DNA methylome profiling identifies novel methylated genes in African American patients with colorectal neoplasia

The identification of genes that are differentially methylated in colorectal cancer (CRC) has potential value for both diagnostic and therapeutic interventions specifically in high-risk populations such as African Americans (AAs). However, DNA methylation patterns in CRC, especially in AAs, have not been systematically explored and remain poorly understood. Here, we performed DNA methylome profiling to identify the methylation status of CpG islands within candidate genes involved in critical pathways important in the initiation and development of CRC. We used reduced representation bisulfite sequencing (RRBS) in colorectal cancer and adenoma tissues that were compared with DNA methylome from a healthy AA subject's colon tissue and peripheral blood DNA. The identified methylation markers were validated in fresh frozen CRC tissues and corresponding normal tissues from AA patients diagnosed with CRC at Howard University Hospital. We identified and validated the methylation status of 355 CpG sites located within 16 gene promoter regions associated with CpG islands. Fifty CpG sites located within CpG islands-in genes ATXN7L1 (2), BMP3 (7), EID3 (15), GAS7 (1), GPR75 (24), and TNFAIP2 (1)-were significantly hypermethylated in tumor vs. normal tissues (P<0.05). The methylation status of BMP3, EID3, GAS7, and GPR75 was confirmed in an independent, validation cohort. Ingenuity pathway analysis mapped three of these markers (GAS7, BMP3 and GPR) in the insulin and TGF-β1 network-the two key pathways in CRC. In addition to hypermethylated genes, our analysis also revealed that LINE-1 repeat elements were progressively hypomethylated in the normal-adenoma-cancer sequence. We conclude that DNA methylome profiling based on RRBS is an effective method for screening aberrantly methylated genes in CRC. While previous studies focused on the limited identification of hypermethylated genes, ours is the first study to systematically and comprehensively identify novel hypermethylated genes, as well as hypomethylated LINE-1 sequences, which may serve as potential biomarkers for CRC in African Americans. Our discovered biomarkers were intimately linked to the insulin/TGF-B1 pathway, further strengthening the association of diabetic disorders with colon oncogenic transformation.

Microbiome analysis of stool samples from African Americans with colon polyps

BACKGROUND

Colonic polyps are common tumors occurring in ~50% of Western populations with ~10% risk of malignant progression. Dietary agents have been considered the primary environmental exposure to promote colorectal cancer (CRC) development. However, the colonic mucosa is permanently in contact with the microbiota and its metabolic products including toxins that also have the potential to trigger oncogenic transformation.

AIM

To analyze fecal DNA for microbiota composition and functional potential in African Americans with pre-neoplastic lesions.

MATERIALS & METHODS

We analyzed the bacterial composition of stool samples from 6 healthy individuals and 6 patients with colon polyps using 16S ribosomal RNA-based phylogenetic microarray; the Human intestinal Tract Chip (HITChip) and 16S rRNA gene barcoded 454 pyrosequencing. The functional potential was determined by sequence-based metagenomics using 454 pyrosequencing.

RESULTS

Fecal microbiota profiling of samples from the healthy and polyp patients using both a phylogenetic microarraying (HITChip) and barcoded 454 pyrosequencing generated similar results. A distinction between both sets of samples was only obtained when the analysis was performed at the sub-genus level. Most of the species leading to the dissociation were from the Bacteroides group. The metagenomic analysis did not reveal major differences in bacterial gene prevalence/abundances between the two groups even when the analysis and comparisons were restricted to available Bacteroides genomes.

CONCLUSION

This study reveals that at the pre-neoplastic stages, there is a trend showing microbiota changes between healthy and colon polyp patients at the sub-genus level. These differences were not reflected at the genome/functions levels. Bacteria and associated functions within the Bacteroides group need to be further analyzed and dissected to pinpoint potential actors in the early colon oncogenic transformation in a large sample size.

Epigenetic silencing of CHD5, a novel tumor-suppressor gene, occurs in early colorectal cancer stages

BACKGROUND

Chromodomain helicase DNA binding protein 5 (CHD5) is a family member of chromatin remodeling factors. The epigenetic silencing mechanisms of CHD5 in colorectal cancer have not been well studied.

METHODS

Here we analyzed CHD5 methylation and mRNA expression in vitro and in clinical samples from African American patients. DNA and RNA were isolated from formalin fixed paraffin embedded (FFPE) colon tissues. DNA was tested for methylation using methylation-specific polymerase chain reation (PCR) and bisulfite sequencing. RNA was used for mRNA quantification using qRT-PCR. The RKO cell line was treated with 5-Aza-dC and SAHA. RKO cells were also stably transfected with a CHD5-expressing vector. The transcriptional activity was studied in the 1 kb upstream region of the CHD5 promoter using the dual reporter assay. We performed cell proliferation, migration, and invasion assays using the RKO cell line.

RESULTS

In most adenoma samples, CHD5 expression was not detected in contrast to normal tissues. In RKO cells, CHD5 silencing was associated with DNA methylation and repressive histone modifications. CHD5 expression was restored after treatment with 5-Aza-dC and SAHA. CHD5 reactivation reduced cell proliferation, migration, and invasion. The reporter assay indicated that the main regulatory region of the CHD5 promoter is encompassed in the -489 to -823 region with important transcriptional regulatory sites (TCF/LEF, SP1, and AP-2).

CONCLUSIONS

The CHD5 gene is repressed in all types of adenomas, either epigenetically or by chromosomal deletion. CHD5 activity is regulated by DNA methylation and repressive histone modifications. CHD5 likely acts as a tumor-suppressor gene in early colorectal carcinogenesis.

