Structural remodeling of the endoplasmic reticulum in response to extracellular signals requires αTAT1-induced microtubule acetylation

Dynamic changes in the endoplasmic reticulum (ER) morphology are central to maintaining cellular homeostasis. Microtubules (MT) facilitate the continuous remodeling of the ER network into sheets and tubules by coordinating with many ER-shaping protein complexes, although how this process is controlled by extracellular signals remains unknown. Here we report that TAK1, a kinase responsive to numerous growth factors and cytokines including TGF-β and TNF-α, triggers ER tubulation by activating αTAT1, an MT-acetylating enzyme that enhances ER-sliding. We show that this TAK1/αTAT-dependent ER remodeling promotes cell survival by actively downregulating BOK, an ER membrane-associated proapoptotic effector. While BOK is normally protected from degradation when complexed with IP3R, it is rapidly degraded upon their dissociation during the ER sheets-to-tubules conversion. These findings demonstrate a distinct mechanism of ligand-induced ER remodeling and suggest that the TAK1/αTAT pathway may be a key target in ER stress and dysfunction.

Clear cell renal cell carcinoma molecular variations in non-Hispanic White and Hispanic patients

BACKGROUND

The United States is becoming increasingly diverse, but few molecular studies have assessed the progression of clear cell renal cell carcinoma (ccRCC) in diverse patient populations. This study examined ccRCC molecular variations in non-Hispanic White (NHW) and Hispanic patients and their effect on the association of gene expression with high-grade (Grade 3 or 4) ccRCC and overall mortality.

METHODS

A total of 156 patients were included in VHL sequencing and/or TempO-Seq analysis. DESeq2 was used to identify the genes associated with high-grade ccRCC. Logistic regression analysis was performed to assess whether race and ethnicity was associated with high/moderate impact VHL somatic mutations and the ccA/ccB subtype. Cox regression analysis was performed to assess association of molecular subtype and gene expression with overall mortality.

RESULTS

NHWs had moderate or high impact mutations in the VHL gene at a higher frequency than Hispanics (40.2% vs. 27.4%), while Hispanics had a higher frequency of the ccA subtype than NHWs (61.9% vs. 45.8%). ccA was more common in patients with BMI≥35 (65.2%) than in those with BMI < 25 (45.0%). There were 11 differentially expressed genes between high- and low-grade tumors. The Haptoglobin (HP) gene was most significantly overexpressed in high- compared to low-grade ccRCC in all samples (p-adj = 1.7 × 10^-12 ). When stratified by subtype, the 11 genes were significantly differentially expressed in the ccB subtype, but none of them were significant after adjusting for multiple testing in ccA. Finally, patients with the ccB subtype had a significantly increased risk of overall mortality (HR 4.87; p = 0.01) compared to patients with ccA, and patients with high HP expression and ccB, had a significantly increased risk of mortality compared to those with low HP expression and ccA (HR 6.45, p = 0.04).

CONCLUSION

This study reports ccRCC molecular variations in Hispanic patients who were previously underrepresented.

Linkage of NAMPT promoter variants to eNAMPT secretion, plasma eNAMPT levels, and ARDS severity

BACKGROUND AND OBJECTIVES

eNAMPT (extracellular nicotinamide phosphoribosyltransferase), a novel DAMP and TLR4 ligand, is a druggable ARDS therapeutic target with NAMPT promoter SNPs associated with ARDS severity. This study assesses the previously unknown influence of NAMPT promoter SNPs on NAMPT transcription, eNAMPT secretion, and ARDS severity.

METHODS AND DESIGN

Human lung endothelial cells (ECs) transfected with NAMPT promoter luciferase reporters harboring SNPs G-1535A, A-1001 C, and C-948A, were exposed to LPS or LPS/18% cyclic stretch (CS) and NAMPT promoter activity, NAMPT protein expression, and secretion assessed. NAMPT genotypes and eNAMPT plasma measurements (Days 0/7) were assessed in two ARDS cohorts (DISCOVERY n = 428; ALVEOLI n = 103).

RESULTS

Comparisons of minor allelic frequency (MAF) in both ARDS cohorts with the 1000 Human Genome Project revealed the G-1535A and C-948A SNPs to be significantly associated with ARDS in Blacks compared with controls and trended toward significance in non-Hispanic Whites. LPS-challenged and LPS/18% CS-challenged EC harboring the -1535G wild-type allele exhibited significantly increased NAMPT promoter activity (compared with -1535A) with the -1535G/-948A diplotype exhibiting significantly increased NAMPT promoter activity, NAMPT protein expression, and eNAMPT secretion compared with the -1535A/-948 C diplotype. Highly significant increases in Day 0 eNAMPT plasma values were observed in both DISCOVERY and ALVEOLI ARDS cohorts (compared with healthy controls). Among subjects surviving to Day 7, Day 7 eNAMPT values were significantly increased in Day 28 non-survivors versus survivors. The protective -1535A SNP allele drove -1535A/-1001A and -1535A/-948 C diplotypes that confer significantly reduced ARDS risk (compared with -1535G, -1535G/-1001 C, -1535G/-948A), particularly in Black ARDS subjects. NAMPT SNP comparisons within the two ARDS cohorts did not identify significant association with either APACHE III scores or plasma eNAMPT levels.

CONCLUSION

NAMPT SNPs influence promoter activity, eNAMPT protein expression/secretion, plasma eNAMPT levels, and ARDS severity. NAMPT genotypes are a potential tool for stratification in eNAMPT-focused ARDS clinical trials.

Live-cell imaging in human colonic monolayers reveals ERK waves limit the stem cell compartment to maintain epithelial homeostasis

The establishment and maintenance of different cellular compartments in tissues is a universal requirement across all metazoans. Maintaining the correct ratio of cell types in time and space allows tissues to form patterned compartments and perform complex functions. Patterning is especially evident in the human colon, where tissue homeostasis is maintained by stem cells in crypt structures that balance proliferation and differentiation. Here, we developed a human 2D patient derived organoid (PDO) screening platform to study tissue patterning and kinase pathway dynamics in single cells. Using this system, we discovered that waves of ERK signaling induced by apoptotic cells play a critical role in maintaining tissue patterning and homeostasis. If ERK is activated acutely across all cells instead of in wavelike patterns, then tissue patterning and stem cells are lost. Conversely, if ERK activity is inhibited, then stem cells become unrestricted and expand dramatically. This work demonstrates that the colonic epithelium requires coordinated ERK signaling dynamics to maintain patterning and tissue homeostasis. Our work reveals how ERK can antagonize stem cells while supporting cell replacement and the function of the gut.

Mutational signature profiling classifies subtypes of clinically different mismatch-repair-deficient tumours with a differential immunogenic response potential

BACKGROUND

Mismatch repair (MMR) deficiency is the hallmark of tumours from Lynch syndrome (LS), sporadic MLH1 hypermethylated and Lynch-like syndrome (LLS), but there is a lack of understanding of the variability in their mutational profiles based on clinical phenotypes. The aim of this study was to perform a molecular characterisation to identify novel features that can impact tumour behaviour and clinical management.

METHODS

We tested 105 MMR-deficient colorectal cancer tumours (25 LS, 35 LLS and 45 sporadic) for global exome microsatellite instability, cancer mutational signatures, mutational spectrum and neoepitope load.

RESULTS

Fifty-three percent of tumours showed high contribution of MMR-deficient mutational signatures, high level of global exome microsatellite instability, loss of MLH1/PMS2 protein expression and included sporadic tumours. Thirty-one percent of tumours showed weaker features of MMR deficiency, 62% lost MSH2/MSH6 expression and included 60% of LS and 44% of LLS tumours. Remarkably, 9% of all tumours lacked global exome microsatellite instability. Lastly, HLA-B07:02 could be triggering the neoantigen presentation in tumours that show the strongest contribution of MMR-deficient tumours.

CONCLUSIONS

Next-generation sequencing approaches allow for a granular molecular characterisation of MMR-deficient tumours, which can be essential to properly diagnose and treat patients with these tumours in the setting of personalised medicine.

BLM Sumoylation Is Required for Replication Stability and Normal Fork Velocity During DNA Replication

BLM is sumoylated in response to replication stress. We have studied the role of BLM sumoylation in physiologically normal and replication-stressed conditions by expressing in BLM-deficient cells a BLM with SUMO acceptor-site mutations, which we refer to as SUMO-mutant BLM cells. SUMO-mutant BLM cells exhibited multiple defects in both stressed and unstressed DNA replication conditions, including, in hydroxyurea-treated cells, reduced fork restart and increased fork collapse and, in untreated cells, slower fork velocity and increased fork instability as assayed by track-length asymmetry. We further showed by fluorescence recovery after photobleaching that SUMO-mutant BLM protein was less dynamic than normal BLM and comprised a higher immobile fraction at collapsed replication forks. BLM sumoylation has previously been linked to the recruitment of RAD51 to stressed forks in hydroxyurea-treated cells. An important unresolved question is whether the failure to efficiently recruit RAD51 is the explanation for replication stress in untreated SUMO-mutant BLM cells.

Genome-Wide Association Study of Response to Selenium Supplementation and Circulating Selenium Concentrations in Adults of European Descent

BACKGROUND

Selenium (Se) is a trace element that has been linked to many health conditions. Genome-wide association studies (GWAS) have identified variants for blood and toenail Se levels, but no GWAS has been conducted to date on responses to Se supplementation.

OBJECTIVES

A GWAS was performed to identify the single nucleotide polymorphisms (SNPs) associated with changes in Se concentrations after 1 year of supplementation. A GWAS of basal plasma Se concentrations at study entry was conducted to evaluate whether SNPs for Se responses overlap with SNPs for basal Se levels.

METHODS

A total of 428 participants aged 40-80 years of European descent from the Selenium and Celecoxib Trial (Sel/Cel Trial) who received daily supplementation with 200 µg of selenized yeast were included for the GWAS of responses to supplementation. Plasma Se concentrations were measured from blood samples collected at the time of recruitment and after 1 year of supplementation. Linear regression analyses were performed to assess the relationship between each SNP and changes in Se concentrations. We further examined whether the identified SNPs overlapped with those related to basal Se concentrations.

RESULTS

No SNP was significantly associated with changes in Se concentration at a genome-wide significance level. However, rs56856693, located upstream of the NEK6, was nominally associated with changes in Se concentrations after supplementation (P = 4.41 × 10-7), as were 2 additional SNPs, rs11960388 and rs6887869, located in the dimethylglycine dehydrogenase (DMGDH)/betaine-homocysteine S-methyltransferase (BHMT) region (P = 0.01). Alleles of 2 SNPs in the DMGDH/BHMT region associated with greater increases in Se concentrations after supplementation were also strongly associated with higher basal Se concentrations (P = 8.67 × 10-8).

CONCLUSIONS

This first GWAS of responses to Se supplementation in participants of European descent from the Sel/Cel Trial suggests that SNPs in the NEK6 and DMGDH/BHMT regions influence responses to supplementation.

