to Signature 5, and 17.3% were similar (cs = 0.635) to Signature 25. Groupwise comparisons of gene mutations and mutation signatures showed that 8 of the 29 tumors (p ≤ 0.06), having a Signature 1 similar signature, contained a BCR frameshift insertion (c.3275_3278dup), which duplicates a four-nucleotide CCGG sequence in exon 19. The relationship between BCR and prostate cancer is still poorly understood; however, within the TCGA PRAD cohort, low BCR expression does significantly (p ≤ 0.024) correlate with poor survival. These results suggest that mutations within BCR result in a disruption of methylation and expression patterns that could contribute to worse outcomes in Nigerian PCa patients. Without tumor/normal matched pairs, more analysis is needed to ensure the accuracy of this characterization; however, completion of this study would comprise the largest mutational analysis of Nigerian PCa to date. Understanding the genetic underpinnings of PCa in Nigerian patients will add much-needed context to the study of the disease in MAA, further illuminating clinical interventions that may prove beneficial in diminishing outcome disparities.

This abstract is also being presented as Poster B079.

Citation Format: Prostate Cancer Transatlantic Consortium Members, Jason White, Wei Tang, Stefan Ambs, Solomon Rotimi, Mohammed Faruuk, Folakemi Odedina, Clayton Yates. Using whole exome sequencing of archived FFPE tissue to characterize the mutational landscape of prostate cancer in Nigerian men [abstract]. In: Proceedings of the Twelfth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2019 Sep 20-23; San Francisco, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl_2):Abstract nr PR12.

DNA methylation patterns in bladder tumors of African American patients point to distinct alterations in xenobiotic metabolism

Racial/ethnic disparities have a significant impact on bladder cancer outcomes with African American patients demonstrating inferior survival over European-American patients. We hypothesized that epigenetic difference in methylation of tumor DNA is an underlying cause of this survival health disparity. We analyzed bladder tumors from African American and European-American patients using reduced representation bisulfite sequencing (RRBS) to annotate differentially methylated DNA regions. Liquid chromatography-mass spectrometry (LC-MS/MS) based metabolomics and flux studies were performed to examine metabolic pathways that showed significant association to the discovered DNA methylation patterns. RRBS analysis showed frequent hypermethylated CpG islands in African American patients. Further analysis showed that these hypermethylated CpG islands in patients are commonly located in the promoter regions of xenobiotic enzymes that are involved in bladder cancer progression. On follow-up, LC-MS/MS revealed accumulation of glucuronic acid, S-adenosylhomocysteine, and a decrease in S-adenosylmethionine, corroborating findings from the RRBS and mRNA expression analysis indicating increased glucuronidation and methylation capacities in African American patients. Flux analysis experiments with 13C-labeled glucose in cultured African American bladder cancer cells confirmed these findings. Collectively, our studies revealed robust differences in methylation-related metabolism and expression of enzymes regulating xenobiotic metabolism in African American patients indicate that race/ethnic differences in tumor biology may exist in bladder cancer.

Epigenetic regulation of REX1 expression and chromatin binding specificity by HMGNs

HMGN proteins localize to chromatin regulatory sites and modulate the cell-type specific transcription profile; however, the molecular mechanism whereby these ubiquitous nucleosome binding proteins affect gene expression is not fully understood. Here, we show that HMGNs regulate the expression of Rex1, one of the most highly transcribed genes in mouse embryonic stem cells (ESCs), by recruiting the transcription factors NANOG, OCT4 and SOX2 to an ESC-specific super enhancer located in the 5' region of Rex1. HMGNs facilitate the establishment of an epigenetic landscape characteristic of active chromatin and enhancer promoter interactions, as seen by chromatin conformation capture. Loss of HMGNs alters the local epigenetic profile, increases histone H1 occupancy, decreases transcription factors binding and reduces enhancer promoter interactions, thereby downregulating, but not abolishing Rex1 expression. ChIP-seq analyses show high colocalization of HMGNs and of REX1, a zinc finger protein, at promoters and enhancers. Loss of HMGNs preferentially reduces the specific binding of REX1 to these chromatin regulatory sites. Thus, HMGNs affects both the expression and the chromatin binding specificity of REX1. We suggest that HMGNs affect cell-type specific gene expression by modulating the binding specificity of transcription factors to chromatin.

Liver- and Microbiome-derived Bile Acids Accumulate in Human Breast Tumors and Inhibit Growth and Improve Patient Survival

PURPOSE

Metabolomics is a discovery tool for novel associations of metabolites with disease. Here, we interrogated the metabolome of human breast tumors to describe metabolites whose accumulation affects tumor biology.

EXPERIMENTAL DESIGN

We applied large-scale metabolomics followed by absolute quantification and machine learning-based feature selection using LASSO to identify metabolites that show a robust association with tumor biology and disease outcome. Key observations were validated with the analysis of an independent dataset and cell culture experiments.