Toward a comprehensive and systematic methylome signature in colorectal cancers

CpG Island Methylator Phenotype (CIMP) is one of the underlying mechanisms in colorectal cancer (CRC). This study aimed to define a methylome signature in CRC through a methylation microarray analysis and a compilation of promising CIMP markers from the literature. Illumina HumanMethylation27 (IHM27) array data was generated and analyzed based on statistical differences in methylation data (1st approach) or based on overall differences in methylation percentages using lower 95% CI (2nd approach). Pyrosequencing was performed for the validation of nine genes. A meta-analysis was used to identify CIMP and non-CIMP markers that were hypermethylated in CRC but did not yet make it to the CIMP genes' list. Our 1st approach for array data analysis demonstrated the limitations in selecting genes for further validation, highlighting the need for the 2nd bioinformatics approach to adequately select genes with differential aberrant methylation. A more comprehensive list, which included non-CIMP genes, such as APC, EVL, CD109, PTEN, TWIST1, DCC, PTPRD, SFRP1, ICAM5, RASSF1A, EYA4, 30ST2, LAMA1, KCNQ5, ADHEF1, and TFPI2, was established. Array data are useful to categorize and cluster colonic lesions based on their global methylation profiles; however, its usefulness in identifying robust methylation markers is limited and rely on the data analysis method. We have identified 16 non-CIMP-panel genes for which we provide rationale for inclusion in a more comprehensive characterization of CIMP+ CRCs. The identification of a definitive list for methylome specific genes in CRC will contribute to better clinical management of CRC patients.

Role of life events in the presence of colon polyps among African Americans

Background

African Americans have disproportionately higher incidence and death rates of colorectal cancer among all ethnic groups in the United States. Several lifestyle factors (e.g. diet, physical activity and alcohol intake) have been suggested as risk factors for colorectal cancer. Stressful life events have also been identified as risk factors for colorectal cancer. The association between stressful life events and colon polyps, which are precursors of colorectal cancer, has yet to be determined.

We aimed to evaluate the relationship between stressful life events and the presence of colon polyps and adenomas in African American men and women.

Methods

In this cross-sectional study, 110 participants were recruited from a colon cancer screening program at Howard University Hospital. Participants completed an 82-item Life Events Questionnaire (Norbeck 1984), assessing major events that have occurred in the participants’ life within the past 12 months. Participants also reported whether the event had a positive or negative impact. Three scores were derived (total, positive, and negative).

Results

Total life events scores were higher (Median [M] = 29 and Interquartile range [IQR] = 18-43) in patients with one or more polyps compared to patients without polyps (M, IQR = 21,13-38; P = 0.029). Total, positive or negative Life Events scores did not differ significantly between normal and adenoma patients. Total, negative and positive Life Events scores did not differ between patients who underwent diagnostic colonoscopy (symptomatic) and patients who underwent colonoscopy for colon cancer screening (asymptomatic) and patients for surveillance colonoscopies due to a personal history of colon polyps. Linear regression analysis indicated that male gender is associated with 9.0 unit lower total Life Events score (P = 0.025).

Conclusion

This study suggests that patients who experienced total life events may be at higher risk of having colon polyps and adenomas which indicates an association between stress and the development of colorectal polyps.

Abstract 3589: Microbiomic analysis of colon cancer tumors and their matched normal reveals distinct gut floras

Background: The gut flora has long been suspected to play a role in colon carcinogenesis either through their secreted toxins or through their processing of ingested nutrients leading to the production of carcinogenic products. We previously have shown that stool samples flora from patients with pre-neoplastic colon lesions differ from those from healthy individuals. However, bacteria in stool samples are not representative of the colon adherent bacteria that are more prone to affect colon mucosa homeostasis. Here we analyzed the microbiota composition in 10 colon tumors and their matched normal tissue from 10 African American patients.

Materials & Methods: DNA extracts from 10 pairs of colon tumors and matched normal tissue, was used to amplify the V1-V3 regions of the 16S rRNA gene. The PCR primers included the A and B adaptor sequences for 454 pyrosequencing as well as a unique 12 bp barcode incorporated onto the reverse primer such that each sample receives its own unique barcode. The amplicons were purified, quantified, normalized, and then pooled in preparation for emulsion PCR followed by 454 sequencing using Titanium chemistry. After deconvolution and trimming, the sequences were put through chimera checking (using chimera slayer). Those sequences of length &gt;=100 bp that were not labeled as chimeras were then processed using RDP's classifier.

Results: Overall, each tumor sample microbiota was the closest to its matched normal based on the general bacterial profile. Bacteroidetes and Firmicutes were the dominant bacterial groups in all analyzed samples. Using a Principal Component Analysis at the genus level with bacterial genera that are represented at least 5% in one sample revealed two distinctly separated healthy tissue groups, one defined primarily by Bacteroides and the second defined by Prevotella bacteria. No tumor sample was within these two groups. It is noteworthy that Fusobacteria, that was shown by other similar studies as primarily abundant in tumors, was not defining any tumor group in our study.

Conclusion: Our study reveals the presence of significant microbiota changes between tumor samples and matched normal tissue even though our analysis were done only at the genus level. Further analysis at the Operational Taxonomic Units (sub-genus level) for each pair of samples are underway and will further dissect the observed differences.

Citation Format: Hassan Brim, Shibu Yooseph, Manolito Torralba, Edward Lee, Karen Nelson, Hassan Ashktorab. Microbiomic analysis of colon cancer tumors and their matched normal reveals distinct gut floras. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3589. doi:10.1158/1538-7445.AM2013-3589

Abstract 5307: Paired analysis of matched colon normal and tumor using whole exome sequencing

Background: Whole Exome sequencing (WES) is a tool that is revolutionizing screening for pathogeni single nucleotide variations (SNV) in complex disorders such as cancers. Using matched normal-tumor pairs, it is possible to identify exome-wide germline and somatic variant alterations that may have an effect on disease progression or response to different interventions. The existing analysis pipelines are under continuous enhancements. In analyzing matched pairs, there is a critical assumption that the sequenced data are matched, without any quality check. Identification of germline and rare somatic variants depend on the normal sample being the qualified matched pair. Our aim was to determine if Identity By State (IBS), a genetics concept on measuring relatedness between individuals (matched tumor-normal pairs) can assess somatic landscape between individual using WES data. Materials and Methods: Genomic DNA was extracted from 8 normal-tumor pair tissues from African Americans (males n=3, females n=5) with colorectal cancer (CRC). WES was performed for identification of SNV according to manufacturer recommendations (Illumina HiScan SQ). The low quality reads were discarded and the clean reads were aligned against the human reference genome (HG19) and base quality calibration was completed using SAMTools, and GATK for variant calling and annotation. Pairs with no shared allele, one shared allele, and two shared allele assigned as IBS 0, IBS 1, and IBS 2 respectfully. Alleles in the dataset were coded using A and B and pairwise IBS was computed between all samples. Display of the IBS landscape was done using GenomeRelator. Results: The frequency of IBS from WGS data sets showed that most of the changes were IBS-1 which were heterozygous variants; i.e. AA/BB&gt;AB (somatic) or AB&gt;AA/BB (LOH). Frequency of LOH varied from 4.36% to 73.61%. Homozygous variant (i.e. IBS-0, AA&gt;BB) on the other hand was not common, from 0.00% to 4.17%. Distribution of IBS across genome for matched pairs reveals that most of the IBS were IBS-2, indicating that both alleles between matched normal and tumor were similar. Frequency of IBS-1 and IBS-0 varied amongst the samples. Sample CC1053 had the most allele changes in chr1-22, and Xq, and sample CC1054 showed the second highest allele changes in chr1,3,4,6,8,9,10,11,13, 16, 17,19,20 and 22. Conclusion: Our results showed that the SNV difference between normal-tumor matched pair is relatively small consistent with the assumption of low mutation rate in cancer. IBS approach provides the tumor contents as well as assurance in the selection of samples for sequencing using SNP data. In our samples 88% similarly was found, as shown in IBS landscape across the chromosomes. We concluded that our matched pair samples are appropriately selected and are suitable for analysis of mutation across the samples.