Decreased copy-neutral loss of heterozygosity in African American colorectal cancers

Despite improvements over the past 20 years, African Americans continue to have the highest incidence and mortality rates of colorectal cancer (CRC) in the United States. While previous studies have found that copy number variations (CNVs) occur at similar frequency in African American and White CRCs, copy-neutral loss of heterozygosity (cnLOH) has not been investigated. In the present study, we used publicly available data from The Cancer Genome Atlas (TCGA) as well as data from an African American CRC cohort, the Chicago Colorectal Cancer Consortium (CCCC), to compare frequencies of CNVs and cnLOH events in CRCs in the two racial groups. Using genotype microarray data, we analyzed large-scale CNV and cnLOH events from 166 microsatellite stable CRCs-31 and 39 African American CRCs from TCGA and the CCCC, respectively, and 96 White CRCs from TCGA. As reported previously, the frequencies of CNVs were similar between African American and White CRCs; however, there was a significantly lower frequency of cnLOH events in African American CRCs compared to White CRCs, even after adjusting for demographic and clinical covariates. Although larger differences for chromosome 18 were observed, a lower frequency of cnLOH events in African American CRCs was observed for nearly all chromosomes. These results suggest that mechanistic differences, including differences in the frequency of cnLOH, could contribute to clinicopathological disparities between African Americans and Whites. Additionally, we observed a previously uncharacterized phenomenon we refer to as small interstitial cnLOH, in which segments of chromosomes from 1 to 5 Mb long were affected by cnLOH.

Implication of DNA repair genes in Lynch-like syndrome

Many colorectal cancers (CRCs) that exhibit microsatellite instability (MSI) are not explained by MLH1 promoter methylation or germline mutations in mismatch repair (MMR) genes, which cause Lynch syndrome (LS). Instead, these Lynch-like syndrome (LLS) patients have somatic mutations in MMR genes. However, many of these patients are young and have relatives with cancer, suggesting a hereditary entity. We performed germline sequence analysis in LLS patients and determined their tumor's mutational profiles using FFPE DNA. Six hundred and fifty-four consecutive CRC patients were screened for suspected LS using MSI and absence of MLH1 methylation. Suspected LS cases were exome sequenced to identify germline and somatic mutations. Single nucleotide variants were used to characterize mutational signatures. We identified 23 suspected LS cases. Germline sequence analysis of 16 available samples identified five cases with LS mutations and 11 cases without LS mutations, LLS. Most LLS tumors had a combination of somatic MMR gene mutation and loss of heterozygosity. LLS patients were relatively young and had excess first-degree relatives with cancer. Four of the 11 LLS patients had rare likely pathogenic variants in genes that maintain genome integrity. Moreover, tumors from this group had a distinct mutational signature compared to tumors from LLS patients lacking germline mutations in these genes. In summary, more than a third of the LLS patients studied had germline mutations in genes that maintain genome integrity and their tumors had a distinct mutational signature. The possibility of hereditary factors in LLS warrants further studies so counseling can be properly informed.

Chromosome instability syndromes

Fanconi anaemia (FA), ataxia telangiectasia (A-T), Nijmegen breakage syndrome (NBS) and Bloom syndrome (BS) are clinically distinct, chromosome instability (or breakage) disorders. Each disorder has its own pattern of chromosomal damage, with cells from these patients being hypersensitive to particular genotoxic drugs, indicating that the underlying defect in each case is likely to be different. In addition, each syndrome shows a predisposition to cancer. Study of the molecular and genetic basis of these disorders has revealed mechanisms of recognition and repair of DNA double-strand breaks, DNA interstrand crosslinks and DNA damage during DNA replication. Specialist clinics for each disorder have provided the concentration of expertise needed to tackle their characteristic clinical problems and improve outcomes. Although some treatments of the consequences of a disorder may be possible, for example, haematopoietic stem cell transplantation in FA and NBS, future early intervention to prevent complications of disease will depend on a greater understanding of the roles of the affected DNA repair pathways in development. An important realization has been the predisposition to cancer in carriers of some of these gene mutations.

Lack of APC somatic mutation is associated with early-onset colorectal cancer in African Americans

African Americans (AAs) have higher incidence and mortality rates of colorectal cancer (CRC) compared with other US populations. They present with more right-sided, microsatellite stable disease and are diagnosed at earlier ages compared with non-Hispanic Whites (NHWs). To gain insight into these trends, we conducted exome sequencing (n = 45), copy number (n = 33) and methylation analysis (n = 11) of microsatellite stable AA CRCs. Results were compared with data from The Cancer Genome Atlas (TCGA). Two of the 45 tumors contained POLE mutations. In the remaining 43 tumors, only 27 (63%) contained loss-of-function mutations in APC compared with 80% of TCGA NHW CRCs. APC-mutation-negative CRCs were associated with an earlier onset of CRC (P = 0.01). They were also associated with lower overall mutation burden, fewer copy number variants and a DNA methylation signature that was distinct from the CpG island methylator phenotype characterized in microsatellite unstable disease. Three of the APC-mutation-negative CRCs had loss-of-function mutations in BCL9L. Mutations in driver genes identified by TCGA exome analysis were less frequent in AA CRC cases than TCGA NHWs. Genes that regulate the WNT signaling pathway, including SOX9, GATA6, TET1, GLIS1 and FAT1, were differentially hypermethylated in APC-mutation-negative CRCs, suggesting a novel mechanism for cancer development in these tumors. In summary, we have identified a subtype of CRC that is associated with younger age of diagnosis, lack of APC mutation, microsatellite and chromosome stability, lower mutation burden and distinctive methylation changes.

DNA methylation among firefighters

Firefighters are exposed to carcinogens and have elevated cancer rates. We hypothesized that occupational exposures in firefighters would lead to DNA methylation changes associated with activation of cancer pathways and increased cancer risk. To address this hypothesis, we collected peripheral blood samples from 45 incumbent and 41 new recruit non-smoking male firefighters and analyzed the samples for DNA methylation using an Illumina Methylation EPIC 850k chip. Adjusting for age and ethnicity, we performed: 1) genome-wide differential methylation analysis; 2) genome-wide prediction for firefighter status (incumbent or new recruit) and years of service; and 3) Ingenuity Pathway Analysis (IPA). Four CpGs, including three in the YIPF6, MPST, and PCED1B genes, demonstrated above 1.5-fold statistically significant differential methylation after Bonferroni correction. Genome-wide methylation predicted with high accuracy incumbent and new recruit status as well as years of service among incumbent firefighters. Using IPA, the top pathways with more than 5 gene members annotated from differentially methylated probes included Sirtuin signaling pathway, p53 signaling, and 5' AMP-activated protein kinase (AMPK) signaling. These DNA methylation findings suggest potential cellular mechanisms associated with increased cancer risk in firefighters.

Rescue of collapsed replication forks is dependent on NSMCE2 to prevent mitotic DNA damage

NSMCE2 is an E3 SUMO ligase and a subunit of the SMC5/6 complex that associates with the replication fork and protects against genomic instability. Here, we study the fate of collapsed replication forks generated by prolonged hydroxyurea treatment in human NSMCE2-deficient cells. Double strand breaks accumulate during rescue by converging forks in normal cells but not in NSMCE2-deficient cells. Un-rescued forks persist into mitosis, leading to increased mitotic DNA damage. Excess RAD51 accumulates and persists at collapsed forks in NSMCE2-deficient cells, possibly due to lack of BLM recruitment to stalled forks. Despite failure of BLM to accumulate at stalled forks, NSMCE2-deficient cells exhibit lower levels of hydroxyurea-induced sister chromatid exchange. In cells deficient in both NSMCE2 and BLM, hydroxyurea-induced double strand breaks and sister chromatid exchange resembled levels found in NSCME2-deficient cells. We conclude that the rescue of collapsed forks by converging forks is dependent on NSMCE2.

DNA damage encountered by the replication fork causes fork stalling and is a major source of mutations when not adequately repaired. Fork stalling can lead to fork collapse, that is, a state of the fork in which normal DNA synthesis cannot be resumed at the site of stalling. Collapsed forks must be rescued by replication forks initiated nearby, but little is known about the rescue mechanism by which an active fork merges with a collapsed fork. We used an inhibitor of DNA replication to generate collapsed replication forks and then studied genetic control of collapsed-fork rescue. We found that NSMCE2, which is a gene product that is known to regulate repair responses to replication stress, is required for cells to effectively rescue collapsed replication forks in order to complete DNA synthesis. DNA double strand breaks that are associated with normal collapsed-fork rescue do not accumulate in cells that are deficient for NSMCE2, suggesting that DNA breakage is part of the rescue and repair mechanism. Failure to rescue collapsed forks leads to DNA damage in mitosis and DNA damage in the following cell cycle. Our work highlights a unique role for NSMCE2 in rescue of collapsed replication forks.

Selenium supplementation and insulin resistance in a randomized, clinical trial

OBJECTIVE

While controversial, observational and randomized clinical trial data implicate the micronutrient selenium (Se) in the development of type 2 diabetes (T2D). The aim of this study was to test the hypothesis that Se supplementation adversely affects pancreatic β-cell function and insulin sensitivity.

RESEARCH DESIGN AND METHODS

In a subset of 400 individuals participating in a randomized, placebo-controlled trial of Se at 200 µg/day for colorectal adenomatous polyps, fasting plasma glucose and insulin were measured before randomization and within 6 months of completing intervention. Change in the homeostasis model assessment-β cell function (HOMA2-%β) and insulin sensitivity (HOMA2-%S) were compared between arms. A subgroup of 175 (79 Se and 96 placebo) participants underwent a modified oral glucose tolerance test (mOGTT) at the end of intervention and change in glucose values was assessed.

RESULTS

No statistically significant differences were observed for changes in HOMA2-%β or HOMA2-%S between those who received Se compared with placebo. After a mean of 2.9 years on study, mean HOMA2-%β values were 3.1±24.0 and 3.1±29.8 for the Se and placebo groups, respectively (p=0.99). For HOMA2-%S, the values were -0.5±223.2 and 80.9±1530.9 for the Se and placebo groups, respectively (p=1.00). Stratification by sex or age did not reveal any statistically significant effects on insulin sensitivity by treatment group. For mOGTT, mean baseline fasting blood glucose concentrations were significantly higher among participants in the placebo group compared with the Se group (96.6±14.6 and 92.3±12.0, respectively; p=0.04), a trend which remained through the 20 min assessment.

CONCLUSIONS

These findings do not support a significant adverse effect of daily Se supplementation with 200 µg/day of selenized yeast on β-cell function or insulin sensitivity as an explanation for previously reported associations between Se and T2D. Further clarification of longer term effects of Se is needed.

CLINICAL TRIAL REGISTRY

NIH Clinical Trials.gov number NCT00078897.