RESULTS

LASSO-based feature selection revealed an association of tumor glycochenodeoxycholate levels with improved breast cancer survival, which was confirmed using a Cox proportional hazards model. Absolute quantification of four bile acids, including glycochenodeoxycholate and microbiome-derived deoxycholate, corroborated the accumulation of bile acids in breast tumors. Levels of glycochenodeoxycholate and other bile acids showed an inverse association with the proliferation score in tumors and the expression of cell-cycle and G₂-M checkpoint genes, which was corroborated with cell culture experiments. Moreover, tumor levels of these bile acids markedly correlated with metabolites in the steroid metabolism pathway and increased expression of key genes in this pathway, suggesting that bile acids may interfere with hormonal pathways in the breast. Finally, a proteome analysis identified the complement and coagulation cascade as being upregulated in glycochenodeoxycholate-high tumors.

CONCLUSIONS

We describe the unexpected accumulation of liver- and microbiome-derived bile acids in breast tumors. Tumors with increased bile acids show decreased proliferation, thus fall into a good prognosis category, and exhibit significant changes in steroid metabolism.

Abstract 625: Association between obesity and prostate cancer disease risk and mortality among African American men

Prostate cancer (PCa) is a major cause of cancer death in U.S. men. Age-adjusted mortality rates for men of African ancestry (40.8 per 100,000) are more than twice that of men of European ancestry (18.2 per 100,000). Men of African ancestry are more likely to have advanced stage cancer at diagnosis and lower prostate cancer survival rates relative to men of European ancestry of similar age and stage at diagnosis. Risk factors that may explain this survival disparity remain poorly understood. Obesity, a major risk factor for cancer development, aggressiveness and progression, disproportionately affects US men of African ancestry. Age-adjusted prevalence of obesity are higher among men of African ancestry (38.0%) compared to men of European ancestry (34.7%). While it has been previously suggested that obesity may worsen disease-related outcomes among prostate cancer patients, the relationship of obesity and prostate cancer mortality remains unclear, with studies showing mixed or null results in men of African ancestry. Less is known about the underlying biological mechanisms that may contribute to the racial differences observed in the link between obesity and prostate cancer. We previously reported an obesity paradox among African-American men in the NCI-Maryland Prostate Cancer-Case Control Study, with overweight and obese men having a lower risk of being diagnosed with the disease. Here, using Cox proportional hazard regression modeling, we estimated the risk of a PCa mortality for the 976 cases in the study. Our primary analysis suggests an obesity paradox, where obesity may protect against disease mortality among the African-American men. In subsequent analyses, we will examine the role of immune and inflammation markers in mediating or moderating the observed relationship of obesity with PCa in these men.

Citation Format: Margaret Saira Pichardo, Tsion Minas, Wei Tang, Tiffany H. Dorsey, Stefan Ambs. Association between obesity and prostate cancer disease risk and mortality among African American men [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 625.

Abstract LB-296: Breast cancer metabolism in association with diabetes

Diabetes and cancer are diseases that have a tremendous impact on health worldwide. Epidemiologic evidence suggests that people with diabetes are at an increased risk of various cancers including liver, pancreas and breast cancer. In line with this, we are finding that breast cancer patients who have diabetes (both type I and II) have decreased breast cancer-specific survival, indicating that diabetes may affect tumor biology and increase disease aggressiveness. To further investigate how diabetes promotes the progression of breast cancer, we performed global metabolic profiling and gene expression analysis of matched tumors from 18 diabetes and 18 non-diabetes breast cancer patients. Patient characteristics in each group included 12 estrogen receptor-positive (ER+) and 6 ER-negative tumors from 14 African American and 4 European American patients. We also performed immunohistochemistry of key disease-associated marker proteins in tumors of these patients. Results from the metabolomic analysis showed a significant accumulation of glycogen metabolic intermediates in breast tumors of diabetes patients, indicating changes in glycogen metabolism in tumor biology. Gene expression analysis showed differential expression of more numerous transcripts in the diabetic vs non-diabetic tumors. Interestingly, the top gene on this list was PPP1R3C, a gene involved in regulation of glycogen metabolism. We validated the higher expression of PPP1R3C in diabetic breast tumors by qRT-PCR and are currently performing an immunohistochemical evaluation of FFPE tumors. Other immunohistochemical staining of tumors from diabetic and non-diabetic patients showed significantly higher stromal expression of indolamine-2,3-dioxgenase (IDO) in breast tumors associated with diabetes, which indicates an immunosuppressive tumor microenvironment. To further corroborate our patient studies in cell culture systems, we began to use cytokine arrays in order to examine media of breast cancer cells treated with high glucose, which potentially mimics diabetes condition in cell culture. As a preliminary observation, we noticed a decrease in the level of certain cytokines in ER+ breast cancer cells (MCF7 and T47D). Notably, these cytokines remained unaltered in the conditioned media of non-neoplastic cells (MCF10A, MCF12A) grown under high glucose. Thus, under high glucose condition, ER+ breast cancer cells may secret a different cytokine repertoire, which would prevent recruiting immune cells into the tumor microenvironment and thereby may create an immunosuppressive tumor microenvironment. In conclusion, our current data indicate that diabetes may promote breast cancer progression by altering glycogen metabolism and by creating an immunosuppressive tumor microenvironment, which we currently further investigate.