Citation Format: Mohammad Daremipouran, Hassan Hassanzadeh Namin, Sohaila Soltani, Joe Devaney, Wayne Frederick, Edward L. Lee, Hassan Brim, Hassan Ashktorab. Paired analysis of matched colon normal and tumor using whole exome sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5307. doi:10.1158/1538-7445.AM2013-5307

Abstract 4247: Identification of new hypermethylated candidate genes in colorectal cancer using reduced representation bisulfite next generation sequencing

Background: The identification and validation of genes that are frequently methylated in CRC will have potential value for both diagnostic and therapeutic implications. However, the DNA methylation patterns in CRC especially in African Americans have not been well investigated. Here we aimed to determine the methylation status of CpG islands of candidate genes in critical pathways important in the initiation and development of CRC.

Materials and Methods: Genomic DNA from 7 individuals (1 normal, 2 adenomas, and 4 adenocarcinomas) was used for global methylation analysis using Reduced Representation Bisulfite Sequencing (RRBS). Based on literature review, differential methylation ratio, gene ontology, WNT, Notch, EGFR, RAS-MPK, PI3K, TGF-b, and P53 pathways analysis, RGS3, EID3, GNAS, ATXN7L1, GAS7, HNRNPF, GPR7, SOX15, and TNFAIP2 genes were selected for methylation validation . Established methylation status of NDRG4, BMP3, Septin 9, Vimentin, and B-Actin were used as validation controls. Forty-four paired colorectal tumors and normal adjacent colonic tissue samples were used for validation. Samples were first bisulfite converted and then amplified at specific loci using 48.48 Access Array (Fluidigm). Amplicon pools were barcoded and adapterized prior to 150-bp paired-end sequencing on the Illumina MiSeq Reads were de-multiplexed using the Fluidigm indexes and mapped back to the reference genome (Hg18). A paired t-test was used for p-value and meth-diff estimation.

Results: We validated the methylation status of 355 CpG sites located in 16 gene promoter regions associated with CpG islands. Fifty-nine CpG sites located on CpG islands of ATXN7L1 (2), BMP3 (7), EID3 (15), GAS7 (1), GPR75 (24), NDRG4 (2), Sept9 (6), and TNFAIP2 (1), were significantly methylated in tumor vs. normal (p&lt;0.05). Most of these genes showed significant hypermethylation in tumors compared to normal mucosa, According to gene ontology analysis, GAS7 methylation is associated with the cadherin signaling (WNT) pathway.

Conclusion: Methylation profiling based on RRBS is an effective method for screening aberrantly methylated genes in CRC. We identified novel methylated genes that are potential biomarkers for CRC. In consistence with other reports, our study showed that GAS7 is also hypermethylated in African American CRC patients. Investigations into the possible roles of this gene as a potential biomarker in the context of early diagnosis and prognosis of CRC are underway.

Citation Format: Hassan Ashktorab, Mohammad Daremipouran, Hamed Rahi, Eward L. Lee, Wayne Frederick, Adeyinka O. Laiyemo, Ron Leavitt, Xueguang Sun, Sudhir Varma, Hassan Brim. Identification of new hypermethylated candidate genes in colorectal cancer using reduced representation bisulfite next generation sequencing. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4247. doi:10.1158/1538-7445.AM2013-4247

Abstract 1934: Novel mutation and hypomethylation define distinct biological subgroups of altered KRAS colon tumors

Background: Several driver mutations have been discovered in colorectal cancer (CRC) progressions including KRAS and BRAF that has a practical significant therapeutic and prognostic value. Sequencing technology has advanced and now provides a tool for the discovery of novel driver mutations. In addition, sequencing technologies now provide a tool for whole genome methylation analysis. Here, we performed whole exome sequencing (WES) and whole genome methylation analysis to elucidate the involvement of novel candidate genes the KRAS pathway that may effect colorectal carcinogenesis.

Patients and Methods: WES was carried out on genomic DNA extracted from 8 normal-tumor pairs of frozen biopsies from African Americans patients with CRC. WES and Reduced Representation Bisulfite Sequencing (RRBS) were performed. Pyrosequencing and sanger sequencing used for validation of methylation and single nucleotide variants (SNV) respectively. For WES, base call quality recalibration, realignment around indels, SNV calling and variant call recalibration were carried out using Genome Analysis Tool Kit. Variants were then annotated using Annovar.

Results: WES uncovered somatic mutations alteration in many genes that are known be mutated in CRC including APC, BRAF, KRAS, Notch1, PIK3C2A, and NDRG4. We discovered a number of Novel SNVs in EID3, RGS3, HNRNPF, and GNAS in tumor samples. One GNAS missense mutation was discovered among KRAS mutated tumors. In addition, the tumor with the GNAS mutation was significantly hypomethylated (P&lt;0.05) in the CpG sites of GNAS promoter as compared with paired normal tissue. The tumor was located in the cecum and identified to be invasive adenocarcinoma with stage IV1b (T4b, N2a, M1). Ingenuity pathway analysis (IPA) showed that GNAS were involved in CRC metastasis signaling via APC, BRAF, GSK3A, KRAS, MLH1, MLH2, MLH3, Notch family, and PIK3C family.

