European American Patients Research Articles

Abstract 1525: Kaiso influences immune signaling of breast cancer exosomes

Abstract Introduction: Exosomes are communication vesicles between tumor cells and immune cells. However, the mechanism underlining this cell-cell communication is not well understanding, particularly in African American (AA) breast cancer patients. Kaiso, a bi-modal transcription factor is highly expressed in AA patients and high Kaiso expression correlates with aggressiveness and the disparity in survival outcomes compared to European American (EA) patients. However, the biological consequences of Kaiso in immune signaling of breast cancer exosomes has not been studied. Herein we demonstrate the biological role of Kaiso in immune signaling in breast cancer exosomes. Methods: We utilized Nanostring immune profiling technology along with multiple in vitro and in vivo assays to study the role of Kaiso in breast cancer immune escape. Results: Nanostring pan cancer immune profiling showed that EA breast cancer exosomes exhibited higher expression of TILs markers, T cell activation markers and CD8+T Cells markers compared to AA, while we observed an increase in the expression of anti-phagocytic molecule CD47 in breast cancer patient exosomes of AA compared to EA. In addition to that CD47 and SIRP-α (Signal Regulatory Protein) are highly expressed in Kaiso-scrambled MDA-MB-231 cells (sh-SCR) and exosomes, whereas THBS1, which is a regulator of CD47 expression and is regarded as angiogenesis inhibitor is significantly increased in sh-Kaiso MDA-231 cells and exosomes. Additionally, we observed that Kaiso directly binds methylated sequences in the promoter region of CD47 and THBS1 by ChIP assay. Furthermore, in vivo sh-Kaiso cells injected into athymic mice exhibited delayed tumor formation after four weeks with smaller tumor size as compared to sh-SCR cells, and we observed higher expression of THBS1 with lower expression of CD47 and SIRP-α molecules by IHC and exosomes isolated from invivo tumors, indicating that Kaiso is associated with macrophage mediated immune escape. Conclusion: Our findings demonstrate the role of kaiso in immune signaling through exosomes which may be related with more aggressive cancer phenotype in breast cancer specially in African Americans. Citation Format: Md Shakir U. Ahmed, Brittany Jenkins, Benjamin Adu-Addai, Balasubramanyam Karanam, Melissa B. Davis, William E. Grizzle, Honghe Wang, Clayton C. Yates. Kaiso influences immune signaling of breast cancer exosomes [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 1525.

Abstract 5133: Identification of distinct gene expression profiles in African Americans and Caucasian men with prostate cancer

Abstract Introduction African Americans (AA) are disproportionately affected by prostate cancer (PCa) compared to European Americans (EA). Genetic and epigenetic differences have been implicated in this racial disparity. Present PCa diagnostic and treatment regimens have focused mainly on gene fusion product involving the androgen driven transmembrane protease serine 2 (TMPRSS2) and the transcription factor, ETS related gene (ERG). However, TMPRSS2:ERG (T2E) fusion product is common mainly to EA (50-80% of patients) and has lower prevalence amongst other ethnicities including AAs (10-30%), Japanese and Chinese patients. In addition, T2E negative PCa subtype has been associated with increased risk of developing castration resistant PCa (CRPC). This study aims at classifying PCa by molecular and pathologic subtypes that drive disease aggressiveness in patients of AA and EA ancestry. Methodology Prostate cancer tissue slides obtained from EA and AA patients were stained for ERG expression. Laser-capture micro-dissected RNAs from formalin-fixed paraffin-embedded tissues were used for RNA-seq. DESeq2 was used as a statistical procedure to call differentially expressed genes (DEGs) in different samples. Data set from Powell was also analyzed for DEGs between ERG positive and ERG negative samples. Leading-Edge Analysis (GSEA v2.2.4) was performed to determine the representation of DEGs across enriched gene sets. Results 32.4% of EA were ERG positive compared to 29% of AA that stained positive. More EA samples (26.4%) had high intensity staining (2≥ on a 1 - 3 scale) compared to AA samples (25.8%). Over 11% of EA samples had high (4) distribution of ERG positive staining compared 6.5% in AA samples. Analysis of the Powell dataset (GSE41696) revealed 301 DEGs and gene set enrichment analysis identified immune system process, regulation of cellular component and homeostatic process as most biological processes affected by DEGs. Other processes significantly affected included: cell motility, cell activation and regulation of locomotion. At least 15 genes including: CCL5, TLR4, PIK3CB, CD86, KIT, CD40, ITGB3, PDGFRA, LEF1, HIF1A, CLU, PLA2G6, GLI3, PIK3CA and TNNB1, were present in at least 10 enriched gene sets. The DEGs across enriched gene sets showed gene signatures involved in Wnt signaling, PI3K, chemokines and receptor tyrosine kinases. Conclusion Specific sets of genes are differentially enriched between EGR-/AR- and ERG+/AR+. These findings suggest that PCas have a distinct gene expression profile in the absence of the T2E fusion, which may act as a driver of disease aggressiveness and racial health disparities in PCa. Identifying these differences in gene-signature expression and signaling transduction pathways will allow stratification of men across races and identify, early on, those individuals who are likely to develop the most aggressive disease. Citation Format: Joakin Mori, Raven Williams, Hui-Xian Lin, Alahni Becks, Jason White, Balasubramanyam Karanam, Clayton Yates, Honghe Wang. Identification of distinct gene expression profiles in African Americans and Caucasian men with prostate cancer [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 5133.