Citation Format: Gatikrushna Panigrahi, Tiffany H. Dorsey, Wei Tang, Stefan Ambs. Breast cancer metabolism in association with diabetes [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 LB-296.

Abstract 1623: Autoantibodies to human endogenous retrovirus K envelope protein (HERV-K ENV) are associated with features of prostate cancer aggressiveness in African American men

Prostate cancer (PCa) is the most commonly diagnosed cancer and the second leading cause of cancer-related deaths in American men. African-American (AA) men are more likely to develop PCa at a younger age and are twice as likely to die from the disease compared to men from other ethnic/racial backgrounds. Even when normalized with equal access to healthcare, socioeconomic status and familial PCa history, AA men still die disproportionately from PCa. Thus, it is paramount to improve the early detection of aggressive PCa. A cancer patient’s humoral immune response to a tumor offers us a minimally invasive opportunity to detect aggressive cancers before a symptomatic tumor emerges. Previous studies indicate that genes associated with immunity and inflammation are significantly upregulated in prostate tumors from AA men compared to European-American (EA) men, suggesting that there are racial differences in the anti-tumor immune response in patients with PCa. This has prompted our laboratory to evaluate the autoantibody repertoire to tumor-associated antigens (TAA) in ethnically diverse patients. Previous studies showed a higher frequency of autoantibodies to the human endogenous retrovirus K (HERV-K) GAG protein in men with late stage PCa. In addition, investigators in this team reported previously an elevated expression of the envelope (ENV) protein in PCa tumors from AA men compared to PCa tumors from EA men. Given the emerging role of HERV-K in human cancers and the potential use of autoantibodies to the ENV and GAG viral proteins as cancer serum biomarkers and immunotherapeutic tools, we investigated the antibody response to the HERV-K ENV in AA and EA men with and without PCa. Using an enzyme-linked immunosorbent assay (ELISA), we detected a significant increase in the frequency of autoantibodies to HERV-K ENV in AA men with PCa compared to EA men with PCa (N=100, p<0.05) and AA men without PCa (N=100, p<0.0001). The frequency of autoantibodies to ENV was also significantly higher in AA men with stage IV (29%, p<0.0001) and AA men with PCa metastasis (40%, p<0.0001) compared to AA men without PCa or EA men with and without PCa. The immunoreactivity of the sera against ENV was confirmed by immunoblotting. To our knowledge this is the first report of an increased autoantibody frequency to HERV-K ENV in PCa patients and the first report of autoantibodies associated with racial differences in PCa. The observation that these autoantibodies are significantly linked to a more aggressive PCa in AA men is also consistent with previous observation of increased upregulation of HERV-K ENV in prostate tumors from AA men. The biological and clinical significance of anti-HERV-K ENV and GAG autoantibodies in PCa, and the racial differences in their frequency and clinical associations, warrant further investigation.

Citation Format: Tino W. Sanchez, Shannalee R. Martinez, Greisha Ortiz-Hernandez, Evelyn Sanchez-Hernandez, Christopher Montgomery, Benjamin Becerra, Tiffany Dorsey, Feng Wang-Johanning, Stefan Ambs, Carlos A. Casiano. Autoantibodies to human endogenous retrovirus K envelope protein (HERV-K ENV) are associated with features of prostate cancer aggressiveness in African American men [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 1623.

Methionine-Homocysteine Pathway in African-American Prostate Cancer

African American (AA) men have a 60% higher incidence and two times greater risk of dying of prostate cancer (PCa) than European American men, yet there is limited insight into the molecular mechanisms driving this difference. To our knowledge, metabolic alterations, a cancer-associated hallmark, have not been reported in AA PCa, despite their importance in tumor biology. Therefore, we measured 190 metabolites across ancestry-verified AA PCa/benign adjacent tissue pairs (n = 33 each) and identified alterations in the methionine-homocysteine pathway utilizing two-sided statistical tests for all comparisons. Consistent with this finding, methionine and homocysteine were elevated in plasma from AA PCa patients using case-control (AA PCa vs AA control, methionine: P = .0007 and homocysteine: P < .0001), biopsy cohorts (AA biopsy positive vs AA biopsy negative, methionine: P = .0002 and homocysteine: P < .0001), and race assignments based on either self-report (AA PCa vs European American PCa, methionine: P = .001, homocysteine: P < .0001) or West African ancestry (upper tertile vs middle tertile, homocysteine: P < .0001; upper tertile vs low tertile, homocysteine: P = .002). These findings demonstrate reprogrammed metabolism in AA PCa patients and provide a potential biological basis for PCa disparities.