Conclusion: This work provides insight into identification of novel somatic mutations in GNAS coupled with promoter hypomethylation at the same locus using WES and RRBS. GNAS SNV resulted in gain of function of G-protein signaling that may play a pivotal role in CRC Identification the biological significance of GNAS in CRC may introduce a new target for colorectal cancer diagnosis and treatment.

Citation Format: Hamed Rahi, Sohaila Soltani, Mohammad Daremipouran, Hassan Brim, Eward L. Lee, Alfreda Woods, Wayne Frederick, Adeyinka O. Laiyemo, Joe Devaney, Ron Leavitt, Xueguang Sun, Hassan Ashktorab. Novel mutation and hypomethylation define distinct biological subgroups of altered KRAS colon tumors. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1934. doi:10.1158/1538-7445.AM2013-1934

Short- and long-term risk of colorectal adenoma recurrence among whites and blacks

BACKGROUND

It is unclear whether the higher burden from colorectal cancer among blacks is due to an increased biological susceptibility.

OBJECTIVE

To determine whether non-Hispanic blacks (blacks) have a higher risk of adenoma recurrence than non-Hispanic whites (whites) after removal of colorectal adenoma.

DESIGN

Secondary analysis of the Polyp Prevention Trial (PPT) data.

SETTING

United States.

PATIENTS

Patients were 1668 self-identified whites and 153 blacks who completed the 4-year trial. Of these, 688 whites and 55 blacks enrolled in a posttrial, passive Polyp Prevention Trial Continued Follow-up Study (PPT-CFS) and underwent another colonoscopy.

MAIN OUTCOME MEASUREMENTS

Recurrence and location of the adenoma and advanced adenoma by race-ethnicity during PPT and cumulative recurrence over a mean follow-up of 8.3 years (range, 4.9-12.4 years) among PPT-CFS enrollees.

RESULTS

Blacks had similar risk of recurrence of adenoma (39.2% vs 39.4%; incidence risk ratio [RR] = .98; 95% CI, .80-1.20) and advanced adenoma (8.5% vs 6.4%; RR = 1.18; 95% CI, .68-2.05) as whites at the end of PPT. Recurrence risk did not differ by colon subsite. Among PPT-CFS enrollees, the cumulative recurrence rate over a maximal follow-up period of 12 years was similar for blacks and whites for adenoma (67.3% vs 67.0%; RR = 1.01; 95% CI, .84-1.21) and advanced adenoma (14.5% vs 16.9%; RR = 1.03; 95% CI, .60-1.79).

LIMITATION

There were few blacks in the long-term follow-up study.

CONCLUSIONS

Adenoma and advanced adenoma recurrence did not differ by race. Our study does not support more frequent surveillance colonoscopies for blacks with a personal history of adenoma as an intervention to reduce colorectal cancer disparity.

Apoptotic DNA fragmentation may be a cooperative activity between caspase-activated deoxyribonuclease and the poly(ADP-ribose) polymerase-regulated DNAS1L3, an endoplasmic reticulum-localized endonuclease that translocates to the nucleus during apoptosis

Caspase-activated DNase (CAD) is the most favorable candidate for chromatin degradation during apoptosis. Ca(2+)-dependent endonucleases are equally important in internucleosomal DNA fragmentation (INDF), including the PARP-1-regulated DNAS1L3. Despite the elaborate work on these endonucleases, the question of whether these enzymes cooperate during INDF was not addressed. Here, we show a lack of correlation between INDF and CAD expression levels and inactivation by cleavage of its inhibitor (ICAD) during apoptosis. The cells that failed to induce INDF accumulated large amounts of 50-kb breaks, which is suggestive of incomplete chromatin processing. Similarly, INDF was blocked by Ca(2+) chelation without a block in ICAD cleavage or caspase-3 activation, which is consistent with the involvement of CAD in 50-kb DNA fragmentation and its Ca(2+) independence. However, DNAS1L3 expression in INDF-deficient cells promoted INDF during apoptosis and was blocked by Ca(2+) chelation. Interestingly, expression of DNAS1L3 in ICAD-deficient cells failed to promote tumor necrosis factor α-induced INDF but required the coexpression of ICAD. These results suggest a cooperative activity between CAD and DNAS1L3 to accomplish INDF. In HT-29 cells, endogenous DNAS1L3 localized to the endoplasmic reticulum (ER) and translocated to the nucleus upon apoptosis induction but prior to INDF manifestation, making it the first reported Ca(2+)-dependent endonuclease to migrate from the ER to the nucleus. The nuclear accumulation of DNAS1L3, but not its exit out of the ER, required the activity of cysteine and serine proteases. Interestingly, the endonuclease accumulated in the cytosol upon inhibition of serine, but not cysteine, proteases. These results exemplify the complexity of chromatin degradation during apoptosis.

Abstract 4414: Distinct taxonomic, metagenomic and metabolomic profiles from a comprehensive gut flora analysis in healthy and colon adenoma African Americans

Background: Gut flora has long been suspected to play a role in colorectal cancer (CRC) pathogenesis. Elegant experiments have substantiated such claims with the use of single pathogenic bacteria in germ free colon cancer mouse models. Here we run a comprehensive taxonomic, metagenomic and metabolomics analysis of stool samples from healthy and colon adenoma African American (AA) patients to define further this role. Patients & Methods: DNA extracts from stool samples of 6 healthy and 6 colon adenoma patients were used for the taxonomic and metagenomic analysis. The sequencing was done using a 454 pyrosequencer and the generated data was processed using informatics pipeline for phylogenetic bacterial affiliation and for bacterial functions assignment. For the metabolomics analysis, 10 fecal water extracts from healthy individuals and 10 from colon adenoma patients were analysed for their metabolites’ contents using NMR spectrometry. Results: The analysis of 16S-rDNA sequences revealed the existence of 22 groups of bacteria. A phylogenetic clustering revealed colon adenoma cases clustering together. Most predominant groups in both sets of samples were Clostridia and Bacteroides. No Lactobacilli or Bifidobacteria (good bacteria) were detected. The synergistetes_Dynergistia group -involved in gastrointestinal infections and Firmicutes phylum: Firmicutes group - involved in energy resorption and obesity were 20 and 10 folds more prevalent in adenoma patients, respectively. Bacteria TM7 group that contain active agents in IBD was 5 folds more represented in the control compared to the adenoma group. The metagenomic experiment have led to the generation of about 100,000 reads per sample, 80% of which were successfully annotated. Among the annotated functions, many were differentially present in the colon adenoma compared to healthy individuals. The metabolomics analysis led to a strong clustering of the adenoma samples metabolomes further consolidating the role of bacteria and their metabolites in colon cancer pathology. Conclusion: Our taxonomic, metagenomic and metabolomics analysis have led the presence of clear differential profiles in colon adenoma patients vs. healthy persons. Lack of detection of “good bacteria” (Lactobacilli and Bifidobacteria) in this study defines already a first level of intervention in this high risk CRC population. A comprehensive analysis of all the results is underway to bridge the Taxo, Meta and metabolomics data.