Whole-transcriptome sequencing identified gene expression signatures associated with aggressive clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most prevalent subtype of kidney cancer, yet molecular biomarkers have not been used for the prognosis of ccRCC to aide clinical decision making. This study aimed to identify genes associated with ccRCC aggressiveness and overall survival (OS). Samples of ccRCC tumor tissue were obtained from 33 patients who underwent nephrectomy. Gene expression was determined using whole-transcriptome sequencing. The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) RNA-seq data was used to test association with OS. 290 genes were differentially expressed between tumors with high and low stage, size, grade, and necrosis (SSIGN) score (≥7 vs. ≤3) with P_ADJ<0.05. Four genes, G6PD, APLP1, GCNT3, and PLPP2, were also over-expressed in advanced stage (III and IV) and high grade (3 and 4) ccRCC and tumor with necrosis (P_ADJ<0.05). Investigation stratifying by stage found that APLP1 and PLPP2 overexpression were significantly associated with poorer OS in the early stage (Quartile 1 vs. Quartile 4, HR = 3.87, 95% CI:1.25-11.97, P = 0.02 and HR = 4.77, 95% CI:1.37-16.57, P = 0.04 respectively). These genes are potential biomarkers of ccRCC aggressiveness and prognosis that direct clinical and surgical management.

Health supervision for people with Bloom syndrome

Bloom Syndrome (BSyn) is an autosomal recessive disorder that causes growth deficiency, endocrine abnormalities, photosensitive skin rash, immune abnormalities, and predisposition to early-onset cancer. The available treatments for BSyn are symptomatic, and early identification of complications has the potential to improve outcomes. To accomplish this, standardized recommendations for health supervision are needed for early diagnosis and treatment. The purpose of this report is to use information from the BSyn Registry, published literature, and expertise from clinicians and researchers with experience in BSyn to develop recommendations for diagnosis, screening, and treatment of the clinical manifestations in people with BSyn. These health supervision recommendations can be incorporated into the routine clinical care of people with BSyn and can be revised as more knowledge is gained regarding their clinical utility.

Is increased colorectal screening effective in preventing distant disease?

BACKGROUND

Screening in the average risk population for colorectal cancer (CRC) is expected to reduce the incidence of distant (i.e., metastatic) CRCs at least as much as less advanced CRCs. Indeed, since 2000, during which time colonoscopy became widely used as a screening tool, the overall incidence of CRC has been reduced by 29%.

OBJECTIVE

The purpose of the current study was to determine whether the reduction of incidence rates is the same for all stages of disease.

METHODS

We evaluated incidence data from the Surveillance, Epidemiology, and End Results (SEER) program from 2000-2014 for Localized, Regional, and Distant disease. Joinpoint models were compared to assess parallelism of trends. Data were stratified by race, age, tumor location, and sex to determine whether these subgroupings could explain overall trends.

RESULTS

Inconsistent with the expectations of a successful screening program, the reduction in incidence rates of distant CRCs from 2000-2014 has been slower than the reductions in incidence rates of both regional and localized CRCs. This trend is evident even when the data are stratified by age at diagnosis, sex, race, or tumor location.

CONCLUSIONS

The slower decrease in the incidence rate of distant disease is not consistent with a screening effect, that is, CRC screening may not be effective in preventing many distant CRCs. As a consequence, distant CRCs represent an increasing fraction of all CRCs, accounting for 21% of all CRCs in 2014. The analysis indicates that inadequate screening does not explain the slower decrease in incidence of distant CRCs. Consequently, we suggest that a subtype of CRC exists that advances rapidly, evading detection because screening intervals are too long to prevent it. Microsatellite unstable tumors represent a known subtype that advances more rapidly, and we suggest that another rapidly advancing subtype very likely exists that is microsatellite stable.

Abstract B52: Copy-neutral loss of heterozygosity is decreased in African American colorectal cancers

Background: Recent reports have shown that chromosomal copy number gains and losses associated with the development of colorectal cancer (CRC) occur at similar frequencies in Whites and African Americans (AAs), but no studies have compared copy-neutral loss of heterozygosity (cnLOH) between these two populations. cnLOH can arise by at least two different mechanisms. One involves recombination between homologous chromosomes, but cnLOH most commonly arises from mis-segregation of chromosomes via a mitotic form of uniparental disomy. Preliminary analysis of copy number data from Chicago AA CRC cases by our lab suggested that cnLOH occurred less frequently in AA CRCs. The present study aimed to use publicly available data from The Cancer Genome Atlas (TCGA) to test whether cnLOH was less frequent in AA CRC cases in the TCGA.

Methods: Raw Affymetrix GenomeWide SNP Array 6.0 files were obtained from TCGA Data Portal and processed using R package Rawcopy and PennCNV to determine segments of loss, gain, and cnLOH. Samples from AAs and Whites were processed separately, using normals from their respective populations as reference. cnLOH events involving less than 20 markers were removed, and the proportion of each chromosome arm affected by cnLOH was calculated for each tumor. Chromosome arms with over 50% cnLOH were counted as cnLOH events. Linear regression models were used to determine associations between the number of chromosome arm events and clinical variables. AA and White cases were identified per TCGA clinical data. Additionally, logistic regression models were used to determine associations between affected and unaffected tumors, defining affected as a tumor with &gt; 2 cnLOH events. The value of 2 was chosen because it was the median value of cnLOH events per tumor among all samples. Chromosome arm-specific differences were tested by Fisher exact tests, using a Bonferroni correction to adjust for multiple testing.

Results: Data from 56 AA and 210 White CRCs were analyzed. Race was associated with a decreased number of cnLOH events per tumor, with AA CRCs on average having significantly fewer chromosome arms affected than White CRCs (p = 0.01). This difference remained significant after correction for age at diagnosis, sex, stage, and BMI. Additionally, AA CRCs were half as likely to have developed more than two cnLOH events compared to White CRCs. In AA CRCs, the frequency of cnLOH events was lower on 32 of the 39 chromosome arms compared to frequency of cnLOH events in White CRCs. Chromosomes 17p and 5q were the arms most frequently subject to cnLOH, comprising 13% of all cnLOH events in White tumors and 15% of all cnLOH events in AA tumors. 19.6% and 17.9% of AA CRC cases had cnLOH events on 17p and 5p, respectively, whereas 24.8% and 24.3% of White CRC cases had events on 17p and 5p. These differences were not significant. cnLOH of chromosome 6p was nominally significantly different (3% of AA cases vs 17% of White cases, p = 0.009); however, that difference did not remain significant after adjustment for multiple testing. No other differences were significant. No differences were found in chromosome arm gains or losses.

Conclusions: The results in our present study show that cnLOH affects AA CRCs less than White CRCs. cnLOH is not a rare event in CRC. Only 64 of 266 CRCs examined from TCGA (~24%) had zero chromosome arms affected. This mechanism of genomic instability is more frequent for certain chromosome arms, specifically chromosomes 5q and 17p, where the known tumor suppressors APC and TP53 are located. In AA CRCs, the majority of chromosome arms showed lower levels of cnLOH, suggesting that the difference in the frequency of cnLOH events is the result of a reduced susceptibility to cnLOH and not of the selective action of different cancer driver genes. Taken together, these results suggest that there is a racial difference in mechanisms that drive genomic instability as it affects and drives CRC.

Citation Format: Gaius J. Augustus, Nathan A. Ellis. Copy-neutral loss of heterozygosity is decreased in African American colorectal cancers [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 B52.

Clinical and Molecular Characteristics and Burden of Kidney Cancer Among Hispanics and Native Americans: Steps Toward Precision Medicine

Cancer disparities in Native Americans (NAs) and Hispanic Americans (HAs) vary significantly in terms of cancer incidence and mortality rates across geographic regions. This review reports that kidney and renal pelvis cancers are unevenly affecting HAs and NAs compared to European Americans of non-Hispanic origin, and that currently there is significant need for improved data and reporting to be able to advance toward genomic-based precision medicine for the assessment of such cancers in these medically underserved populations. More specifically, in states along the US-Mexico border, HAs and NAs have higher kidney cancer incidence rates as well as a higher prevalence of kidney cancer risk factors, including obesity and chronic kidney disease. They are also more likely to receive suboptimal care compared to European Americans. Furthermore, they are underrepresented in epidemiologic, clinical, and molecular genomic studies of kidney cancer. Therefore, we maintain that progress in precision medicine for kidney cancer care requires an understanding of various factors among HAs and NAs, including the real kidney cancer burden, variations in clinical care, issues related to access to care, and specific clinical and molecular characteristics.

Colorectal Cancer Disparity in African Americans: Risk Factors and Carcinogenic Mechanisms

African Americans have the highest incidence and mortality rates of colorectal cancer (CRC) of any ethnic group in the United States. Although some of these disparities can be explained by differences in access to care, cancer screening, and other socioeconomic factors, disparities remain after adjustment for these factors. Consequently, an examination of recent advances in the understanding of ethnicity-specific factors, including genetic and environmental factors relating to risk of CRC, the biology of CRC progression, and the changes in screening and mortality, is important for evaluating our progress toward eliminating the disparities. An overarching limitation in this field is the number and sample size of studies performed to characterize the etiological bases of CRC incidence and mortality in African Americans. Despite this limitation, significant differences in etiology are manifest in many studies. These differences need validation, and their impacts on disparities need more detailed investigation. Perhaps most heartening, improvements in CRC screening can be attributed to the smallest difference in CRC incidence between African Americans and whites since the late 1980s. Cancer mortality, however, remains a persistent difference.

Race-dependent association of sulfidogenic bacteria with colorectal cancer

OBJECTIVE

Colorectal cancer (CRC) incidence is higher in African Americans (AAs) compared with non-Hispanic whites (NHWs). A diet high in animal protein and fat is an environmental risk factor for CRC development. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC. Hydrogen sulfide, produced by autochthonous sulfidogenic bacteria, triggers proinflammatory pathways and hyperproliferation, and is genotoxic. We hypothesised that sulfidogenic bacterial abundance in colonic mucosa may be an environmental CRC risk factor that distinguishes AA and NHW.

DESIGN

Colonic biopsies from uninvolved or healthy mucosa from CRC cases and tumour-free controls were collected prospectively from five medical centres in Chicago for association studies. Sulfidogenic bacterial abundance in uninvolved colonic mucosa of AA and NHW CRC cases was compared with normal mucosa of AA and NHW controls. In addition, 16S rDNA sequencing was performed in AA cases and controls. Correlations were examined among bacterial targets, race, disease status and dietary intake.

RESULTS

AAs harboured a greater abundance of sulfidogenic bacteria compared with NHWs regardless of disease status. Bilophila wadsworthia-specific dsrA was more abundant in AA cases than controls. Linear discriminant analysis of 16S rRNA gene sequences revealed five sulfidogenic genera that were more abundant in AA cases. Fat and protein intake and daily servings of meat were significantly higher in AAs compared with NHWs, and multiple dietary components correlated with a higher abundance of sulfidogenic bacteria.

CONCLUSIONS

These results implicate sulfidogenic bacteria as a potential environmental risk factor contributing to CRC development in AAs.