Large-scale profiling of serum metabolites in African American and European American patients with bladder cancer reveals metabolic pathways associated with patient survival

BACKGROUND

African Americans (AAs) experience a disproportionally high rate of bladder cancer (BLCA) deaths even though their incidence rates are lower than those of other patient groups. Using a metabolomics approach, this study investigated how AA BLCA may differ molecularly from European Americans (EAs) BLCA, and it examined serum samples from patients with BLCA with the aim of identifying druggable metabolic pathways in AA patients.

METHODS

Targeted metabolomics was applied to measure more than 300 metabolites in serum samples from 2 independent cohorts of EA and AA patients with BLCA and healthy EA and AA controls via liquid chromatography-mass spectrometry, and this was followed by the identification of altered metabolic pathways with a focus on AA BLCA. A subset of the differential metabolites was validated via absolute quantification with the Biocrates AbsoluteIDQ p180 kit. The clinical significance of the findings was further examined in The Cancer Genomic Atlas BLCA data set.

RESULTS

Fifty-three metabolites, mainly related to amino acid, lipid, and nucleotide metabolism, were identified that showed significant differences in abundance between AA and EA BLCA. For example, the levels of taurine, glutamine, glutamate, aspartate, and serine were elevated in serum samples from AA patients versus EA patients. By mapping these metabolites to genes, this study identified significant relations with regulators of metabolism such as malic enzyme 3, prolyl 3-hydroxylase 2, and lysine demethylase 2A that predicted patient survival exclusively in AA patients with BLCA.

CONCLUSIONS

This metabolic profile of serum samples might be used to assess risk progression in AA BLCA. These first-in-field findings describe metabolic alterations in AA BLCA and emphasize a potential biological basis for BLCA health disparities.

Binding of HMGN proteins to cell specific enhancers stabilizes cell identity

The dynamic nature of the chromatin epigenetic landscape plays a key role in the establishment and maintenance of cell identity, yet the factors that affect the dynamics of the epigenome are not fully known. Here we find that the ubiquitous nucleosome binding proteins HMGN1 and HMGN2 preferentially colocalize with epigenetic marks of active chromatin, and with cell-type specific enhancers. Loss of HMGNs enhances the rate of OSKM induced reprogramming of mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs), and the ASCL1 induced conversion of fibroblast into neurons. During transcription factor induced reprogramming to pluripotency, loss of HMGNs accelerates the erasure of the MEF-specific epigenetic landscape and the establishment of an iPSCs-specific chromatin landscape, without affecting the pluripotency potential and the differentiation potential of the reprogrammed cells. Thus, HMGN proteins modulate the plasticity of the chromatin epigenetic landscape thereby stabilizing, rather than determining cell identity.

HMGN1 and HMGN2 are ubiquitous nucleosome binding proteins. Here the authors provide evidence that HMGN proteins preferentially localize to chromatin regulatory sites to modulate the plasticity of the epigenetic landscape, proposing that HGMNs stabilize, rather than determine, cell identity.

Integrated proteotranscriptomics of breast cancer reveals globally increased protein-mRNA concordance associated with subtypes and survival

Background

Transcriptome analysis of breast cancer discovered distinct disease subtypes of clinical significance. However, it remains a challenge to define disease biology solely based on gene expression because tumor biology is often the result of protein function. Here, we measured global proteome and transcriptome expression in human breast tumors and adjacent non-cancerous tissue and performed an integrated proteotranscriptomic analysis.

Methods

We applied a quantitative liquid chromatography/mass spectrometry-based proteome analysis using an untargeted approach and analyzed protein extracts from 65 breast tumors and 53 adjacent non-cancerous tissues. Additional gene expression data from Affymetrix Gene Chip Human Gene ST Arrays were available for 59 tumors and 38 non-cancerous tissues in our study. We then applied an integrated analysis of the proteomic and transcriptomic data to examine relationships between them, disease characteristics, and patient survival. Findings were validated in a second dataset using proteome and transcriptome data from “The Cancer Genome Atlas” and the Clinical Proteomic Tumor Analysis Consortium.

Results

We found that the proteome describes differences between cancerous and non-cancerous tissues that are not revealed by the transcriptome. The proteome, but not the transcriptome, revealed an activation of infection-related signal pathways in basal-like and triple-negative tumors. We also observed that proteins rather than mRNAs are increased in tumors and show that this observation could be related to shortening of the 3′ untranslated region of mRNAs in tumors. The integrated analysis of the two technologies further revealed a global increase in protein-mRNA concordance in tumors. Highly correlated protein-gene pairs were enriched in protein processing and disease metabolic pathways. The increased concordance between transcript and protein levels was additionally associated with aggressive disease, including basal-like/triple-negative tumors, and decreased patient survival. We also uncovered a strong positive association between protein-mRNA concordance and proliferation of tumors. Finally, we observed that protein expression profiles co-segregate with a Myc activation signature and separate breast tumors into two subgroups with different survival outcomes.