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 4414. doi:1538-7445.AM2012-4414

Abstract 3096: ICAD deficiency in human colon cancer and predisposition to colon tumorigenesis in mice: Linkage to resistance to apoptosis and susceptibility to genomic instability

We previously showed that DNA fragmentation factor, which comprises a caspase-3-activated DNase (CAD) and its inhibitor (ICAD), may influence the rate of cell death by generating PARP-1-activating DNA breaks. Here we tested the hypothesis that ICAD-deficient colon epithelial cells (CECs) exhibiting resistance to death stimuli may accumulate additional genetic modifications, leading to a tumorigenic phenotype. We show that ICAD deficiency is highly associated with colon malignancy in humans. Upon DNA damage caused by a low dose of irradiation, ICAD-/- cells acquire a tumorigenic phenotype. CECs derived from ICAD-/- mice showed a marked resistance to death induced by the colon carcinogen dimethylhydrazine (DMH) in vitro and in mice. Such resistance was associated with a decrease in PARP-1 activation. In an animal model of DMH-induced colon tumorigenesis, ICAD-/- mice developed significantly higher numbers of tumors with markedly larger sizes than the wild-type counterparts. Interestingly, the phenotype of the ICAD-/- mice was not associated with a significant increase in the precancerous aberrant crypt foci suggesting a link to tumor progression rather than initiation. More importantly, ICAD deficiency was associated with severe genomic instability, constituting most prominently of amplifications but with sizable deletions as compared to the wild-type counterparts affecting several cancer-related genes including RAF-1, GSN, LMO3, and Fzd6 independently of p53. Our results present a strong case for involvement of ICAD deficiency in colon carcinogenesis and show that apoptosis and genomic instability may comprise the means by which such deficiency may contribute to the process of increasing susceptibility to carcinogen-induced tumorigenesis.

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 3096. doi:1538-7445.AM2012-3096

Abstract 994: Colorectal cancer, adenoma and normal whole genome methylation sequencing in Africa Americans

Background: Colorectal adenoma (CRA) to cancer (CRC) progression involves epigenetic changes including DNA methylation. Here we performed whole genome Bisulfite Next-Generation Sequencing (WGBNGS) on a normal, a tubular adenoma and a tumor patients’ tissue DNA to elucidate epigenetic drivers in normal to cancer progression. Patients and Methods: Genomic DNA was isolated from fresh frozen tissues from a patient with normal colon, from a tubular adenoma lesion (20X depth was performed on these DNA samples., Alignment, mapping and CpG methylation analyses were done. Pyrosequencing and immunohistochemistry (IHC) were used to confirm selected methylation target genes. Results: We identified 94 unique CpG sites hypermethylated in 4 novel genes in adenoma compared to normal and 180 unique CpG sites in 7 genes in cancer. Ingenuity pathway analysis (IPA) showed that the methylated genes including a novel gene ATXN7L1 were involved in WNT pathway, ubiquitination process and cross-talk with B-catenin, in the adenoma. Three of the hypermethylated genes in cancer were, Loc100506436: a novel gene with 17 unique CpG sites (EGFR pathway, cRNA CpG site hypermethylated is part of MEK1/2), GPNMB with 7 unique CpG sites (membrane protein likely in complexes with integrins) and TNFAIP2 with 8 unique CpG sites (its role was noted in Head and neck cancer). IHC confirmed the lack of GPNMB expression in cancer tissues. Conclusion: This work provides insight into differential CpG island methylation profiles in CRA, CRC vs. normal colon tissue and provides a window into the more complex factors, including alteration of known and novel genes as multiple CpG methylation drivers in colorectal carcinogenesis. Investigations into the possible roles of the novel genes targets in the context of early and prognostic methylation biomarker are underway.

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 994. doi:1538-7445.AM2012-994

SEL1L, an UPR response protein, a potential marker of colonic cell transformation

BACKGROUND

SEL1L gene product is implicated in the endoplasmic reticulum (ER)-associated protein degradation and Unfolded Protein Response pathways. This gene and associated miRNAs have been indicated as predictive and prognostic markers of pancreatic cancer.

AIM

Explore the role of SEL1L in colorectal cancer (CRC) progression.

METHODS

SEL1L expression was analysed immunohistochemically in 153 adenomas and 71 CRCs from African American and North Italian patients. The distribution of stained cells was determined by computing median and inter quartile range. The receiver operating characteristics plot was used as discriminate power of SEL1L expression, CRC diagnosis and the effects on patient survival.

RESULTS

SEL1L was low in normal mucosa and confined to few scattered cells at the base crypt of the villi and in the foveolar glandular compartment. The highest levels were in Paneth cells within the lysosomes. The enterocytic progenitor cells and mature enterocytes showed less cytoplasmic staining. In CRCs, SEL1L expression significantly correlated with the progression from adenoma to carcinoma (P = 0.0001) being stronger in well-to-moderately differentiated cancers. No correlation was found with other clinicopathological characteristics or ethnicity.

CONCLUSIONS

SEL1L expression is a potential CRC tissue biomarker since its expression is significantly higher in adenoma cells with respect to normal mucosa. The levels of expression decrease sensibly in undifferentiated CRC cancers. Interestingly, Paneth cells contain high levels of SEL1L protein that could indicate pre-neoplastic mucosa undergoing neoplastic transformation. Since SEL1L's major function lies within ER stress and active ERAD response, it may identify CRCs with differentiated secretory phenotype and acute cellular stress.