A meta-analysis of MSI frequency and race in colorectal cancer

PURPOSE

African Americans (AA) are at a higher risk of colorectal cancer (CRC) and some studies report a higher frequency of microsatellite instability (MSI) in this population while others report lower frequency compared to Caucasians.

AIM

To determine and evaluate the association of race and clinical factors with MSI frequency through meta- analysis.

METHODS

Twenty-two studies out of 15,105 (1997-2015) were evaluated after a search in different literature databases, using keywords “colorectal cancer, microsatellite instability, African Americans, Caucasians and Hispanics”. We used random effect meta-analysis to calculate the MSI frequency in all studies as well as in African American and Caucasian samples. Meta-regression analysis was used to assess the univariate effect of race, gender, age, tumor location and stage on MSI frequency.

RESULTS

The overall MSI frequency among CRCs was 17% (95%CI: 15%-19%, I²=91%). In studies with available race data, The MSI rate among AAs, Hispanics and Caucasians were 12%, 12% and 14% respectively and was not significantly different. Sub-group analysis of studies with racial information indicates MSI OR of 0.78 for AAs compared to Caucasians.

CONCLUSION

CRCs demonstrate an overall MSI frequency of 17%. MSI frequency differences between AAs and Caucasians were not pronounced, suggesting that other factors contribute to the racial disparity. The methodological approaches and biological sources of the variation seen in MSI frequency between different studies need to be further investigated.

Abstract B31: Sulfidogenic bacteria are an important diet-driven exposure promoting colorectal cancer in African Americans

Objectives. Colorectal cancer (CRC) incidence is higher in post-industrial cultures, and the incidences varies among different populations. In the US, there is a higher incidence of CRC in African Americans (AAs) compared to non-Hispanic whites (NHWs). Recent evidence links consumption of a diet high in animal protein and fat as an environmental risk factor for the development of CRC. The intestinal microbiota is postulated to modulate the effects of diet in promoting or preventing CRC development. Hydrogen sulfide, which is produced by normal members of the colonic microenvironment (sulfidogenic bacteria), triggers pro-inflammatory and hyper-proliferative pathways, and it is genotoxic. We hypothesized that the production of hydrogen sulfide by sulfidogenic bacteria is a key environmental carcinogen contributing to CRC risk.

Design. The abundance of sulfidogenic bacteria via quantitative PCR (qPCR) was compared in non-involved colonic mucosa of 97 AA and 56 NHW CRC patients and in 100 AA and 76 NHW healthy controls. In addition, we performed 16S rDNA sequencing in 61 AA cases and 94 AA controls. Additionally, we tested correlations among race, dietary intake, disease status, and sulfidogenic bacterial abundance.

Results. Overall, the functional gene for hydrogen sulfide production in sulfate-reducing bacteria, dissimilatory sulfate reductase (dsrA), was more abundant in AAs than in NHWs, in both cases and controls. In addition, AA CRC cases exhibited a significantly higher abundance of Bilophila wadsworthia-specific dsrA. Linear discriminant analysis of 16S rDNA sequencing results revealed several taxa that differed between AA cases and controls, including the known butyrate producer Faecalibacterium that was more abundant in AA controls, and the sulfidogenic Pyramidobacter that was more abundant in AA CRC cases. Importantly, we found that dietary intake of protein and fat was higher in AAs compared to NHWs, and these dietary components correlated with a higher abundance of sulfidogenic bacteria.

Conclusion. There were significant differences in sulfidogenic bacterial abundance between AAs and NHWs, in both cases and controls, and implicate sulfidogenic bacteria as an important diet-driven environmental exposure that contributes to the increased risk of CRC in AAs. Replication studies are needed to test that effectiveness of using B. wadsworthia as a biomarker for increased CRC risk.

Citation Format: Cemal Yazici, Patricia G. Wolf, Tzu-Wen Liu, Karin Vermillion, Timothy Carroll, Ece Mutlu, Lisa Tussing-Humphreys, Carol Braunschweig, Rosa M. Xicola, Barbara Jung, Xavier Llor, Nathan A. Ellis, H. Rex Gaskins. Sulfidogenic bacteria are an important diet-driven exposure promoting colorectal cancer in African Americans. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr B31.

Bloom's Syndrome: Clinical Spectrum, Molecular Pathogenesis, and Cancer Predisposition

Bloom's syndrome is an autosomal recessive disorder characterized by prenatal and postnatal growth deficiency, photosensitive skin changes, immune deficiency, insulin resistance, and a greatly increased risk of early onset of cancer and for the development of multiple cancers. Loss-of-function mutations of BLM, which codes for a RecQ helicase, cause Bloom's syndrome. The absence of a functional BLM protein causes chromosome instability, excessive homologous recombination, and a greatly increased number of sister chromatid exchanges that are pathognomonic of the syndrome. A common founder mutation designated blmAsh is present in about 1 in 100 persons of Eastern European Jewish ancestry, and there are additional recurrent founder mutations among other populations. Missense, nonsense, and frameshift mutations as well as multiexonic deletions have all been observed. Bloom's syndrome is a prototypical chromosomal instability syndrome, and the somatic mutations that occur as a result of that instability are responsible for the increased cancer risk. Although there is currently no treatment aimed at the underlying genetic abnormality, persons with Bloom's syndrome benefit from sun protection, aggressive treatment of infections, surveillance for insulin resistance, and early identification of cancer.

Association of a let-7 miRNA binding region of TGFBR1 with hereditary mismatch repair proficient colorectal cancer (MSS HNPCC)

The purpose of this study was to identify novel colorectal cancer (CRC)-causing alleles in unexplained familial CRC cases. In order to do so, coding regions in five candidate genes (MGMT, AXIN2, CTNNB1, TGFBR1 and TGFBR2) were sequenced in 11 unrelated microsatellite-stable hereditary non-polyposis CRC (MSS HNPCC) cases. Selected genetic variants were genotyped in a discovery set of 27 MSS HNPCC cases and 85 controls. One genetic variant, rs67687202, in TGFBR1 emerged as significant (P = 0.002), and it was genotyped in a replication set of 87 additional MSS HNPCC-like cases and 338 controls where it was also significantly associated with MSS HNPCC cases (P = 0.041). In the combined genotype data, rs67687202 was associated with a moderate increase in CRC risk (OR = 1.68; 95% CI = 1.13-2.50; P = 0.010). We tested a highly correlated SNP rs868 in 723 non-familial CRC cases compared with 629 controls, and it was not significantly associated with CRC risk (P = 0.370). rs868 is contained in a let-7 miRNA binding site in the 3'UTR of TGFBR1, which might provide a functional basis for the association in MSS HNPCC. In luciferase assays, the risk-associated allele for rs868 was associated with half the luciferase expression in the presence of miRNA let-7b-5p compared with protective allele, suggesting more binding of let-7b-5p and less TGFBR1 expression. Thus, rs868 potentially is a CRC risk-causing allele. Our results support the concept that rs868 is associated with lower TGFBR1 expression thereby increasing CRC risk.

Abstract PR02: Homologous recombination drives African American colorectal carcinogenesis

Background: African Americans (AAs) have the highest incidence and mortality rates of colorectal cancer (CRC) cases in the United States, with higher levels of early-onset and right-sided CRC, yet there are little data on carcinogenesis in AA CRC. Copy number variations (CNVs) affect large portions of the cancer genome, and they provide information about mechanisms of cancer initiation and progression. Given the unique clinical-pathological features of AA CRC, we hypothesized that different mechanisms operate in colorectal carcinogenesis in AAs. To test this hypothesis, we evaluated CNVs in AA CRC as compared to publically available data on CRC from the TCGA.

Methods: Tumor DNA samples from 46 AA CRC cases were available through the Chicago Colorectal Cancer Consortium. Determinations of CNVs were performed using the Affymetrix Cytoscan HD platform, which provides data from 2.67 million copy number probes and 750,000 genotype probes for analysis of loss of heterozygosity (LOH) with and without copy number change. Whole chromosome-arm gains and losses were defined as the gain or loss of &gt;50% of probes on an arm. Gains and losses were tabulated and compared to data from the TCGA. Statistical analyses of arm losses and gains were performed with Fisher exact tests, adjusting for multiple testing using a Bonferroni correction. Statistical analysis of total chromosome number alterations was performed with the chi-square test.

Results: Overall, significantly fewer chromosome-arm gains and losses occurred in AA CRC cases than in TCGA CRC cases with 10% of gains and losses in AA and 34% of gains and losses from TCGA (p &lt; 0.0001). More specifically, we found chromosome-arm gains occurred significantly less frequently for 8p (28% to 0%), 13q (56% to 26%), and 20 p and q (58% to 17% and 72% to 39%, respectively). Similarly, we found chromosome-arm losses occurred significantly less frequently for 1p (19% to 0%), 5q (17% to 0%), 8p (50% to 20%), 14q (30% to 0%), 17p (56% to 24%), 18p and q (61% to 26% and 66% to 28%, respectively), 20p (32% to 7%), and 21q (22% to 2%). All adjusted p values were less than 0.05 for these comparisons. No chromosome-arm gains or losses were significantly more frequent in AA CRC cases than in TCGA cases.

The difference in chromosome-arm gain and loss was not the result of segmental gain or loss. However, analysis of genotype data revealed that copy-number neutral LOH in AA CRC cases substantially compensates for the lower frequency of chromosome-arm losses and focal amplifications for the lower frequency of gains. For example, in AAs, for chromosomal region 17p where TP53 localizes, 24% of cases exhibited 17p loss and 26% exhibited copy-number neutral LOH, for a total of 50% TP53 loss. For chromosomal region 13q where CDK8 localizes, 26% of cases exhibited 13q gain and 28% exhibited focal gains around CDK8, for a total of 54% CDK8 gain. The total frequency of tumor-suppressor gene losses and oncogene gains was similar in AA CRC and TCGA cases.

Conclusion: These data show that, although the major carcinogenesis genes (as identified by LOH and gene amplification) appear to be similar in AA and TCGA CRC cases, the mechanisms of genomic instability that generate these genetic changes are different. Chromosome-arm losses are more frequent in TCGA CRC cases whereas AA CRC is driven by homologous recombination and segregation resulting in copy-number neutral LOH. Chromosome-arm gains are more frequent in TCGA CRC cases whereas AA CRC is driven by focal amplification, which could result from unequal sister chromatid exchange. Thus, these CNV differences could reflect variation in the regulation of fundamental genomic integrity mechanisms in AAs. More studies are needed to confirm these results and elucidate the mechanisms of carcinogenesis in AA CRC.

This abstract is also presented as Poster A62.

Citation Format: Gaius J. Augustus, Rosa Xicola, Arthur R. Brothman, Xavier Llor, Nathan A. Ellis. Homologous recombination drives African American colorectal carcinogenesis. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr PR02.