Conclusions

Our study provides new insights into the relationship between protein and mRNA expression in breast cancer and shows that an integrated analysis of the proteome and transcriptome has the potential of uncovering novel disease characteristics.

Electronic supplementary material

The online version of this article (10.1186/s13073-018-0602-x) contains supplementary material, which is available to authorized users.

IFNL4-ΔG is associated with prostate cancer among men at increased risk of sexually transmitted infections

Sexually transmitted infections can reach the prostate gland where their harmful effects are mediated by innate immunity, including interferons. Humans are polymorphic for the germline dinucleotide variant, rs368234815-TT/ΔG, in the IFNL4 gene encoding interferon λ4. Since the IFNL4-ΔG allele has been linked to impaired viral clearance, we hypothesized that potential exposure to sexually transmitted pathogens, as assessed by the number of lifetime sexual partners, may increase prostate cancer risk in an IFNL4-ΔG-dependent manner. Accordingly, we find that men with 10 or more sexual partners and at least one copy of IFNL4-ΔG have a significantly increased risk of prostate cancer while those with the same number of partners but lacking IFNL4-ΔG do not. Moreover, a test for effect modification shows a positive interaction between the number of lifetime partners and IFNL4-ΔG in the development of aggressive prostate cancer. Based on these findings, we conclude that a gene-environment interaction between IFNL4-ΔG and sexual activity may increase the risk of prostate cancer.

IFNL4-ΔG Allele Is Associated with an Interferon Signature in Tumors and Survival of African-American Men with Prostate Cancer

Purpose: Men of African ancestry experience an excessive prostate cancer mortality that could be related to an aggressive tumor biology. We previously described an immune-inflammation signature in prostate tumors of African-American (AA) patients. Here, we further deconstructed this signature and investigated its relationships with tumor biology, survival, and a common germline variant in the IFNλ4 (IFNL4) gene.Experimental Design: We analyzed gene expression in prostate tissue datasets and performed genotype and survival analyses. We also overexpressed IFNL4 in human prostate cancer cells.Results: We found that a distinct interferon (IFN) signature that is analogous to the previously described "IFN-related DNA damage resistance signature" (IRDS) occurs in prostate tumors. Evaluation of two independent patient cohorts revealed that IRDS is detected about twice as often in prostate tumors of AA than European-American men. Furthermore, analysis in TCGA showed an association of increased IRDS in prostate tumors with decreased disease-free survival. To explain these observations, we assessed whether IRDS is associated with an IFNL4 germline variant (rs368234815-ΔG) that controls production of IFNλ4, a type III IFN, and is most common in individuals of African ancestry. We show that the IFNL4 rs368234815-ΔG allele was significantly associated with IRDS in prostate tumors and overall survival of AA patients. Moreover, IFNL4 overexpression induced IRDS in three human prostate cancer cell lines.Conclusions: Our study links a germline variant that controls production of IFNλ4 to the occurrence of a clinically relevant IFN signature in prostate tumors that may predominantly affect men of African ancestry. Clin Cancer Res; 24(21); 5471-81. ©2018 AACR.

Advanced glycation end products are elevated in estrogen receptor-positive breast cancer patients, alter response to therapy, and can be targeted by lifestyle intervention

Purpose

Lifestyle factors associated with personal behavior can alter tumor-associated biological pathways and thereby increase cancer risk, growth, and disease recurrence. Advanced glycation end products (AGEs) are reactive metabolites produced endogenously as a by-product of normal metabolism. A Western lifestyle also promotes AGE accumulation in the body which is associated with disease phenotypes through modification of the genome, protein crosslinking/dysfunction, and aberrant cell signaling. Given the links between lifestyle, AGEs, and disease, we examined the association between dietary-AGEs and breast cancer.

Methods

We evaluated AGE levels in bio-specimens from estrogen receptor-positive (ER+) and estrogen receptor-negative (ER−) breast cancer patients, examined their role in therapy resistance, and assessed the ability of lifestyle intervention to reduce circulating AGE levels in ER+ breast cancer survivors.

Results

An association between ER status and AGE levels was observed in tumor and serum samples. AGE treatment of ER+ breast cancer cells altered ERα phosphorylation and promoted resistance to tamoxifen therapy. In a proof of concept study, physical activity and dietary intervention was shown to be viable options for reducing circulating AGE levels in breast cancer survivors.

Conclusions

There is a potential prognostic and therapeutic role for lifestyle derived AGEs in breast cancer. Given the potential benefits of lifestyle intervention on incidence and mortality, opportunities exist for the development of community health and nutritional programs aimed at reducing AGE exposure in order to improve breast cancer prevention and treatment outcomes.