Immune-stimulatory gene expression in stroma cells of African-American prostate cancer tissues.

e16544 Background: Prostate cancer (PCa) of African Americans (AA) has a two-fold higher mortality compared to PCa of European Americans (EA). PCa-adjacent stroma cells from these two populations were examined for differences in their cytokine secretion and gene transcription. Methods: Primary PCa-adjacent stroma cells (carcinoma-associated fibroblasts (CAFs)) and PCa-distant normal fibroblasts of the same gland (dNFs) from 15 AA and 27 EA patients were grown to passage 5. A multiplex immunoassay was then used to measure the secretion of 30 cytokines/chemokines in conditioned medium. In addition, RNA-Seq was performed on four AA and four EA CAF lines, and on PCa-adjacent stroma FFPE tissues of seven AA and five EA patients. Self-identified ethnicity was confirmed using the LASER program and SNPs present in the RNA-Seq. Results: Conditioned media from 42 AA and EA CAFs and dNFs were assayed for 30 immuno-regulatory cytokines/chemokines and growth factors, 20 of which (66%) were secreted at lower levels ( p < 0.05) in AA vs. EA CAFs. Remarkably, dNFs did not show this difference. RNA-Seq analysis of AA vs EA CAFs in culture identified 413 upregulated and 893 downregulated genes (FDR < 0.05, ≥ ±1.5 fold). Several interleukins, interferons, and 120 of 154 differentially transcribed interferon-stimulated genes were downregulated in AA vs. EA CAFs. RNA-Seq of PCa-adjacent stroma from FFPE tissues of seven AA and five EA patients revealed significantly reduced transcription of many immunomodulatory genes in AA stroma, including type I IFN-stimulated genes (ISGs). CIBERSORT analysis of the FFPE RNA-Seq data indicated the presence of significantly less numbers of dendritic cells and higher levels of naïve CD4 Th cells in AA vs. EA stroma. Conclusions: We observed reduced transcription of immunomodulators in CAFs of AA vs. EA, accompanied by profound decreases in the levels of many secreted cytokines and chemokines. These differences may indicate reduced innate and adaptive immune responses in AA PCa, compared to EA PCa. The differences observed here in primary cell lines may permit functional studies of the underlying mechanism(s) of the striking dissimilarity in disease outcome of AA PCa compared to EA PCa

Mitochondrial alterations may underlie race-specific differences in cancer risk and outcome.

African Americans are at increased risk of cancer and associated mortalities compared with European American populations. Socioeconomic, cultural, and biological factors have been implicated in this discrepancy. In this issue of the JCI, Piyarathna et al. identify a set of genes that are upregulated in a number of tumor types in African American cancer patients as compared with European American patients. These genes were associated with enhanced oxidative phosphorylation and upregulation of transcription factors that promote mitochondrial biogenesis, resulting in greater numbers of mitochondria in tumor samples from African American subjects. Together, these results indicate that mitochondria dysfunction may underlie the increased cancer incidence and poor outcomes observed in African American patients.

ERR1 and PGC1α associated mitochondrial alterations correlate with pan-cancer disparity in African Americans.