Abstract 4582: Enrichment of colorectal cancer and inflammatory bowel disease risk variants in colon expression quantitative trait loci in African Americans

Background: Genome wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including colorectal cancer (CRC) and inflammatory bowel diseases (IBD). However, the functional role of many of these SNPs is largely unknown. Expression quantitative trait loci (eQTL) mapping is a tool to identify target genes of disease-associated SNPs. We have comprehensively assessed eQTLs in the human colon and tested for enrichment of GWAS-associated variants of colon diseases. We also characterized the genetic and functional properties of colonic eQTLs.

Methods: Distal colonic biopsies were obtained from 48 healthy African American males and total RNA was extracted. Genomic DNA was obtained from the same patients and genotyped using the Axiom Pan-African array. In total, 8.4 million genotyped and imputed SNPs were included. RNA expression levels were estimated using the Illumina HT-12v4 Expression Beadchip. eQTLs were identified using Matrix eQTL. False discovery rate calculations were performed according to the Benjamini and Hochberg method. Significance thresholds for other associations were determined using permutation-based methods.

Results: 1941 significant cis-eQTLs, corresponding to 122 independent signals, were identified at a false discovery rate of 0.01. There was substantial overlap between cis-eQTLs found in liver and ileum and less overlap in lymphoblastoid cells, brain, and skin fibroblasts. Overall, there was enrichment for GWAS variants associated with CRC and IBD, as well as 2 metabolic traits–Type 2 diabetes and body mass index–among colon cis-eQTLs. The CRC-associated eQTL rs3802842 was significantly associated with the expression of C11orf93 (COLCA2). The CRC-associated SNP rs1862748 is associated with 2 cis-eQTLs that are associated with expression differences in the NFATC3 gene, which regulates beta-catenin activation in response to WNT signaling. We also identified UBA7, INPP5E, ERAP2, SFMBT1, NXPE1, REXO2 as target genes for IBD-associated variants. There was significant enrichment of colonic cis-eQTLs near the transcription start sites (TSSs), for active histone marks and for SNPs with high population differentiation.

Conclusion: Through this comprehensive study of eQTLs in the human colon, we have identified novel and known target genes for IBD- and CRC-associated genetic variants. The cis-eQTLs are useful in identification of the causal functional variation underlying IBD and CRC associations. The eQTL catalog is now expanded to include the human colon and the functional characteristics of colonic eQTLs.

Note: This abstract was not presented at the meeting.

Citation Format: Sonia S. Kupfer, Imge Hulur, Eric Gamazon, Andrew Skol, Xavier Llor, Kenan Onel, Nathan A. Ellis. Enrichment of colorectal cancer and inflammatory bowel disease risk variants in colon expression quantitative trait loci in African Americans. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4582. doi:10.1158/1538-7445.AM2015-4582

Abstract 3036: The SUMO-targeted ubiquitin ligase RNF4 regulates BLM helicase's function in dormant origin firing

Regulation of dormant origin firing under conditions of replication stress is poorly understood. The Bloom syndrome DNA helicase BLM functions in maintaining replication fork stability, with sumoylation regulating this function, and BLM deficiency is associated with increased dormant origin firing. We found here that BLM sumoylation levels increase in response to replication stalling by hydroxyurea (HU) and to proteasome inhibition; depletion of the SUMO-targeted ubiquitin ligase RNF4 also causes increased levels of BLM sumoylation. RNF4 directly interacts with BLM and can ubiquitylate sumoylated BLM in vitro. These data indicate that sumoylated BLM is an RNF4 substrate. RNF4 is recruited to DNA repair foci in response to replication stalling. RNF4 depletion causes the accumulation of increased numbers of HU-induced BLM foci, whereas the numbers of RPA, RAD51, and gamma-H2AX foci are unaffected by fork stalling in RNF4-depleted cells. Sister chromatid exchanges are normal in RNF4-depleted cells. These data indicate that RNF4 can regulate BLM retention at stalled forks without affecting repair by homologous recombination. RNF4 depletion reduces cell proliferation and survival of untreated cells, and it confers hypersensitivity to replication stalling by HU. Studies of cell-cycle progression using bromodeoxyuridine incorporation and flow cytometry show that RNF4 depletion causes a delay of re-entry into S phase in HU-treated cells and the replication delay is partially rescued by BLM mutation. The delay is not caused by modification of checkpoint kinase activities. Analysis of replication dynamics using the DNA fiber assay show that RNF4 depletion causes an increase of permanently stalled replication forks and a decrease in activation of dormant origins following recovery from HU-induced replication stress. Co-depletion of RNF4 and BLM partially rescues these defects. Replication dynamics is unaffected by RNF4 depletion in untreated cells. These data indicate that RNF4 regulates BLM's functions in replication fork stability and dormant origin firing, without affecting BLM's roles in homologous recombination. We propose that sumoylation of BLM at stalled replication forks leads to RNF4-mediated ubiquitylation and subsequent proteasome-dependent degradation of BLM, which relieves BLM's active inhibition of dormant origin firing.

Citation Format: Nathan A. Ellis, Wei-Chih Yang, Mary Yagle, Jianmei Zhu, Jing Huang, Michael Seidman, Michael J. Matunis. The SUMO-targeted ubiquitin ligase RNF4 regulates BLM helicase's function in dormant origin firing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3036. doi:10.1158/1538-7445.AM2015-3036

Enrichment of inflammatory bowel disease and colorectal cancer risk variants in colon expression quantitative trait loci

Background

Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with diseases of the colon including inflammatory bowel diseases (IBD) and colorectal cancer (CRC). However, the functional role of many of these SNPs is largely unknown and tissue-specific resources are lacking. Expression quantitative trait loci (eQTL) mapping identifies target genes of disease-associated SNPs. This study provides a comprehensive eQTL map of distal colonic samples obtained from 40 healthy African Americans and demonstrates their relevance for GWAS of colonic diseases.

Results

8.4 million imputed SNPs were tested for their associations with 16,252 expression probes representing 12,363 unique genes. 1,941 significant cis-eQTL, corresponding to 122 independent signals, were identified at a false discovery rate (FDR) of 0.01. Overall, among colon cis-eQTL, there was significant enrichment for GWAS variants for IBD (Crohn’s disease [CD] and ulcerative colitis [UC]) and CRC as well as type 2 diabetes and body mass index. ERAP2, ADCY3, INPP5E, UBA7, SFMBT1, NXPE1 and REXO2 were identified as target genes for IBD-associated variants. The CRC-associated eQTL rs3802842 was associated with the expression of C11orf93 (COLCA2). Enrichment of colon eQTL near transcription start sites and for active histone marks was demonstrated, and eQTL with high population differentiation were identified.

Conclusions

Through the comprehensive study of eQTL in the human colon, this study identified novel target genes for IBD- and CRC-associated genetic variants. Moreover, bioinformatic characterization of colon eQTL provides a tissue-specific tool to improve understanding of biological differences in diseases between different ethnic groups.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1292-z) contains supplementary material, which is available to authorized users.

Abstract 1279: Association between vitamin D levels and colorectal cancer in African Americans

Background. Colorectal cancer (CRC) is the fourth most commonly diagnosed cancer in the world and there is a sizeable disparity in CRC incidence and mortality between African Americans (AAs) and all other US racial groups that remains unexplained. Associations between vitamin D levels and CRC have been widely reported in many populations, but there are few studies in AAs. We hypothesized that vitamin D levels are lower in AAs with CRC. Methods. 401 subjects were prospectively ascertained in endoscopy clinics in the Illinois Medical District: 130 healthy controls, 136 individuals with adenomatous polyps, and 130 individuals with CRC; 270 of 401 subjects were AA. Clinical data included age, gender, and BMI (kg/m2); smoking and drinking status; anti-inflammatory medication use; education and income levels; physical exercise level. Levels of serum 25-(OH) vitamin D2 and D3 were measured by Quest Diagnostics using liquid chromatography and tandem mass spectroscopy. Thirty nine potentially functional SNPs from eight vitamin D-related genes (CYP2R1, CYP24A1, CYP27A1, CYP27B1, CYP3A4, DHCR7, GC, and VDR) were genotyped using the Sequenom MassARRAY platform. We tested associations between vitamin D and CRC using logistic regression models, adjusting for age, gender, and time of year of blood collection, and we tested each clinical covariate in the model. In addition, we tested associations between SNPs and vitamin D levels using logistic regression, adjusting for age, gender, and time of collection. Results. Levels of total vitamin D (D2 + D3) and of vitamin D3 were statistically significantly lower in AAs compared to Non-Hispanic Whites (NHW). Approximately 15% of AAs exhibited detectable levels of vitamin D2, which was evidence of supplementation; only 8% of NHWs supplemented. Supplementation was significantly associated with older ages, female gender, less alcohol use and less exercise. Vitamin D3 levels were 22% lower in AA CRC cases compared to AA controls (18.5 ng/ml vs 23.7 ng/ml; P &lt;0.03); vitamin D3 levels were not significantly different in NHW CRC cases compared to controls (29.8 ng/ml vs. 28.2 ng/ml). Vitamin D3 levels in adenoma cases were not significantly different compared to controls in either group (23.5 ng/ml in AA adenoma cases and 27.3 ng/ml in NHW adenoma cases). The SNP rs1544410 in VDR and rs3829251 in DHCR7 had the smallest p values (0.008 and 0.013, respectively). The minor allele of rs16847024 in GC was associated with lower vitamin D3 levels; this same SNP was associated with left-sided CRC in AAs in a larger case-control study performed by our group. rs3829251 in DHCR7 has been previously associated with serum vitamin D levels in Han Chinese. Conclusion. These data demonstrated that vitamin D levels are associated with protection against CRC in AAs. SNPs in vitamin D-related genes may modulate vitamin D levels and risk of CRC.

Citation Format: Sariya Siddiqi, Fabio Pibiri, Rosa Munoz Xicola, Rick A. Kittles, Xavier Llor, Sonia S. Kupfer, Nathan A. Ellis. Association between vitamin D levels and colorectal cancer in African Americans. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1279. doi:10.1158/1538-7445.AM2014-1279

Excess of proximal microsatellite-stable colorectal cancer in African Americans from a multiethnic study

PURPOSE

African Americans (AA) have the highest incidence of colorectal cancer compared with other U.S. populations and more proximal colorectal cancers. The objective is to elucidate the basis of these cancer disparities.

EXPERIMENTAL DESIGN

Of note, 566 AA and 328 non-Hispanic White (NHW) colorectal cancers were ascertained in five Chicago hospitals. Clinical and exposure data were collected. Microsatellite instability (MSI) and BRAF (V600E) and KRAS mutations were tested. Statistical significance of categorical variables was tested by the Fisher exact test or logistic regression and age by the Mann-Whitney U test.

RESULTS

Over a 10-year period, the median age at diagnosis significantly decreased for both AAs (68-61; P < 0.01) and NHWs (64.5- 62; P = 0.04); more AA patients were diagnosed before age 50 than NHWs (22% vs. 15%; P = 0.01). AAs had more proximal colorectal cancer than NHWs (49.5% vs. 33.7%; P < 0.01), but overall frequencies of MSI, BRAF and KRAS mutations were not different nor were they different by location in the colon. Proximal colorectal cancers often presented with lymphocytic infiltrate (P < 0.01) and were diagnosed at older ages (P = 0.02). Smoking, drinking, and obesity were less common in this group, but results were not statistically significant.