Electronic supplementary material

The online version of this article (10.1007/s10549-018-4992-7) contains supplementary material, which is available to authorized users.

Genetic variation in the Hippo pathway and breast cancer risk in women of African ancestry

Gene expression changes within the Hippo pathway were found to be associated with large tumor size and metastasis in breast cancer. The combined effect of genetic variants in genes of this pathway may have a causal role in breast cancer development. We examined 7086 SNPs that were not highly correlated (r2  < 0.8) in 35 Hippo pathway genes using data from the genome-wide association study of breast cancer from the Root Consortium, which includes 3686 participants of African ancestry from Nigeria, United States of America, and Barbados: 1657 cases (403 estrogen receptor-positive [ER+], 374 ER-) and 2029 controls. Gene-level analyses were conducted using improved AdaJoint test for large-scale genetic association studies adjusting for age, study site and the first four eigenvectors from the principal component analysis. SNP-level analyses were conducted with logistic regression. The Hippo pathway was significantly associated with risk of ER+ breast cancer (pathway-level P = 0.019), with WWC1 (Padj  = 0.04) being the leading gene. The pathway-level significance was lost without WWC1 (P = 0.12). rs147106204 in the WWC1 gene was the most statistically significant SNP after gene-level adjustment for multiple comparisons (OR = 0.53, 95%CI = 0.41-0.70, Padj  = 0.025). We found evidence of an association between genetic variations in the Hippo pathway and ER+ breast cancer. Moreover, WWC1 was identified as the most important genetic susceptibility locus highlighting the importance of genetic epidemiology studies of breast cancer in understudied populations.

Association of Anthropometric Measures with Prostate Cancer among African American Men in the NCI-Maryland Prostate Cancer Case-Control Study

Background: Obesity is a cancer risk factor. Although it does not increase the risk of localized prostate cancer, it raises the risk of the aggressive disease in men of European ancestry. Few studies investigated obesity as a prostate cancer risk factor in men of African ancestry. Findings from those studies were heterogeneous, but some reported an association of excess body fatness with aggressive disease.Methods: We examined the relationship of body mass index (BMI), waist circumference, and waist-hip ratio with prostate cancer in African American (AA) and European American (EA) men in the NCI-Maryland Prostate Cancer Case-Control Study consisting of 798 men with incident prostate cancer (402 AA and 496 EA) and 1,008 population-based controls (474 AA and 534 EA). BMI was self-reported. Waist circumference and waist-hip ratio were calculated from measurements at enrollment.Results: A high BMI either at enrollment or years prior to it was associated with a decreased risk of prostate cancer in AA men. In contrast, an elevated BMI tended to increase the disease risk in EA men. Waist circumference was inversely associated with prostate cancer in both AA and EA men, whereas a high waist-hip ratio did not associate with prostate cancer in AA men but tended to be associated with advanced/aggressive disease in EA men.Conclusions: Our findings reveal an obesity paradox among AA men in this study population, where a high BMI and waist circumference associated with a decreased disease risk.Impact: Our observations expand the knowledge of how obesity may affect prostate cancer risks in AAs. Cancer Epidemiol Biomarkers Prev; 27(8); 936-44. ©2018 AACR.

Abstract B92: Metabolomic landscape of African American prostate cancer: Insights into the biologic basis of the racial disparity

African American (AA) men have an approximately 60% higher incidence of prostate cancer (PCa) and have about two times greater risk of dying of the disease than their European American (EA) counterparts. Despite this staggeringly unequal burden of PCa incidence and outcome between AA and EA men, there is limited insight into the molecular mechanisms associated with this racial disparity. Using state-of-the-art mass spectrometry platform, we uncovered the very first metabolic and lipidomics landscape in PCa/benign adjacent tissue pairs and paired plasma and urine containing epidemiologic meta-data from ancestry-typed AA and EA men. A total of 190 polar and mid-polar metabolites and 495 lipids were measured in tissues and 183 metabolites and lipids were examined in the plasma and urine samples. AA PCa tissue and plasma signatures had unique alterations in metabolites and key enzymes associated with the methionine-homocysteine pathway, including adenosine and inosine levels, compared to corresponding tissues and plasma from EA case controls and EA PCa tissues. Intriguingly, methionine levels in AA PCa were also portrayed by distinct dietary practices in these patients. In addition, AA PCa tissues demonstrated unique patterns of bioenergetic metabolites and accumulated lipids reflecting impaired mitochondrial activity and TCA cycle. Further characterization of these first-in-the-field findings demonstrating reprogrammed metabolism in AA PCa relative to EA tumors could reveal insights into the biologic basis of PCa disparities and novel areas for therapeutic intervention.

Citation Format: Stacy M. Lloyd*, Jie H. Gohlke*, Sumanta Basu*, Vasanta Putluri,Shaiju K Vareed, Rebeca San Martin, Thekkelnaycke Rajendiran, Tiffany A. Dorsey, Bandana Prasad, Rajni Sonavane, Uttam Rasaily, James Henderson, Balasubramanyam Karanam, Harene Venghatakrishnan, Salil Bhowmik, Alexander Zaslavsky,Nilanjan Guha, Rick Kittles, Stefan Ambs, Michael Ittmann,David Rowley, Ganesh Palapattu, Nagireddy Putluri,George Michailidis, Arun Sreekumar. Metabolomic landscape of African American prostate cancer: Insights into the biologic basis of the racial disparity [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B92.

Abstract 3789: Role of NOS2-COX2 crosstalk in tumor microenvironment of estrogen receptor-negative breast cancer and its therapeutic implications

Tumor is often described as a wound that never heals. This leads to a chronic inflammatory tumor microenvironment characterized by infiltration of M2 macrophages and Th2 cells causing dysregulated release of multiple cytokines, chemokines and growth factors, thus creating a conducive environment for tumor growth and metastasis. In spite of significant progress in breast cancer treatment, metastatic breast cancer still remains a major health hazard with a high mortality rate among women. Moreover, there is cellular heterogeneity within and among different breast tumors, which poses a significant challenge in developing effective therapeutics, thus making it important to understand subtype-specific mechanisms. Our laboratory and other groups have previously shown that inducible nitric oxide synthase (NOS2), an enzyme involved in production and regulation of endogenous nitric oxide (NO), is a predictor of poor survival among highly metastatic ER-negative (ER-) breast cancer patients. Another proinflammatory enzyme, cyclooxygenase-2 (COX2,) responsible for conversion of arachidonic acid to prostaglandin E2 (PGE2), is also highly expressed in breast cancer and is detectable in ductal carcinoma in situ, invasive breast carcinoma, and metastatic lesions. We investigated the role of inflammation associated enzymes, NOS2 and COX2, and established that their simultaneous elevated expression significantly reduced patient survival (33%) when compared to greater than 95% survival of ER- patients with low NOS2/COX2 tumor expression. We further investigated their tumor subtype specific novel signaling mechanism in vitro and showed TNFα and/or endoplasmic reticulum stress as key players. Proinflammatory cytokines present in tumor microenvironment play a key role in regulation of this pathway and effectiveness of chemotherapeutics. Moreover, the ability of NOS2 and COX2 to regulate different cytokines in the tumor microenvironment further emphasizes the importance of their crosstalk in tumor progression, metastasis and ability of cancer cells to escape immune surveillance. Last, we demonstrated that simultaneous inhibition of COX2 and NOS2 using commercially available inhibitors significantly reduced tumor growth in murine models of ER- breast cancer, thus suggesting the beneficial effects of dual NOS2/COX2 therapy.

Citation Format: Debashree Basudhar, Sharon Glynn, Madison Greer, Veena Somasundaram, Jae H. No, David A. Scheiblin, Pablo Garrido, William F. Heinz, Aideen E. Ryan, Jonathan M. Weiss, Robert Y. Cheng, Lisa A. Ridnour, Stephen J. Lockett, Daniel W. McVicar, Stefan Ambs, David A. Wink. Role of NOS2-COX2 crosstalk in tumor microenvironment of estrogen receptor-negative breast cancer and its therapeutic implications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3789.

Abstract 2394: Racial disparity in bladder cancer and identification of altered metabolism in African American compared to European American bladder cancer

This abstract has been withheld from publication due to its inclusion in the AACR Annual Meeting 2018 Official Press Program. It will be posted online following its presentation.

Citation Format: Venkata Rao Vantaku, Sri Ramya Donepudi, Tiffany Dorsey, Vasanta Putluri, Chandrashekar Ambati, Tang Wei, Michael M. Ittmann, Martha K. Terris, Seth Lerner, Stefan Ambs, Yair Lotan, Arun Sreekumar, Nagireddy Putluri. Racial disparity in bladder cancer and identification of altered metabolism in African American compared to European American bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2394.

Influence of lifestyle and genetic variants in the aldo-keto reductase 1C3 rs12529 polymorphism in high-risk prostate cancer detection variability assessed between US and New Zealand cohorts

Introduction

The prostate-specific antigen (PSA) based prostate cancer (PC) screening is currently being debated. The current assessment is to understand the variability of detecting high-risk PC in a NZ cohort in comparison to a US cohort with better PSA screening facilities. Aldo-keto reductase 1C3 (AKR1C3) is known for multiple functions with a potential to regulate subsequent PSA levels. Therefore, we wish to understand the influence of tobacco smoking and the AKR1C3 rs12529 gene polymorphism in this variability.