Esophageal carcinoma in African Americans: a five-decade experience

BACKGROUND

Esophageal cancer accounts for a considerable proportion of carcinomas of the upper gastrointestinal tract in African Americans. Our aim was to describe the epidemiology of esophageal squamous cell cancer (ESCC) and esophageal adenocarcinoma (EA) among African Americans in the last five decades.

METHODS

A total of 601 records of patients with documented esophageal cancer between 1959 and 2007 at Howard University Hospital were reviewed. Demographic characteristics, risk factors, clinical stage and histological findings were reviewed. The change in prevalence of the disease and the interaction between main risk factors with tumor stage of the patients were assessed over the years of this study.

RESULT

A total of 552 patients (91.8%) had ESCC while 49 patients (8.2%) had EA. The mean age at diagnosis was 60.1 and 60.6 years for ESCC and EA, respectively (P = 0.8). The peak incidence was in the 1980-1989 decade. Out of 136 ESCC patients with TNM staging information, 130 (95.6%) were diagnosed in stage 2 and above. The majority (73%) of the ESCC were in the mid- and upper third of the esophagus and associated with smoking and alcohol exposure. The majority (81%) of the EA were in the mid- and lower third. The most common presenting symptoms were dysphagia (77.7%), and weight loss (31.9%).

CONCLUSION

ESCC is the predominant esophageal cancer in African Americans and diagnosed in late stages, and its diagnosis in our institution has decreased since 1990. A combination of genetic factors, environmental influences (e.g., those related to diet), and the deleterious changes associated with smoking and alcohol consumption, and differences in tumor histology, are the obvious parameters that should be the focus of future studies, and early diagnosis at an earlier stage should be considered among blacks.

Case-control study of vitamin D, dickkopf homolog 1 (DKK1) gene methylation, VDR gene polymorphism and the risk of colon adenoma in African Americans

BACKGROUND

There are sparse data on genetic, epigenetic and vitamin D exposure in African Americans (AA) with colon polyp. Consequently, we evaluated serum 25(OH) D levels, vitamin D receptor (VDR) polymorphisms and the methylation status of the tumor suppressor gene dickkopf homolog 1 (DKK1) as risk factors for colon polyp in this population.

METHODS

The case-control study consisted of 93 patients with colon polyp (cases) and 187 healthy individuals (controls) at Howard University Hospital. Serum levels of 25(OH)D (including D3, D2, and total) were measured by liquid chromatography-mass spectrometry. DNA analysis focused on 49 single nucleotide polymorphisms (SNPs) in the VDR gene. Promoter methylation analysis of DKK1 was also performed. The resulting data were processed in unadjusted and multivariable logistic regression analyses.

RESULTS

Cases and controls differed in vitamin D status (D(3)<50 nmol/L: Median of 35.5 in cases vs. 36.8 in controls nmol/L; P = 0.05). Low levels of 25(OH)D(3) (<50 nmol/L) were observed in 86% of cases and 68% of controls and it was associated with higher risks of colon polyp (odds ratio of 2.7, 95% confidence interval 1.3-3.4). The SNP analysis showed no association between 46 VDR polymorphisms and colon polyp. The promoter of the DKK1 gene was unmethylated in 96% of the samples.

CONCLUSION

We found an inverse association between serum 25(OH)D(3) and colon polyp in AAs. VDR SNPs and DKK1 methylation were not associated with colon polyp. Vitamin D levels may in part explain the higher incidence of polyp in AAs.

SLC5A8 gene, a transporter of butyrate: a gut flora metabolite, is frequently methylated in African American colon adenomas

Background

Colon cancer is one of the leading causes of cancer related deaths. Its impact on African Americans (AAs) is higher than in the general population both in the incidence and mortality from the disease. Colon cancer aggressiveness in AAs as well as non-frequent check-ups and follow up in this population have been proposed as ways to explain the observed discrepancies. These facts made the detection of early carcinogenesis markers in this population a priority.

Materials and Methods

Here, we analyzed 50 colon adenomas from AA patients for both microsatellite instability (MSI) and the methylation status of SLC5A8 gene. This gene's product is involved in the transport of butyrate that has anti-proliferative properties through its effects on histone acetylation and gene expression. A proteomic analysis to check the expressed histones in adenoma and normal tissues was also performed.

Results

The analyzed samples displayed 82% (n = 41) methylation level of SLC5A8 gene in adenomas. The MSI-H (high) adenoma were about 18% (n = 9) while the rest were mostly MSS (microsatellite stable) with few MSI-L (Low). No association was found between SLC5A8 methylation and the MSI status. Also, there was no association between SLC5A8 methylation and the sex and age of the patients. However, there were more right sided adenomas with SLC5A8 methylation than the left sided ones. The proteomic analysis revealed distinct histone expression profiles between normal and adenoma tissues.

Conclusion

SLC5A8 is highly methylated in AA colon adenomas which points to its potential use as a marker for early detection. The MSI rate is similar to that found in colon cancer tumors in AAs. These findings suggest that both processes stem from the same epigenetic and genetic events occurring at an early stage in colon carcinogenesis in AAs.

Abstract 3871: Expression of MACC1, a metastasis-related protein, associated with the progression of colorectal cancer

Background: Colorectal cancer (CRC) as the second most common cancer in western world has different prognostic basis in contrast to other cancers. Its pathologic staging is the main prognostic factor. Recently, MACC1 has been proposed as an effective marker for identifying patients at high risk for the development of distant metastases when MACC1 is highly expressed in the not (yet) metastasized primary tumor.

Aims and Methods: We aimed to assess the cellular and sub-cellular expression of MACC1 in age matched normal, adenomatous and cancerous colonic tissue samples. Samples were recruited from pathology department of Howard University Hospital. The Tissue Micro Array (TMA) sections were made from all duplicated samples and put in three different TMA slides as normal matched (n=44), adenomatous (n=60) and adenocarcinoma (n=36). Total of 140 samples were stained for MACC1 by Immuno-Histo-Chemistry method. Then, all three TMA were read by two pathologists including one GI pathologist. The expression were reported as staining 0, 1, 2, 3, 4 which refer to none, less than 10%, 10-25%, 25-50%, 50-75%, &gt;75%, respectively. Sub-cellular staining was reported as nuclear, cytoplasmic, or both.