CONCLUSIONS

Patients with colorectal cancer have gotten progressively younger. The excess of colorectal cancer in AAs predominantly consists of more proximal, microsatellite stable tumors, commonly presenting lymphocytic infiltrate and less often associated with toxic exposures or a higher BMI. Younger AAs had more distal colorectal cancers than older ones. These data suggest two different mechanisms driving younger age and proximal location of colorectal cancers in AAs.

Shared and independent colorectal cancer risk alleles in TGFβ-related genes in African and European Americans

Genome-wide association studies (GWAS) in colorectal cancer (CRC) identified five regions near transforming growth factor β-related genes BMP4, GREM1, CDH1, SMAD7 and RPHN2. The true risk alleles remain to be identified in these regions, and their role in CRC risk in non-European populations has been understudied. Our previous work noted significant genetic heterogeneity between African Americans (AAs) and European Americans (EAs) for single nucleotide polymorphisms (SNPs) identified in GWAS. We hypothesized that associations may not have been replicated in AAs due to differential or independent genetic structures. In order to test this hypothesis, we genotyped 195 tagging SNPs across these five gene regions in 1194 CRC cases (795 AAs and 399 EAs) and 1352 controls (985 AAs and 367 EAs). Imputation was performed, and association testing of genotyped and imputed SNPs included ancestry, age and sex as covariates. In two of the five genes originally associated with CRC, we found evidence for association in AAs including rs1862748 in CDH1 (OR(Add) = 0.82, P = 0.02) and in GREM1 the SNPs rs10318 (OR(Rec) = 60.1, P = 0.01), rs11632715 (OR(Rec) = 2.36; P = 0.004) and rs12902616 (OR(Rec) = 1.28, P = 0.005), the latter which is in linkage disequilibrium with the previously identified SNP rs4779584. Testing more broadly for associations in these gene regions in AAs, we noted three statistically significant association peaks in GREM1 and RHPN2 that were not identified in EAs. We conclude that some CRC risk alleles are shared between EAs and AAs and others are population specific.

Genetic variation in vitamin D-related genes and risk of colorectal cancer in African Americans

Purpose

Disparities in both colorectal cancer (CRC) incidence and survival impact African Americans (AAs) more than other US ethnic groups. Because vitamin D is thought to protect against CRC and AAs have lower serum vitamin D levels, genetic variants that modulate the levels of active hormone in the tissues could explain some of the cancer health disparity. Consequently, we hypothesized that genetic variants in vitamin D-related genes are associated with CRC risk.

Methods

To test this hypothesis, we studied 39 potentially functional single-nucleotide polymorphisms (SNPs) in eight genes (CYP2R1, CYP3A4, CYP24A1, CYP27A1, CYP27B1, GC, DHCR7, and VDR) in 961 AA CRC cases and 838 healthy AA controls from Chicago and North Carolina. We tested whether SNPs are associated with CRC incidence using logistic regression models to calculate p values, odds ratios, and 95 % confidence intervals. In the logistic regression, we used a log-additive genetic model and used age, gender, and percent West African ancestry, which we estimated with the program STRUCTURE, as covariates in the models.

Results

A nominally significant association was detected between CRC and the SNP rs12794714 in the vitamin D 25-hydroxylase gene CYP2R1 (p = 0.019), a SNP that has previously been associated with serum vitamin D levels. Two SNPs, rs16847024 in the GC gene and rs6022990 in the CYP24A1 gene, were nominally associated with left-sided CRC (p = 0.015 and p = 0.018, respectively).

Conclusions

Our results strongly suggest that genetic variation in vitamin D-related genes could affect CRC susceptibility in AAs.

Electronic supplementary material

The online version of this article (doi:10.1007/s10552-014-0361-y) contains supplementary material, which is available to authorized users.

BLM SUMOylation regulates ssDNA accumulation at stalled replication forks

Polymerase stalling results in uncoupling of DNA polymerase and the replicative helicase, which generates single-stranded DNA (ssDNA). After stalling, RAD51 accumulates at stalled replication forks to stabilize the fork and to repair by homologous recombination (HR) double-strand breaks (DSBs) that accumulate there. We showed recently that SUMO modification of the BLM helicase is required in order for RAD51 to accumulate at stalled forks. In order to investigate how BLM SUMOylation controls RAD51 accumulation, we characterized the function of HR proteins and ssDNA-binding protein RPA in cells that stably expressed either normal BLM (BLM+) or SUMO-mutant BLM (SM-BLM). In HU-treated SM-BLM cells, mediators BRCA2 and RAD52, which normally substitute RAD51 for RPA on ssDNA, failed to accumulate normally at stalled forks; instead, excess RPA accumulated. SM-BLM cells also exhibited higher levels of HU-induced chromatin-bound RPA than BLM+ cells did. The excess RPA did not result from excessive intrinsic BLM helicase activity, because in vitro SUMOylated BLM unwound similar amounts of replication-fork substrate as unSUMOylated BLM. Nor did BLM SUMOylation inhibit binding of RPA to BLM in vitro; however, in immunoprecipitation experiments, more BLM-RPA complex formed in HU-treated SM-BLM cells, indicating that BLM SUMOylation controls the amount of BLM-RPA complex normally formed at stalled forks. Together, these results showed that BLM SUMOylation regulates the amount of ssDNA that accumulates during polymerase stalling. We conclude that BLM SUMOylation functions as a licensing mechanism that permits and regulates HR at damaged replication forks.

Abstract PR02: Genetic variation in the vitamin D pathway and risk for colorectal cancer in African Americans

Background: Colorectal cancer (CRC) is the third leading cause of cancer-related deaths in both sexes in the United States. There is a large disparity in both CRC incidence and survival between African Americans (AAs) and all other US racial groups. Differences in serum vitamin D levels could contribute to this disparity because vitamin D is thought to protect against CRC and AAs have lower serum vitamin D levels than whites. We hypothesized that genetic variants in vitamin D-related genes are associated with CRC risk in AAs.

Methods: To evaluate association with CRC risk, we genotyped 39 putatively functional single nucleotide polymorphisms (SNPs) in vitamin D-related genes (CYP27A1, GC, CYP3A4, CYP2R1, DHCR7/NADSYN1, VDR, CYP27B1 and CYP24A1, in 961 AA cases (292 right colon, 340 left colon, 113 rectal) and 838 AA controls from the North Carolina Colorectal Cancer Study and the Chicago Colorectal Cancer Consortium. We calculated odds ratios (OR) using logistic regression, assuming an additive genetic model and controlling for age, gender, and West African ancestry. We further evaluated whether the genetic polymorphisms conferred differential risk for right-sided CRC (R-CRC) and left-sided CRC (L-CRC, including rectal).

Results: Nominal associations (p&lt;0.05) were detected between CRC and SNPs in the 24-hydroxylase gene CYP24A1, rs73913755 (OR, 0.73; P = 0.0003), which degrades calcidiol, and the 25-hydroxylase gene CYP2R1, rs12794714 (OR, 0.82; P = 0.032), which converts cholecalciferol into calcidiol. When we analyzed R-CRC and L-CRC separately, no SNPs were associated with R-CRC, whereas 4 SNPs were associated with L-CRC. Two SNPs in the vitamin D binding protein gene GC, rs1155563 (OR, 0.77; P = 0.039) and rs16847024 (OR, 1.56; P = 0.003) and two SNPs in the 24-hydroxylase gene CYP24A1, rs6022990 (OR, 1.48; P = 0.006) and rs73913755 (OR, 0.67; P = 0.0002). The P value for rs73913755 was statistically significant after adjustment for multiple testing.

Conclusion: Our results indicate that several SNPs in the vitamin D pathway contribute to CRC susceptibility in AAs, with the minor allele of rs73913755 conferring increased protection against L-CRC. We hypothesize that the minor allele of rs73913755 causes a reduction in the expression levels of CYP24A1. We further hypothesize that there is a gradient of expression levels of CYP24A1 in the colon with higher levels on the left side than on the right side. The protective effect of rs73913755 would then be explained by increased levels of calcidiol in the tissue in combination with a threshold effect. Because rs73913755 is African-specific, its presence could explain in part the lower proportion of L-CRC in AAs compared to whites. Future studies include analysis of vitamin D pathway gene expression levels relative to genotype and analysis of possible gene-vitamin D level interactions in AA CRC.

This abstract is also presented as Poster B72.

Citation Format: Fabio Pibiri, Rick A. Kittles, Robert S. Sandler, Temitope O. Keku, Sonia S. Kupfer, Rosa Xicola, Xavier Llor, Nathan A. Ellis. Genetic variation in the vitamin D pathway and risk for colorectal cancer in African Americans. [abstract]. In: Proceedings of the Fifth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2012 Oct 27-30; San Diego, CA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(10 Suppl):Abstract nr PR02.

Abstract 1661: Fine-mapping of GWAS variants in BMP4, GREM1, CDH1, and RHPN2 in African American colorectal cancer patients

Background: Genome-wide association studies (GWAS) of colorectal cancer (CRC) have identified risk variants in candidate genes involved in TGF-ß signaling including BMP4, GREM1, CDH1, RHPN2 and SMAD7. We previously replicated the association with a 3′-UTR SNP in GREM1 (rs10318) in African Americans but did not find evidence of associations in the other genes. This finding could be explained by different genomic structure in African Americans. Therefore, we sought to fine-map these genes to identify CRC risk variants in African Americans who are at highest risk of CRC in the US. Methods: DNA from cases and controls was obtained from two US institutions. In total, we included DNA from 795 AA cases and 985 AA controls. TagSNPs with minor allele frequencies &gt;5% and pairwise r2 &gt;0.8 were identified in five genes using YRI Hapmap data. A total of 81 SNPs were genotyped in cases and controls using Sequenom MassARRAY. We calculated odds ratios and 95% confidence intervals using logistic regression controlling for ancestry, age, gender and multiple testing in PLINK. Results: Association analysis was completed for four genes: BMP4, GREM1, CDH1 and RHPN2. The top tagSNP associations for each gene are shown in the Table. None of the SNPs were significant after permutation testing. In GREM1, the strongest SNP associations were found at the 3′ end of the gene. In BMP4, we identified two SNPs (rs1957852 and rs7146040) that are in LD with rs4444235 previously identified in a European GWAS. In CDH1, rs12931189 is located in the same LD block as the strongest association signal (rs7199991) in a recent fine-mapping study in Europeans. Finally, we have no evidence for associations in RHPN2 in African Americans. Conclusion: These results provide preliminary evidence of associations in African American colorectal cancer patients in BMP4, GREM1 and CDH1 identified by GWAS in Europeans. Ongoing work is testing associations in SMAD7 and further fine-mapping by imputation and resequencing in these regions.