Method

NZ cohort (n = 376) consisted of 94% Caucasians while the US cohort consisted of African Americans (AA), n = 202, and European Americans (EA), n = 232. PSA level, PC grade and stage at diagnosis were collected from hospital databases for assigning high-risk PC status. Tobacco smoking status and the AKR1C3 rs12529 SNP genotype were considered as confounding variables. Variation of the cumulative % high-risk PC (outcome variable) with increasing PSA intervals (exposure factor) was compared between the cohorts using the Kolmogorov-Smirnov test. Comparisons were carried out with and without stratifications made using confounding variables.

Results

NZ cohort has been diagnosed at a significantly higher mean age (66.67± (8.08) y) compared to both AA (62.65±8.17y) and EA (64.83+8.56y); median PSA (NZ 8.90ng/ml compared to AA 6.86ng/ml and EA 5.80ng/ml); and Gleason sum (NZ (7) compared EA (6)) (p<0.05). The cumulative % high-risk PC detection shows NZ cohort with a significantly lower diagnosis rates at PSA levels between >6 - <10ng/ml compared to both US groups (p<0.05). These were further compounded significantly by smoking status and genetics.

Conclusions

High-risk PCs recorded at higher PSA levels in NZ could be due to factors including lower levels of PSA screening and subsequent specialist referrals for biopsies. These consequences could be pronounced among NZ ever smokers carrying the AKR1C3 rs12529 G alleles making them a group that requires increased PSA screening attention.

Long Noncoding RNA PURPL Suppresses Basal p53 Levels and Promotes Tumorigenicity in Colorectal Cancer

Basal p53 levels are tightly suppressed under normal conditions. Disrupting this regulation results in elevated p53 levels to induce cell cycle arrest, apoptosis, and tumor suppression. Here, we report the suppression of basal p53 levels by a nuclear, p53-regulated long noncoding RNA that we termed PURPL (p53 upregulated regulator of p53 levels). Targeted depletion of PURPL in colorectal cancer cells results in elevated basal p53 levels and induces growth defects in cell culture and in mouse xenografts. PURPL associates with MYBBP1A, a protein that binds to and stabilizes p53, and inhibits the formation of the p53-MYBBP1A complex. In the absence of PURPL, MYBBP1A interacts with and stabilizes p53. Silencing MYBBP1A significantly rescues basal p53 levels and proliferation in PURPL-deficient cells, suggesting that MYBBP1A mediates the effect of PURPL in regulating p53. These results reveal a p53-PURPL auto-regulatory feedback loop and demonstrate a role for PURPL in maintaining basal p53 levels.

ADHFE1 is a MYC-linked oncogene that induces metabolic reprogramming and cellular de-differentiation in breast cancer

The oncometabolite, D-2-hydroxyglutarate, accumulates in various cancers because of acquired mutations in isocitrate dehydrogenase 1 & 2. Here, we describe a new mechanism for D-2-hydroxyglutarate accumulation in breast cancer. It involves c-Myc signaling and alcohol dehydrogenase, iron-containing protein 1 (ADHFE1) and leads to metabolic reprogramming, de-differentiation, and increased mammary tumorigenesis.

Genome-wide association studies in women of African ancestry identified 3q26.21 as a novel susceptibility locus for oestrogen receptor negative breast cancer

Multiple breast cancer loci have been identified in previous genome-wide association studies, but they were mainly conducted in populations of European ancestry. Women of African ancestry are more likely to have young-onset and oestrogen receptor (ER) negative breast cancer for reasons that are unknown and understudied. To identify genetic risk factors for breast cancer in women of African descent, we conducted a meta-analysis of two genome-wide association studies of breast cancer; one study consists of 1,657 cases and 2,029 controls genotyped with Illumina’s HumanOmni2.5 BeadChip and the other study included 3,016 cases and 2,745 controls genotyped using Illumina Human1M-Duo BeadChip. The top 18,376 single nucleotide polymorphisms (SNP) from the meta-analysis were replicated in the third study that consists of 1,984 African Americans cases and 2,939 controls. We found that SNP rs13074711, 26.5 Kb upstream of TNFSF10 at 3q26.21, was significantly associated with risk of oestrogen receptor (ER)-negative breast cancer (odds ratio [OR]=1.29, 95% CI: 1.18-1.40; P = 1.8 × 10 − 8). Functional annotations suggest that the TNFSF10 gene may be involved in breast cancer aetiology, but further functional experiments are needed. In addition, we confirmed SNP rs10069690 was the best indicator for ER-negative breast cancer at 5p15.33 (OR = 1.30; P = 2.4 × 10 − 10) and identified rs12998806 as the best indicator for ER-positive breast cancer at 2q35 (OR = 1.34; P = 2.2 × 10 − 8) for women of African ancestry. These findings demonstrated additional susceptibility alleles for breast cancer can be revealed in diverse populations and have important public health implications in building race/ethnicity-specific risk prediction model for breast cancer.