Results: Of 140 samples, 36 were adenocarcinomas (mean age: 64.3; M/F: 16/20); 60 adenomatous (mean age: 64.8; M/F: 31/29); 44 normal controls (mean age 65.8; M/F: 22/22). Adenocarcinomas received score 4 in 86.1% of cases which was significantly higher (p&lt;0.05) than normal (15.9%) and adenomatous (28.3%) cases. MACC1 stained more in cytoplasm (88.6%) in contrast to normal (44.7%) and adenomatous cases (32.1%) with P &lt; 0.05. Observationally, high grade adenomas had higher scores (3 or 4) than low grade ones (P=0.1). Of total 18 patients with stage 3 and/or 4, 14 scored 4 and had cytoplasmic stainning.

Conclusions: Our data showed that MACC1 not only can be a prognostic and pathological marker to differentiate high grade from low grade adenoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3871. doi:10.1158/1538-7445.AM2011-3871

Abstract B48: Do the gut flora play a role in the high incidence of colon cancer in African Americans?

Colonic adenomatous polyps are common tumors occurring in 50% of Western populations with 10% risk of malignant progression. To date, the environmental exposures proposed to promote the development of colorectal cancer (CRC) have been primarily dietary agents. However, the local environment to which the colonic mucosa is exposed is created by the bacterial microbiota of the colon and their metabolic products that include toxins. African Americans are known to have a higher incidence of colon cancer than other groups.

We analyzed the gut flora from African Americans patients by both 16S rDNA sequencing and HIT (Human Intestinal Tract) Chip. Our findings reflected a high prevalence of Bacteroidetes and Clostridia groups with the Bacteroidetes slightly more represented in patients with colon polyps than healthy ones. While Bifidobacteria were not detected at all in all samples, Lactobacilliwere present at a very low frequency. Both bacteria are referred to as “good bacteria” and are generally associated with healthy colon. Helicobacter bacteria, associated with gastric cancer, were also detected in all analysed samples. Bacteroides fragilis and relatives were present in all samples at a high frequency. It is noteworthy that an enterotoxigenic Bacteroides fragilis have been found to trigger colon polyps formation in Min mice through a pSTAT3 pathway. A tissue microarray immunohistochemistry experiment on colon adenoma and matched normals revealed a strong expression of pSTAT3 both in colonic epithelial cells and in colonic immune cells in adenoma samples but not as much in normal ones. These findings highlight the presence of a possible ETBF-like induction mechanism in the analysed samples.

Enzyme immunoassay for the detection of antibodies against ETBF toxin would confirm such findings and a metagenomic analysis of the analysed samples would shed light on predominant bacterial functions in adenoma patients that might play a role in colon oncogenic transformation in this population.

Citation Information: Cancer Epidemiol Biomarkers Prev 2010;19(10 Suppl):B48.

Abstract B52: Predictor of distinct genetic alterations in African Americans with colon cancer by genomic analysis

Purpose: Chromosomal instability (CIN), microsatellite instability (MIN), and CpG island methylation phenotype (CIMP) are known processes through which colorectal cancer (CRC) can occur. In a given tumor, one or more of these events might be responsible for tumor development. We previously reported the results of our MSI and CIMP analysis of colorectal tumors in African Americans (AA), a group at high risk. Here, we report our array comparative genomic hybridization (aCGH) population analysis of AA and Caucasian CRC and its implication for the understanding of CRC development in this population.

Experimental design: We used 30 AA and 22 Caucasian CRC patients and applied aCGH (105k chip) to identify copy number aberrations in samples. In addition, we did a population comparative analysis with aCGH data in Caucasians as well as with a widely publicized list of colon cancer candidate genes (CAN genes). Bioinformatics analysis was done to calculate the chromosomal imbalance using Agilent Genomic Workbench 5.0.

Results: There was an average of 30 aberrations per patient with all samples displaying some level of chromosomal instability. Analysis of DNA copy number of frequently altered chromosomes revealed that deletions occurred primarily in chromosomes 4, 8 and 18. Chromosomal duplications occurred in more than 50% of cases on chromosomes 7, 8, 13, 20 and X. The CIN profile showed some differences when compared to alterations in Caucasians.

Conclusions: Prominent chromosome X amplification in male patients and chromosomes 4, 8 and 18 deletions were the primary targets in AAs. Most CAN genes were altered at high frequencies in AAs with EXOC4, EPHB6, GNAS, MLL3 and TBX22 as the most frequently deleted genes and HAPLN1, ADAM29, SMAD2 and SMAD4 as the most frequently amplified genes. CIN seems to be more prominent in AAs and may play a distinctive role in CRC development in this population.

Citation Information: Cancer Epidemiol Biomarkers Prev 2010;19(10 Suppl):B52.

Abstract 2714: Colorectal Cancer in young (&lt;50 years old) African Americans, Could race be a risk factor? A 20 years experience in an inner city teaching hospital

BACKGROUND: Colorectal cancer (CRC) is the third most common cancer, and survival in African Americans (AAs) is worse than Caucasians. Some studies suggest that the incidence of CRC is higher in AA patients below the age of 50 when compared to Caucasians. This study aims to confirm the higher prevalence of CRC in an AA population less than 50, and its implications to the screening guidelines.

METHOD: In a retrospective study demographic data, indication and outcome of colonoscopy, and biopsy data were collected at Howard University Hospital (HUH) over a period of 21 years (1989-2008). All of the study patients were (AA), and cases were classified either symptomatic average risk (91%); or high risk (family history, IBD) (9%). Distribution of variables was studied by median (inter-quartile range) or number (%).

RESULTS: Seventy five CRC cases younger than 50 years old were recorded from 1989 to 2008 at HUH. Median age (inter-quartile range) of these patients were 43 (40-46) years and 35 (47%) were female. Among them 55 (73%) were adenocarcinoma and 43 (57%) were located at left colon. In the same period a total of 671 CRC was recorded in HUH. We compared this data with 4591 CRC cases who were registered at District of Colombia (DC) from 1996 to 2007. While in HUH 11% of all CRC cases were under 50, this ratio for DC area was 9% (P=0.1). Among HUH patients 4%, 16% and 80% were 20-29, 30-39 and 40-49 years old, respectively. In DC area these ratios were 3%, 26% and 70% (P = 0.2). Among HUH tumors with available data 49%, 40%, 11% were local, regional, distant and unknown extension, while these proportions in DC area were 40%, 37%, 23% (P=0.018), respectively.

CONCLUSION: Our data showed a high burden of colorectal CRC in young AAs (&lt;50). CRC rate of 80% (60/75) was seen for the age group of 40-49, which indicates cancer in AAs may starts at younger age than predicted (&lt;45). The American College of Gastroenterology recommends to start screening of AAs at age of 45, but this may not cover many high risk people who are younger than 45. Further study is needed on AAs to confirm these findings.

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 2714.

Abstract 3453: Phylogenetic fingerprinting of the fecal microbiota in colorectal cancer patients

Colonic adenomatous polyps are common tumors occurring in ∼50% of Western populations with ∼10% risk of malignant progression. To date, the environmental exposures proposed to promote the development of colorectal cancer (CRC) have been primarily dietary agents. However, the local environment to which the colonic mucosa is exposed is created by the bacterial microbiota of the colon and their metabolic products that include toxins. A member of the Bacteroidetes division, Bacteroides fragilis is a common human commensal, occupying a mucosal niche in the colon. One molecular class of B. fragilis, enterotoxigenic B. fragilis (ETBF) induces polyp formation in Min (multiple intestinal neopplasia) mice through a STAT3 pathway.

Here we analyzed fecal DNA for gut flora composition in African Americans (n=12) with colon adenoma. A 16S rDNA cloning/sequencing experiment revealed that patients with colon adenomas have a higher rate of Bacteroides bacteria than healthy ones. These data was further confirmed using a HITChip (Human Intestinal Tract Chip) where samples from adenoma patients tended to cluster together pointing to common bacterial profiles.

STAT3 induced in adenoma and tumor by IHC, indicating, signal activation perhaps through ETBF like bacteria.

In conclusion, High throughput and sequencing approaches may help to better detect gut flora components including Bacteroides fragilis that induces colorectal carcinogenesis. In addition, the STAT3 expression results would confirm possible ETBF involvement on colon cancer risk via activating STAT3 downstream factor and molecules that are known to play a key role in the regulation of epithelial proliferation

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 3453.

Abstract 3445: Helicobacter pylori increases the risk of colorectal polyps in African Americans

Background: H. Pylori infection have linked to colorectal polyps, mainly through hypergastrinemia and its trophic effect on colon mucosa. African Americans were under represented despite both common diseases are more prevalent in them.

Aim: The aim of this study was to investigate whether H. Pylori infection has a role in development of colorectal polyps in Africans Americans.

Methods: Retrospectively, Africans Americans (n=1262) greater than 40 years old who underwent bidirectional gastrointestinal endoscopy on the same day were enrolled. The pre-procedure indication and post-procedure diagnosis were recorded (n=1262). H. Pylori status was assessed by immunohistochemistry on gastric specimens. Colorectal polyps were confirmed by histological examination of biopsies from complete colonoscopy. Multivariable logistic regression was used to assess the independent risk factors of polyp occurrence.

Results: Colorectal polyps (regardless polyp pathology) were more prevalent in H. Pylori-infected subjects (43%; 160/368) compared to (34%; 302/894) uninfected subjects (OR=1.5; 95 %CI=1.2-1.9). Furthermore, there was a trend toward larger polyp size ≥ 1cm in H. Pylori positive patients (P=0.07). There was no difference in histopathology or location of polyps in regard to H. Pylori status. Among the participants, 21 (2%) were defined with baseline above average risk for colorectal polyps justifying colonoscopy and of those; the polyps were detected in 62% (OR; 95%CI=2.9; 1.2-7.1). Age and male gender were independent risk factors for colorectal polyps.

Conclusion: H. Pylori increases the risk of developing colorectal polyps and may increase the chances for having a larger size polyp in Africans Americans. These findings suggest that H. Pylori might have a role in the initiation and/or promotion of polyps. Further studies are needed to explore its mechanisms.

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 3445.

Abstract 5018: Transcriptional and functional analysis of the CHD5 gene in Colorectal Cancer

Background: CHD5 is a family member of chromatin remodeling factors that functions as a tumor suppressor in neuroblastoma and ovarian cancer. The transcriptional activity of CHD5 is silenced by hypermethylation. It has been found that CHD5 is a biomarker in colon carcinogenesis. In this study, we have investigated the transcriptional regulation and function of the CHD5 in CRC.

Methods: The transcriptional activity of CHD5 was tested by reporter luciferase assay. The 1kb large fragment upstream of CHD5 transcription start site (TSS) showed luciferase activity; while the 400 bp subfragment upstream of TSS was inactive in both RKO (CHD5 endogenous non-expressing) and HCT116 (CHD5 endogenous expressing) cell lines. This suggests that the transcriptionally active sites of CHD5 are located within −400 to −1000. There are two consensus TCF binding sites in the 1 kb promoter region. In order to investigate whether Wnt pathway affects the CHD5 transcriptional activity, we treated the RKO and HCT116 cell lines with 6-bromoindirubin-3′oxime (BIO), the GSK-3a inhibitor, which activates the β-Catenin. We tested the Wnt pathway activity in RKO and HCT116 cell lines by using the TCF/LEF responsive luciferase construct. Methylation profiles of CHD5 in 51 CRC and 6 adenomas from African Americans analyzed by MSP. Microdeletion analysis of the CHD5 region (1p36) was performed by aCGH.

Results: The activity of TCF/LEF responsive element increased by 17.5 folds in RKO cell line and by 7.3 in HCT116 cell line after BIO treatment. Interestingly, the luciferase activity of 1kb CHD5 promoter increased after treating with BIO, and no changes were observed in activity of the 400 bp fragment. This suggests that the TCF/LEF and β-Catenin might act as coactivators for CHD5 transcriptional regulation. We also analyzed the proliferation of the RKO cell line after stably transfecting with CHD5 expressing plasmid (pcDNA). The results showed that the exogenous expression of CHD5 reduces the proliferation of the RKO cell line by two folds compared to the wild type and the mock controls. CHD5 was hypermethylated in 78% of the tested patients samples and deleted in 36%.

Conclusion: The function of CHD5 is not well understood in CRC. Here, we suggest that the wnt/β-catenin pathway may be involved in the transcriptional regulation of CHD5. In addition in vivo CHD5 microdeletion and methylation excrement suggest that CHD5 act as tumor suppressor in CRC.

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 5018.