Abstract 1653: Genetic variation in the vitamin D pathway and risk for colorectal cancer in African Americans

Background: Colorectal cancer (CRC) is the third leading cause of cancer-related death in both sexes in the United States. There is a large disparity in both CRC incidence and survival between African Americans (AAs) and all other US racial groups. Differences in serum vitamin D levels could contribute to this disparity because vitamin D is thought to protect against CRC and AAs have lower serum vitamin D levels. In addition, genetic variants in vitamin D-related genes could modify the association between vitamin D levels and CRC risk. Methods: We tested for associations between CRC and 39 single nucleotide polymorphisms (SNPs) in vitamin D-related genes (CYP27A1, GC, CYP3A4, CYP2R1, DHCR7/NADSYN1, VDR, CYP27B1 and CYP24A1). We genotyped 357 AAs cases and 443 AA controls from the North Carolina Colorectal Cancer Study. We calculated odds ratios (OR) using logistic regression, assuming an additive genetic model and controlling for age, gender, and ancestry. We also analyzed SNP associations for colon and rectal cancer cases separately. We analyzed linkage disequilibrium and haplotype association using Haploview. Results: Associations (p&lt;0.05) were detected between CRC and two SNPs in the vitamin D binding protein gene GC, rs3755967 (OR, 0.69; P = .039,) and rs16847024 (OR, 1.50; P = .047,). We also detected an association with a SNP in the 24-hydroxylase gene CYP24A1, rs73913755 (OR, 0.75; P = .034,), which degrades vitamin D. A trend for association was detected in the 25-hydroxylase gene CYP2R1, rs10741657 (OR, 0.79; P = .051), which converts cholecalciferol into calcidiol. When we analyzed colon and rectal cancers separately, only one SNP was associated with colon cancer whereas 9 SNPs were associated with rectal cancer. In particular, rs73913755 (OR, 0.39; P = 3 x 10-7) was statistically significant even after adjustment for multiple testing. Conclusion: We tested vitamin D-related SNPs and found suggestive evidence that they influence the risk of developing CRC in AAs, with differences in risk between the colon and rectum. Comparison of these data with data from US whites could shed light on disparities in these different US populations.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1653. doi:1538-7445.AM2012-1653

Genetic associations in the vitamin D receptor and colorectal cancer in African Americans and Caucasians

Low vitamin D levels are associated with an increased incidence of colorectal cancer (CRC) and higher mortality from the disease. In the US, African Americans (AAs) have the highest CRC incidence and mortality and the lowest levels of vitamin D. Single nucleotide polymorphisms (SNPs) in the vitamin D receptor (VDR) gene have been previously associated with CRC, but few studies have included AAs. We studied 795 AA CRC cases and 985 AA controls from Chicago and North Carolina as well as 1324 Caucasian cases and 990 Caucasian controls from Chicago and Spain. We genotyped 54 tagSNPs in VDR (46586959 to 46521297 Mb) and tested for association adjusting for West African ancestry, age, gender, and multiple testing. Untyped markers were imputed using MACH1.0. We analyzed associations by gender and anatomic location in the whole study group as well as by vitamin D intake in the North Carolina AA group. In the joint analysis, none of the SNPs tested was significantly associated with CRC. For four previously tested restriction fragment length polymorphisms, only one (referred to as ApaI), tagged by the SNP rs79628898, had a nominally significant p-value in AAs; none of these polymorphisms were associated with CRC in Caucasians. In the North Carolina AAs, for whom we had vitamin D intake data, we found a significant association between an intronic SNP rs11574041 and vitamin D intake, which is evidence for a VDR gene-environment interaction in AAs. In summary, using a systematic tagSNP approach, we have not found evidence for significant associations between VDR and CRC in AAs or Caucasians.

Abstract PL08-02: Fine mapping of genetic associations in African American colorectal cancer

Genome-wide association studies (GWAS) of colorectal cancer (CRC) have identified risk variants in 14 genomic regions through the study of Europeans with CRC. In genotype analysis of a European American CRC case-control group, effects sizes and directions of association for 24 SNPs tested, which localize to 10 of the 14 previously identified regions, were consistent with GWAS results; in contrast, in an African American CRC case-control group, the associations ran in the opposite direction for 9 of 22 SNPs tested, indicating significant genetic heterogeneity in CRC associations in African Americans compared to European Americans. We conclude that genetic markers that identify CRC risk in persons of European ancestry do not identify CRC risk in African Americans. Two hypotheses may explain the genetic heterogeneity between European and African Americans: (i) The risk alleles in both populations are the same, however, the genetic architecture differs such that other SNPs that are linked to these same risk alleles will make better markers for African American CRC risk. (ii) The underlying risk alleles are different between the two populations. A corollary of this hypothesis is that the allele frequencies of the risk alleles must be low (&lt;5%), because most the frequent genetic polymorphisms are shared between European and African populations. Distinguishing these hypotheses is important because genetic risk associated with rare alleles could have larger effect sizes (ORs&gt;2, for example), which could make genetic risk modeling more determinative. Furthermore, identification of multiple rare alleles, each with a moderate risk effect, could explain the missing heritability problem. To address these hypotheses, we have drilled down on each of the genetic regions identified in the European GWAS using systematic genotyping and deep re-sequencing in African American CRC cases and population-matched controls. Analysis of tagSNPs in two genes so far analyzed, GREM1 and BMP4, have demonstrated multiple, independent SNP associations, which are not correlated with SNPs previously identified in persons of European descent. Because novel SNP associations are detected in each of these genes, we suggest that rare alleles underlie these genetic risk associations. We are presently using the deep re-sequencing analysis to identify candidate risk variants, which we will then test in functional studies. Ultimately, the analysis will permit better quantification of CRC risk, and it may lead to risk assessment models that can be used clinically for screening and surveillance.

Citation Information: Cancer Epidemiol Biomarkers Prev 2011;20(10 Suppl):PL08-02.

A large-scale meta-analysis to refine colorectal cancer risk estimates associated with MUTYH variants

Background:

Defective DNA repair has a causal role in hereditary colorectal cancer (CRC). Defects in the base excision repair gene MUTYH are responsible for MUTYH-associated polyposis and CRC predisposition as an autosomal recessive trait. Numerous reports have suggested MUTYH mono-allelic variants to be low penetrance risk alleles. We report a large collaborative meta-analysis to assess and refine CRC risk estimates associated with bi-allelic and mono-allelic MUTYH variants and investigate age and sex influence on risk.

Methods:

MUTYH genotype data were included from 20 565 cases and 15 524 controls. Three logistic regression models were tested: a crude model; adjusted for age and sex; adjusted for age, sex and study.

Results:

All three models produced very similar results. MUTYH bi-allelic carriers demonstrated a 28-fold increase in risk (95% confidence interval (CI): 6.95–115). Significant bi-allelic effects were also observed for G396D and Y179C/G396D compound heterozygotes and a marginal mono-allelic effect for variant Y179C (odds ratio (OR)=1.34; 95% CI: 1.00–1.80). A pooled meta-analysis of all published and unpublished datasets submitted showed bi-allelic effects for MUTYH, G396D and Y179C (OR=10.8, 95% CI: 5.02–23.2; OR=6.47, 95% CI: 2.33–18.0; OR=3.35, 95% CI: 1.14–9.89) and marginal mono-allelic effect for variants MUTYH (OR=1.16, 95% CI: 1.00–1.34) and Y179C alone (OR=1.34, 95% CI: 1.01–1.77).

Conclusions:

Overall, this large study refines estimates of disease risk associated with mono-allelic and bi-allelic MUTYH carriers.

Genetic heterogeneity in colorectal cancer associations between African and European americans

BACKGROUND & AIMS

Genome-wide association studies of colorectal cancer (CRC) have identified risk variants in 10 genomic regions. None of these studies included African Americans, who have the highest incidence and mortality from CRC in the United States. For the 10 genomic regions, we performed an association study of Americans of African and European descent.

METHODS

We genotyped 22 single nucleotide polymorphisms (SNPs) in DNA samples from 1194 patients with CRC (795 African Americans and 399 European Americans) and 1352 controls (985 African Americans and 367 European Americans). At chromosome 8q24.21 region 3, we analyzed 6 SNPs from 1000 African American cases and 1393 controls. Association testing was done using multivariate logistic regression controlling for ancestry, age, and sex.

RESULTS

Among African Americans, the SNP rs6983267 at 8q24.21 was not associated with CRC (odds ratio, 1.18; P = .12); instead, the 8q24.21 SNP rs7014346 (odds ratio, 1.15; P = .03) was associated with CRC in this population. At 15q13.3, rs10318 was associated with CRC in both populations. At 11q23.1, rs3802842 was significantly associated with rectal cancer risk only among African Americans (odds ratio, 1.34; P = .01); this observation was made in previous studies. Among European Americans, SNPs at 8q24.21, 11q23.1, and 16q22.1 were significantly associated with CRC, and the odds ratios were of the same magnitude and direction for all SNPs tested, consistent with previously published studies. In contrast, in African Americans, the opposite allele of rs10795668 at 10p14 was associated with colorectal cancer (odds ratio, 1.35; P = .04), and altogether the odds ratios were in the opposite direction for 9 of the 22 SNPs tested.

CONCLUSIONS

There is genetic heterogeneity in CRC associations in Americans of African versus European descent.

Abstract PR-4: Genetic heterogeneity in colorectal cancer associations in African Americans

Background: Genome-wide association studies of colorectal cancer (CRC) have identified risk variants in 10 genomic regions. None of these studies included African Americans, who have the highest incidence and mortality from CRC in the U.S. For the 10 genomic regions, we performed an association study in African and European Americans. Methods: We genotyped 22 single nucleotide polymorphisms (SNPs) in DNA samples from 1194 patients with CRC (795 African Americans and 399 European Americans) and 1352 controls (985 African Americans and 367 European Americans). At chromosome 8q24.21 region 3, we analyzed five additional SNPs from 1000 African American cases and 1393 controls. Association testing was done using multivariate logistic regression controlling for ancestry, age, and sex.

Results: Whereas effects sizes and directions of association for all SNPs tested in European Americans were consistent with previously published studies, the associations ran in the opposite direction for 9 of 22 SNPs tested in African Americans. Among African Americans, the SNP rs6983267 at 8q24.21 was not associated with CRC (OR=1.18; P=0.12); instead, the 8q24.21 SNP rs7014346 (OR=1.15; p=0.03) was associated with CRC in this population. On chromosome 15q13.3, rs10318 was associated with CRC in both populations. On chromosome 10p14, the opposite allele of rs10795668 was associated with CRC in African Americans (OR=1.35; P=0.04). On chromosome 11 q23.1, rs3802842 was significantly associated with rectal cancer risk only among African Americans (OR 1.34; P=0.01); a similar observation was made in previous studies of Europeans. Among European Americans, SNPs on chromosomes 8q24.21,11 q23.1, and 16q22.1 were associated with CRC, in agreement with previous reports.