African American (AA) patients have higher cancer mortality rates and shorter survival times compared to European American (EA) patients. Despite a significant focus on socioeconomic factors, recent findings strongly argue the existence of biological factors driving this disparity. Most of these factors have been described in a cancer-type specific context rather than a pan-cancer setting. A novel in silico approach based on Gene Set Enrichment Analysis (GSEA) coupled to Transcription Factor enrichment was carried out to identify common biological drivers of pan-cancer racial disparity using The Cancer Genome Atlas (TCGA) dataset. Mitochondrial content in patient tissues was examined using a multi-cancer tissue microarray approach (TMA). Mitochondrial oxidative phosphorylation was uniquely enriched in AA tumors compared to EA tumors across various cancer types. AA tumors also showed strong enrichment for the ERR1-PGC1α-mediated transcriptional program, which has been implicated in mitochondrial biogenesis. TMA analysis revealed that AA cancers harbor significantly more mitochondria compared to their EA counterparts. These findings highlight changes in mitochondria as a common distinguishing feature between AA and EA tumors in a pan-cancer setting, and provide the rationale for the repurposing of mitochondrial inhibitors to treat AA cancers.

Type I IFN and IL-4R define B cell checkpoint defects in systemic lupus erythematosus

Abstract The development of pathogenic autoantibody producing B cells is normally limited at the early transitional (Tr) stage and a later T-dependent developmental checkpoint. The precise molecular mechanisms underlying defective autoreactive B cell deletion/anergy at each checkpoint have been difficult to define. We utilized a combined single-cell B cell transcriptome and high dimensional flow cytometry analysis approach for a parallel understanding of B-cell developmental checkpoint defects at multiple stages in SLE. We found that while high levels of B-cell endogenous interferon-β (IFNβ) is an important risk factor for autoantibody positive African American (AA) SLE patients, low expression of IL-4R was a risk factor of both AA and European-Americans (EA) patients for development of pathogenic autoantibodies. The molecular signature of autoreactive B cells that escape deletion at the Tr stage include type I IFN stimulated genes (ISGs), including IRF7, ISG15, ISG20, MX1, and STAT1. The molecular signature of autoreactive B cells that escape the second T-dependent checkpoint, include low expression of IL4R and the transcriptional repressor BACH2, and high levels of TBX21, ITGAX, FCRL5 and IFI30. Interestingly, in vitro culture stimulation confirmed that the presence of IL-4 signaling significantly suppressed the development of pathogenic CD21−CD27−IgD−CD11c+T-bet+ double negative 2 (DN2) B cells in SLE. These results suggest that B-cell checkpoint defects can be used to stratify SLE patients according to high type I IFN or low IL-4R and their response signatures. These immune phenotype and transcriptome signatures offer the potential to predict therapy responses to type I IFN blockade or other therapies.

CC chemokines are differentially expressed in Breast Cancer and are associated with disparity in overall survival

Despite recent advances, breast cancer (BrCa) still affects many women and the impact is disproportional in African Americans (AA) compared to European Americans (EA). Addressing socioeconomic and behavioral status has not been enough to reduce disparity, suggesting contribution of biological differences in BrCa disparity. Our laboratory was first to show involvement of CC chemokines in BrCa. In this study, using ONCOMINE, TCGA, bc-GenExMiner and KMplotter, we examined the association of CC chemokines in BrCa outcomes and disparity. We show over-expression of CCL5, -7, -11, -17, -20, -22 and -25 in BrCa tissues. High mRNA levels of CCL7, -8, -17, -20 and -25 predicted a decrease in overall survival (OS). CCL7 and CCL8 were associated with decreased relapse-free survival. Expression of CCL17 and CCL25 was associated with decreased OS in AA. In EA, CCL8 was associated with decreased OS. Expression of CCL5, -7, -8, -17, -20 and -25 was highest in TNBC. Expression of CCL11 and CCL22 was associated with HER2. CCL7, -8, -17, -20 and -25 were elevated in AAs. In conclusion, our analysis suggests significant association of CC-chemokines in BrCa progression, OS and disparate disease outcome in AA compared to EA patients.

TP53 missense mutation is associated with increased tumor-infiltrating T cells in primary prostate cancer

The makeup of the tumor immune microenvironment may be associated with tumor somatic genomic alterations and plays a key role in tumor progression and response to immunotherapy. We examined the association of tumor-infiltrating T-cell density with TP53 status in surgically treated primary prostate cancer using 3 independent tissue microarray sets, including one set of tumors from grade-matched patients of European American or African American ancestry (n = 391), a retrospective case-cohort of intermediate- and high-risk patients enriched for adverse outcomes (n = 267), and a set of tumors with primary Gleason pattern 5 (n = 77). The presence of TP53 missense mutation, indicated by p53 nuclear accumulation using a genetically validated assay, was significantly associated with increased CD3+ T-cell density (median, 341 versus 231 CD3+ T cells/mm2; P = .004) in the matched European American and African American ancestry patient sets. The same association was present in patients of both ancestries when analyzed separately, despite the fact that p53 nuclear accumulation was less frequent among African American compared with European American tumors (7% versus 3%, P = .2). The validation cohorts of intermediate/high-risk and primary Gleason pattern 5 patients corroborated the association of increased CD3+ T-cell density with presence of p53 nuclear accumulation. In a pooled analysis of all sets, adjusting for clinicopathological variables, CD3+ and CD8+, but not FOXP3+, T-cell densities remained significantly higher in tumors with p53 nuclear accumulation compared with those without. TP53 mutation is associated with higher tumor-infiltrating T-cell density, which may be relevant in future clinical trials of immunotherapy in prostate cancer.

Differences in Genomic Profiles and Outcomes Between Thoracic and Adrenal Neuroblastoma

Neuroblastoma is a biologically and clinically heterogeneous disease. Based on recent studies demonstrating an association between the primary tumor site, prognosis, and commonly measured tumor biological features, we hypothesized that neuroblastomas arising in different sites would show distinct genomic features reflective of the developmental biology of the sympathicoadrenal nervous system. We first compared genomic and epigenomic data of primary diagnostic neuroblastomas originating in the adrenal gland (n = 646) compared to thoracic sympathetic ganglia (n = 118). We also evaluated association of common germline variation with these primary sites in 1027 European-American neuroblastoma patients. We observed higher rates of MYCN amplification, chromosome 1q gain, and chromosome 11q deletion among adrenal tumors, which were highly predictive of functional RNA signatures. Surprisingly, thoracic neuroblastomas were more likely to harbor ALK driver mutations than adrenal cases among all cases (odds ratio = 1.89, 95% confidence interval = 1.04 to 3.43), and among cases without MYCN amplification (odds ratio = 2.86, 95% confidence interval = 1.48 to 5.49). Common germline single nucleotide polymorphisms (SNPs) in BARD1 (previously associated with high-risk neuroblastoma) were found to be strongly associated with predisposition for origin at adrenal, rather than thoracic, sites. Neuroblastomas arising in the adrenal gland are more likely to harbor structural DNA aberrations including MYCN amplification, whereas thoracic tumors show defects in mitotic checkpoints resulting in hyperdiploidy. Despite the general association of ALK mutations with high-risk disease, thoracic tumors are more likely to harbor gain-of-function ALK aberrations. Site of origin is likely reflective of stage of sympathetic nervous system development when malignant transformation occurs and is a surrogate for underlying tumor biology.

Novel genetic associations with interferon in systemic lupus erythematosus identified by replication and fine-mapping of trait-stratified genome-wide screen

Background/PurposeHigh serum interferon alpha (IFN-α) is an important heritable phenotype in systemic lupus erythematosus (SLE) which is involved in primary disease pathogenesis. High vs. low levels of IFN-α are associated with disease severity and account for some of the biological heterogeneity between SLE patients. The aim of the study was to replicate and fine-map previously detected genetic associations with serum IFN-α in SLE. MethodsWe previously undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci identified in this screen were selected for follow up in a large independent cohort of 1370 SLE patients (703 European-ancestry, 432 African ancestry, and 235 Amerindian ancestry). Each ancestral background was analyzed separately, and ancestry-informative markers were used to control for ancestry and admixture. ResultsWe find a rare haplotype spanning the promoter region of EFNA5 that is strongly associated with serum IFN-α in both African-American and European-American SLE patients (OR = 3.0, p = 3.7 × 10−6). We also find SNPs in the PPM1H, PTPRM, and NRGN regions associated with IFN-α levels in European-American, Amerindian, and African-American SLE patients respectively. Many of these associations are within regulatory regions of the gene, suggesting an impact on transcription. ConclusionThis study demonstrates the power of molecular sub-phenotypes to reveal genetic factors involved in complex autoimmune disease. The distinct associations observed in different ancestral backgrounds emphasize the heterogeneity of molecular pathogenesis in SLE.

SU86 - VALIDATION STUDY IN TWO GENOME-WIDE SIGNIFICANT RISK VARIANTS FOR ANTIPSYCHOTIC INDUCED WEIGHT GAIN

Background Antipsychotic drugs are the primary intervention in the treatment of psychotic disorders, however, the use of antipsychotics is often accompanied by weight gain and metabolic syndrome. A recent Genome-Wide Association Study (GWAS) investigating a Han Chinese sample suggested a possible role of rs1097714 and rs10977154 variants of the protein tyrosine phosphatase, receptor type D (PTPRD) gene in antipsychotic induced weight gain (AIWG). Additionally, two upstream variants (rs1886243 and rs6915627) of T-complex 11 (TCP11) were among the 20 most significant SNPs in the original study. The purpose of this study was to replicate the association of the top 20 variants from the aforementioned GWAS in two independent samples to evaluate whether these associations are also present in patients of European and African American ancestry. Methods The following two independent samples were used: 1) schizophrenia or schizoaffective disorder patients (based on DSM III and DSM IV criteria) primary undergoing first exposure to atypical antipsychotic drugs and 2) patients in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE) sample. Samples 1 and 2 were genotyped using Illumina Omni 2.5 Chip, Affymetrix 500 K “A” chipset, and the Perlegen custom 164 K chip, respectively. In the main analyses in two replication samples. Analysis of Covariance (ANCOVA) was used to investigate the percentage of change in weight (Sample 1) or Body Mass Index (BMI) (Sample 2) from baseline to last observation carried forward (LOCF), where genotypes were coded as factors. Models in both samples were corrected for study duration, and additionally for age in Sample 1, and medications used in Sample 2. Results In Sample 1 (122 men (65.9%), mean±SD age; 36±11 years, baseline body weight; 79.72±15.9 kg % of weight change (LOCF); 5.08±7.11, weight gainer (>7%); n=57 (31.0%), medication: clozapine, olanzapine, and risperidone were mainly used), none of 14 genetic variants showed a significant association with % of weight change in the European population. In African Americans, the nominal association was observed (F2,50=4.814; p=0.034) between rs3853114 variant of dynein axonemal heavy chain 5 (DNAH5). In Sample 2 (118 men (78.1%), mean±SD age; 40±12 years, baseline BMI; 28.63±5.43, % of BMI change (LOCF); 2.95±7.79, weight gainer (>7%); n=31 (20.5%), medication: olanzapine, risperidone, and quetiapine were used), nominal associations with two TCP11 variants rs1886243 (F2,148=3.14; p=0.046) and AIWG were observed. None of the variants described above survived correction for multiple testing. Discussion To the best of our knowledge, this is the first genetic association study evaluating PTPRD and TCP11 in European and African American patients. However, the associations between PTPRD variants and AIWG were not replicated; whereas the effects of TCP11 remained nominally significant. More studies across different ancestries are needed to examine if PTPRD and TCP11 can be considered susceptibility genes for AIWG.

The persisting puzzle of racial disparity in triple negative breast cancer: looking through a new lens.

Triple-negative breast cancer (TNBC) is characterized by the absence of estrogen and progesterone receptors and absence of amplification of human epidermal growth factor receptor (HER2). This disease has no approved treatment with a poor prognosis particularly in African-American (AA) as compared to European-American (EA) patients. Gene ontology analysis showed specific gene pathways that are differentially regulated and gene signatures that are differentially expressed in AA as compared to EA. Such differences might underlie the basis for the aggressive nature and poor prognosis of TNBC in AA patients. In-depth studies of these pathways and differential genetic signature might give significant clues to improve our understanding of tumor biology associated with AA TNBC to advance the prognosis and survival rates. Along with gene ontology analysis, we suggest that post-translational modifications (PTM) could also play a crucial role in the dismal survival rate of AA TNBC patients. Further investigations are necessary to explore this terrain of PTMs to identify the racially disparate burden in TNBC.

Elevation of Stromal-Derived Mediators of Inflammation Promote Prostate Cancer Progression in African-American Men.

Progress in prostate cancer racial disparity research has been hampered by a lack of appropriate research tools and better understanding of the tumor biology. Recent gene expression studies suggest that the tumor microenvironment (TME) may contribute to racially disparate clinical outcomes in prostate cancer. Analysis of the prostate TME has shown increased reactive stroma associated with chronic inflammatory infiltrates in African-American (AA) compared with European-American (EA) patients with prostate cancer. To better understand stromal drivers of changes in TME, we isolated prostate fibroblasts (PrF) from AA (PrF-AA) and EA (PrF-EA) prostate cancer tissues and studied their functional characteristics. PrF-AA showed increased growth response to androgens FGF2 and platelet-derived growth factor. Compared with PrF-EA, conditioned media from PrF-AA significantly enhanced the proliferation and motility of prostate cancer cell lines. Expression of markers associated with myofibroblast activation (αSMA, vimentin, and tenascin-C) was elevated in PrF-AA In vivo tumorigenicity of an AA patient-derived prostatic epithelial cell line E006AA was significantly increased in the presence of PrF-AA compared with PrF-EA, and RNA-seq data and cytokine array analysis identified a panel of potential proinflammatory paracrine mediators (BDNF, CHI3L1, DPPIV, FGF7, IL18BP, IL6, and VEGF) to be enriched in PrF-AA E006AA cell lines showed increased responsiveness to BDNF ligand compared with EA-derived LNCaP and C4-2B cells. Addition of a TrkB-specific antagonist significantly reduced the protumorigenic effects induced by PrF-AA compared with PrF-EA These findings suggest that fibroblasts in the TME of AA patients may contribute to the health disparity observed in the incidence and progression of prostate cancer tumors.Significance: These findings suggest that stromal cells in the tumor microenvironment of African-American men promote progression of prostate cancer by increasing levels of a specific set of pro-inflammatory molecules compared with European-American men.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/21/6134/F1.large.jpg Cancer Res; 78(21); 6134-45. ©2018 AACR.

Racial and Ethnic Disparities in Renal Cell Carcinoma: An Analysis of Clinical Characteristics.

Racial/ethnic minority groups, including Hispanic Americans (HAs) and Native Americans (NAs), have a heavier burden of kidney cancer than European Americans (EAs). We investigated variations in clinical characteristics of HA and NA patients with renal cell carcinoma (RCC) who were previously underrepresented. Clinical records of 294 patients with RCC (151 EAs, 95 HAs, 22 NAs, and 26 others) without prior diagnosis of cancer were reviewed. Logistic regression analysis was performed to understand patients' clinical characteristics. HAs had about 5 years younger average age at diagnosis than EAs (55.8 vs. 60.5 years) and an almost 3-fold increased odds of diagnosis before age 50 years (odds ratio [OR], 2.77; 95% confidence interval [CI], 1.39-5.54). The mean age of diagnosis among NAs was 49.7 years, and NAs had an over 6-fold higher odds of diagnosis at a younger age (OR, 6.23; 95% CI, 2.00-19.46). Clear-cell RCC (ccRCC) was more common in HAs and NAs than EAs. Over 90% of HA patients had ccRCC, whereas only 78.8% of EA patients had ccRCC. HAs had increased odds of diagnosis with ccRCC compared with EAs (OR, 2.79; 95% CI, 1.15-6.80). Among HAs, older patients and patients who spoke Spanish as their primary language were more likely to have advanced stage RCC at diagnosis (OR, 10.48; 95% CI, 1.69-64.89 and OR, 4.61; 95% CI, 1.38-15.40). HA and NA patients with RCC had different clinical characteristics than EA patients. It is necessary to better understand the clinical characteristics of these underserved HA and NA populations with high kidney cancer burden.

The association between method of solicitation and patient permissions for use of surplus tissues and contact for future research.

ObjectiveObtaining patient permissions for research contact and for surplus tissue use as part of routine clinical practice can improve research participation. This study aims to investigate the difference in patient permissions for use of surplus tissues, and for direct contact for research, using 2 different methods of solicitation.MethodsAn opt-in, population-based approach for gathering research permissions was implemented in 2 methods. The first method, applied a 2-item patient questionnaire delivered through the electronic health record patient portal. The questionnaire composed of 2 questions (1) whether de-identified surplus specimens may be used for research and (2) whether patients could be contacted about research. In the second method, the same questionnaire was physically presented in clinic within the clinical workflow. We used 1 to 1 propensity score matching and multivariate logistic regression to estimate the odds of obtaining permission and the difference between the 2 methods of solicitation.ResultsThe propensity score model matched 8044 observations (4114 submissions in each group). Among the in-clinic submission group, 70.13% provided permission for surplus tissue compared with 66.65% in the patient portal submission group (odds ratio [OR] = 1.20; 95% confidence interval [CI] 1.09–1.32; P < 0.001). Permission for future research contact was similar among in-clinic (65.07%) and patient portal submission (66.65%) groups (OR = 0.94; 95% CI 0.85–1.03; P = 0.175). These trends were consistent among European Americans and African American patients. However, among patients of other race, higher permission for both future contact (OR = 0.58; 95% CI 0.39–0.86; P < 0.007) and surplus tissue use (OR = 0.65; 95% CI 0.43–0.97; P = 0.036) was observed among patient portal submission.DiscussionOur findings suggest that in-clinic solicitation of patient permissions may provide the same opportunity to patients who do not use patient portals and may be associated with higher permission rate for surplus tissue. However, this was primary true for European American and African Americans patients. Patients of other race minorities might respond better to online approaches.ConclusionAdopting a patient-centric approach that combines in-clinic and portal-based administration may be feasible and promising. Further research is required in this area.

Atopic dermatitis in African American patients is TH2/TH22-skewed with TH1/TH17 attenuation

BackgroundAfrican Americans (AA) are disproportionately impacted by atopic dermatitis (AD), with increased prevalence and therapeutic challenges unique to this population. Molecular profiling data informing development of targeted therapeutics for AD are derived primarily from European American (EA) patients. These studies are absent in AA, hindering development of effective treatments for this population. ObjectiveWe sought to characterize the global molecular profile of AD in the skin of AA patients as compared with that of EA AD and healthy controls. MethodsWe performed RNA-Seq with reverse transcription polymerase chain reaction validation and immunohistochemistry studies in lesional and nonlesional skin of AA and EA AD patients vs healthy controls. ResultsAfrican American AD lesions were characterized by greater infiltration of dendritic cells (DCs) marked by the high-affinity immunoglobulin E (IgE) receptor (FcεR1+) compared with EA AD (P < .05). Both AD cohorts showed similarly robust up-regulation of Th2-related (CCL17/18/26) and Th22-related markers (interleukin [IL]-22, S100A8/9/12), but AA AD featured decreased expression of innate immune (tumor necrosis factor [TNF], IL-1β), Th1-related (interferon gamma [IFN-γ], MX1, IL-12RB1), and Th17-related markers (IL-23p19, IL-36G, CXCL1) vs EA AD (P < .05). The Th2 (IL-13) and Th22-related products (IL-22, S100A8/9/12) and serum IgE were significantly correlated with clinical severity (Scoring of Atopic Dermatitis [SCORAD]) in AA. Fillagrin (FLG) was exclusively down-regulated in EA AD, whereas loricrin (LOR) was down-regulated in both AD cohorts and negatively correlated with SCORAD in AA. ConclusionThe molecular phenotype of AA AD skin is characterized by attenuated Th1 and Th17 but similar Th2/Th22-skewing to EA AD. Our data encourages a personalized medicine approach accounting for phenotype-specific characteristics in future development of targeted therapeutics and clinical trial design for AD.

Abstract A33: Race, DNA methylation, and regulation of cancer immunotherapy response genes: A comparison of non-small cell lung cancers from African Americans and European Americans

Abstract African Americans (AA) have the highest non-small cell lung cancer incidence and lowest 5-year survival rates compared with any other population in the United States. Smoking is the strongest risk factor for lung cancer development. Paradoxically, AA smoke less than European Americans (EA). Even AA never-smokers have higher rates of lung cancer when compared with EA. This suggests other factors may contribute to lung cancer health disparities, both nonbiologic and biologic in scope. Biologic determinants are largely understudied. Recently, breakthroughs in cancer immunotherapy have revolutionized treatment paradigms. However, AA lung cancer patients may not benefit from these therapeutic advances as much as their EA counterparts if the underlying lung tumor biology differs in cancer immunotherapy response gene regulation. Previous work across cancers has shown clear immune system differences in AA compared with EA patients. Additionally, smoking is known to mediate DNA methylation. We hypothesize that population-specific differences in DNA methylation regulate cancer immunotherapy response genes. Comparative integrative genomics was performed using clinical demographic and lung tumor tissue data from TCGA (Illumina 450K methylation array, mRNA-seq). The DNA methylation status of 554 recently identified essential genes for cancer immunotherapy response was assessed in both LUAD (n=53 AA, 367 EA) and LUSC (n=48 AA, 274 EA) patients. Although many genes varied significantly by race (P value + FDR = ≤0.01) in both histologies (n=285), some gene signatures were LUAD-enriched (n=19), while others were LUSC-enriched (n=101). Significant DNA methylation decreases at a LUAD-enriched gene (SHISA4) in AA compared with EA corresponded with upregulation of this gene in 15% AA and 14% EA LUAD patients, respectively. Similarly, we observed significant decreases in DNA methylation at a LUSC-enriched gene (RAD1) in AA compared with EA, and this correlated with mRNA upregulation in 15% AA and 49% EA LUSC patients. Decreased immunotherapy response gene expression in AA suggests that targeted immunotherapy would be less effective in this population. This work is the first study to explore how DNA methylation differences between AA and EA with lung cancer may translate to differences in cancer immunotherapy drug response. Future studies include exploring other LUAD- and LUSC-enriched genes and their relationship with smoking, validating these findings in lung cancer cell lines from AA and EA, and elucidating novel biologic mechanisms for therapeutic purposes. Citation Format: Allison McHayle, Amy Boles, Lysa Diarra, Khadijah A. Mitchell. Race, DNA methylation, and regulation of cancer immunotherapy response genes: A comparison of non-small cell lung cancers from African Americans and European Americans [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr A33.

Secular change in dental development in New Mexican females

Recent research has indicated a dramatic acceleration of dental development in 20th century European Americans in Tennessee and Arizona, resulting in developmental stages being reached at earlier calendar ages. In order to determine whether this rate change is also observed in New Mexico, radiographs from two cohorts of European American female orthodontic patients with known ages were used to compare age by stage of development. The cohorts date to the 1970’s (n=101) and the 1990’s (n=93) and were between 5-11 years of age. Dental developmental stages were recorded for five mandibular teeth.The average calendar age difference between cohorts per tooth and developmental stage combination was less than one month, but varies among tooth/stage combinations by up to 13 months. A Pearson’s chi square test found no significant difference between the two cohorts for the 22 tooth/stage combinations. However, Cox Hazards Analysis demonstrated significant differences between the cohorts for five of the 22 tooth and stage combinations. Contrary to previous findings, the calendar age of the 1990’s cohort is older for 16 of the 22 tooth/stage combinations than the 1970’s cohort. This runs counter to the general trend of acceleration in development observed in multiple systems.

Frequency and phenotype consequence of APOC3 rare variants in patients with very low triglyceride levels

BackgroundHigh levels of triglycerides (TG ≥200 mg/dL) are an emerging risk factor for cardiovascular disease. Conversely, very low levels of TG are associated with decreased risk for cardiovascular disease. Precision medicine aims to capitalize on recent findings that rare variants such as APOC3 R19X (rs76353203) are associated with risk of disease, but it is unclear how population-based associations can be best translated in clinical settings at the individual-patient level.MethodsTo explore the potential usefulness of screening for genetic predictors of cardiovascular disease, we surveyed BioVU, the Vanderbilt University Medical Center’s biorepository linked to de-identified electronic health records (EHRs), for APOC3 19X mutations among adult European American patients (> 45 and > 55 years of age for men and women, respectively) with the lowest percentile of TG levels. The initial search identified 262 patients with the lowest TG levels in the biorepository; among these, 184 patients with sufficient DNA and the lowest TG levels were chosen for Illumina ExomeChip genotyping.ResultsA total of two patients were identified as heterozygotes of APOC3 R19X for a minor allele frequency (MAF) of 0.55% in this patient population. Both heterozygous patients had only a single mention of TG in the EHR (31 and 35 mg/dL, respectively), and one patient had evidence of previous cardiovascular disease.ConclusionsIn this patient population, we identified two patients who were carriers of the APOC3 19X null variant, but only one lacked evidence of disease in the EHR highlighting the challenges of inclusion of functional or previously associated genetic variation in clinical risk assessment.

Brief Report: Whole-Exome Sequencing to Identify Rare Variants and Gene Networks That Increase Susceptibility to Scleroderma in African Americans.

Whole-exome sequencing (WES) studies in systemic sclerosis (SSc) patients of European American (EA) ancestry have identified variants in the ATP8B4 gene and enrichment of variants in genes in the extracellular matrix (ECM)-related pathway that increase SSc susceptibility. This study was undertaken to evaluate the association of the ATP8B4 gene and the ECM-related pathway with SSc in a cohort of African American (AA) patients. SSc patients of AA ancestry were enrolled from 23 academic centers across the US under the Genome Research in African American Scleroderma Patients consortium. Unrelated AA individuals without serologic evidence of autoimmunity who were enrolled in the Howard University Family Study were used as unaffected controls. Functional variants in genes reported in the 2 WES studies in EA patients with SSc were selected for gene association testing using the optimized sequence kernel association test (SKAT-O) and pathway analysis by Ingenuity Pathway Analysis in 379 patients and 411 controls. Principal components analysis demonstrated that the patients and controls had similar ancestral backgrounds, with roughly equal proportions of mean European admixture. Using SKAT-O, we examined the association of individual genes that were previously reported in EA patients and none remained significant, including ATP8B4 (P = 0.98). However, we confirmed the previously reported association of the ECM-related pathway with enrichment of variants within the COL13A1, COL18A1, COL22A1, COL4A3, COL4A4, COL5A2, PROK1, and SERPINE1 genes (corrected P = 1.95 × 10-4 ). In the largest genetic study in AA patients with SSc to date, our findings corroborate the role of functional variants that aggregate in a fibrotic pathway and increase SSc susceptibility.