Conclusion: There is genetic heterogeneity in CRC associations in Americans of African vs. European descent.

Citation Information: Cancer Epidemiol Biomarkers Prev 2010;19(10 Suppl):PR-4.

Abstract B65: Targeted resequencing of the EphB2 gene in colorectal cancer for SNP discovery using next generation sequencing

Colorectal cancer (CRC) remains a leading cause of cancer morbidity and mortality in the United States. CRC is the third most common cause of deaths in the U. S. with the highest incidence observed in the African American (AA) population compared to other American populations. Our group was the first to implicate the EphB2 tyrosine kinase receptor as a tumor suppressor in prostate cancer (PC), where we reported somatic inactivating mutations occurring in 5%-10% of sporadic tumors. With its role in maintaining normal epithelial architecture and functional data suggestive of a tumor suppressor in both prostate and colon cancer.

Recent advances in next-generation sequencing (NGS) afford new opportunities for large scale SNP discovery using a targeted resequencing approach. Several methodologies have been developed for targeted resequencing. Among these methods is the RainDance picoliter massive single-plex PCR assay, which provides the capability to assess up to 10,000 independent amplicons in a single reaction. We designed a RainDance PCR assay containing 700 amplicons, encompassing the entire 225,000bp genomic region of the EphB2 gene. These individual pools of amplicons from each sample were then used as template for NGS and barcoded to generate pools of 16 unique individuals using the Life Technologies SOLiD version 3-Plus system. Utilizing this method we screened 20 colorectal cancer cases and 27 sporadic prostate cancer cases. Thus far we have identified both known and novel variants within the EphB2 gene region among of which are several common coding variants including the 2055A&gt;T nonsense mutation (K1019X) in three of 10 female CRC cases. We will provide data on the number of novel and known single nucleotide polymorphisms (SNPs) for all CRC and PC cases as well as quality assessment and overall performance of the RainDance method and performance metrics for SOliD NGS along with a comparison of utilizing several different analyses pipelines to identify the novel and known SNPs. These data will provide us with unprecedented details of the genetic variation of the EphB2 gene in African Americans.

Citation Information: Cancer Epidemiol Biomarkers Prev 2010;19(10 Suppl):B65.

African-derived genetic polymorphisms in TNFAIP3 mediate risk for autoimmunity

The TNF alpha-induced protein 3 (TNFAIP3) is an ubiquitin-modifying enzyme and an essential negative regulator of inflammation. Genome-wide association studies have implicated the TNFAIP3 locus in susceptibility to autoimmune disorders in European cohorts, including rheumatoid arthritis, coronary artery disease, psoriasis, celiac disease, type 1 diabetes, inflammatory bowel disease, and systemic lupus erythematosus (SLE). There are two nonsynonymous coding polymorphisms in the deubiquitinating (DUB) domain of TNFAIP3: F127C, which is in high-linkage disequilibrium with reported SLE-risk variants, and A125V, which has not been previously studied. We conducted a case-control study in African-American SLE patients using these coding variants, along with tagging polymorphisms in TNFAIP3, and identified a novel African-derived risk haplotype that is distinct from previously reported risk variants (odds ratio=1.6, p=0.006). In addition, a rare protective haplotype was defined by A125V (odds ratio=0.31, p=0.027). Although A125V was associated with protection from SLE, surprisingly the same allele was associated with increased risk of inflammatory bowel disease. We tested the functional activity of nonsynonymous coding polymorphisms within TNFAIP3, and found that the A125V coding-change variant alters the DUB activity of the protein. Finally, we used computer modeling to depict how the A125V amino acid change in TNFAIP3 may affect the three-dimensional structure of the DUB domain to a greater extent than F127C. This is the first report of an association between TNFAIP3 polymorphisms and autoimmunity in African-Americans.

Abstract 4734: Validation of genome-wide colorectal cancer genetic risk factors in African- and European-Americans

Background: Genome-wide association studies have identified several colorectal cancer (CRC) genetic risk factors. However, these studies have been performed primarily in individuals of European descent and none include African Americans (AAs). Determining CRC genetic risk factors in AAs is important because CRC incidence and mortality rates are highest of all US populations.

Aim: To validate genome-wide CRC genetic risk factors, we tested single nucleotide polymorphism (SNP) associations in ten chromosome (chr) regions in AAs and European-Americans (EAs).

Methods: We genotyped 22 SNPs in 1725 AA and 883 EA CRC cases and controls using Sequenom iPLEX. Ancestry estimates were obtained using STRUCTURE 2.1. We tested for allelic association and calculated odds ratios and confidence intervals using logistic regression adjusting for ancestry, age and gender.

Results: Association results are shown in the Table. In AAs, rs10795668 (chr 10) and rs10318 (chr 15) were significantly associated with CRC. rs7014346 (chr 8) and rs355527 (chr 20) trended toward significant associations. In EAs, three SNPs on chr 8 were significantly associated with CRC. In addition, two chr 11 SNPs (rs3802842 & rs1074997) and rs1862748 (chr 16) were significantly associated with disease in EAs. SNPs on chr 15 and chr 16 are located in or near genes GREM1 and CDH1 respectively. SNPs on chr 8, 10, 11 and 20 are in gene deserts.

Conclusion: This is the first study to validate genome-wide SNP associations in AAs. We also confirm several associations in EAs. SNPs on chr 15 & 16 are located in genes involved in TGFβ signaling (GREM1 & CDH1) which has been implicated in CRC pathogenesis, while those on chr 8, 10, 11 and 20 are in gene deserts. Future fine-mapping in these regions is warranted to identify functional variants.Genome-wide SNP associations in African- and European-AmericansChr (gene)SNPReference alleleAllele frequency casesAllele frequency controlsOR [95% CI]p*African Americans      8rs7014346A0.420.391.14 [0.99-1.31]0.0710rs10795668A0.080.061.41 [1.07-1.87]0.0415 (GREM1)rs10318T0.050.031.45 [1.02-2.05]0.0520rs355527A0.180.200.87 [0.73-1.04]0.09European Americans      8rs6983626T0.120.091.38 [1.00-1.91]0.058rs6983267G0.520.471.24 [1.01-1.51]0.048rs7837328A0.430.371.30 [1.06-1.60]0.0111rs3802842C0.330.281.26 [1.02-1.57]0.0211rs10749971G0.410.331.42 [1.15-1.74]0.000216 (CDH1)rs1862748T0.280.320.80 [0.64-0.99]0.04

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4734.

Novel single nucleotide polymorphism associations with colorectal cancer on chromosome 8q24 in African and European Americans

Regions on chromosome 8q24 harbor susceptibility alleles for multiple cancers including colorectal (region 3) and prostate cancer (regions 1-4). The objectives of the present study were (i) to test whether single-nucleotide polymorphisms (SNPs) in region 4 are associated with colorectal cancer (CRC) in European or African Americans; (ii) to test whether 8q24 SNPs previously shown to be associated with colorectal and prostate cancer also show association in our multiethnic series and (iii) to test for association between 100 ancestry informative markers (AIMs) and CRC in both the African American and European American cohorts. In total, we genotyped nine markers on 8q24 and 100 unlinked AIMs in 569 CRC cases and 439 controls (490 European Americans and 518 African Americans) obtained retrospectively from a hospital-based sample. We found rs7008482 in 8q24 region 4 to be significantly associated with CRC in European Americans (P = 0.03). Also in region 4, we found that a second SNP, rs16900305, trended toward association with CRC in African Americans. The rs6983267 in region 3, previously implicated in CRC risk, trended toward association with disease in European Americans but not in African Americans. Finally, none of the 100 AIMs tested for association reached statistical significance after correction for multiple hypothesis testing. In summary, these results are evidence that 8q24 region 4 contains novel CRC-associated alleles in European and African Americans.

Bloom's syndrome workshop focuses on the functional specificities of RecQ helicases

Human cells express five DNA helicases that are paralogs of Escherichia coli RecQ and which constitute the family of human RecQ helicases. Disease-causing mutations in three of these five human DNA helicases, BLM, WRN, and RECQL4, cause rare severe human genetic diseases with distinct clinical phenotypes characterized by developmental defects, skin abnormalities, genomic instability, and cancer susceptibility. Although biochemical and genetic evidence support roles for all five human RecQ helicases in DNA replication, DNA recombination, and the biological responses to DNA damage, many questions concerning the various functions of the human RecQ helicases remain unanswered. Researchers investigating human and non-human RecQ helicases held a workshop on May 27-28, 2008, at the University of Chicago Gleacher Center, during which they shared insights, discussed recent progress in understanding the biochemistry, biology, and genetics of the RecQ helicases, and developed research strategies that might lead to therapeutic approaches to the human diseases that result from mutations in RecQ helicase genes. Some workshop sessions were held jointly with members of a recently formed advocacy and support group for persons with Bloom's syndrome and their families. This report describes the outcomes and main discussion points of the workshop.

Small ubiquitin-related modifier (SUMO) binding determines substrate recognition and paralog-selective SUMO modification

Small ubiquitin-related modifiers (SUMOs) regulate diverse cellular processes through their covalent attachment to target proteins. Vertebrates express three SUMO paralogs: SUMO-1, SUMO-2, and SUMO-3 (SUMO-2 and SUMO-3 are approximately 96% identical and referred to as SUMO-2/3). SUMO-1 and SUMO-2/3 are conjugated, at least in part, to unique subsets of proteins and thus regulate distinct cellular pathways. However, how different proteins are selectively modified by SUMO-1 and SUMO-2/3 is unknown. We demonstrate that BLM, the RecQ DNA helicase mutated in Bloom syndrome, is preferentially modified by SUMO-2/3 both in vitro and in vivo. Our findings indicate that non-covalent interactions between SUMO and BLM are required for modification at non-consensus sites and that preferential SUMO-2/3 modification is determined by preferential SUMO-2/3 binding. We also present evidence that sumoylation of a C-terminal fragment of HIPK2 is dependent on SUMO binding, indicating that non-covalent interactions between SUMO and target proteins provide a general mechanism for SUMO substrate selection and possible paralog-selective modification.

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

BACKGROUND

Genetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups.

RESULTS

A small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P < 0.001); large regions that differed were found on chromosomes 2 and 6. Haplotype blocks inferred from pairwise linkage disequilibrium (LD) statistics (Haploview) as well as by expectation-maximization haplotype phase inference (HAP) showed a greater number of haplotype blocks in AJ compared to CEU by Haploview (50,397 vs. 44,169) or by HAP (59,269 vs. 54,457). Average haplotype blocks were smaller in AJ compared to CEU (e.g., 36.8 kb vs. 40.5 kb HAP). Analysis of global patterns of local LD decay for closely-spaced SNPs in CEU demonstrated more LD, while for SNPs further apart, LD was slightly greater in the AJ. A likelihood ratio approach showed that runs of homozygous SNPs were approximately 20% longer in AJ. A principal components analysis was sufficient to completely resolve the CEU from the AJ.

CONCLUSION

LD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure.