Five Quantitative Trait Loci Control Radiation-Induced Adenoma Multiplicity in Mom1R ApcMin/+ Mice

Ionising radiation is a carcinogen capable of inducing tumours, including colorectal cancer, in both humans and animals. By backcrossing a recombinant line of ApcMin/+ mice to the inbred BALB/c mouse strain, which is unusually sensitive to radiation–induced tumour development, we obtained panels of 2Gy-irradiated and sham-irradiated N2 ApcMin/+ mice for genotyping with a genome-wide panel of microsatellites at ∼15 cM density and phenotyping by counting adenomas in the small intestine. Interval and composite interval mapping along with permutation testing identified five significant susceptibility quantitative trait loci (QTLs) responsible for radiation induced tumour multiplicity in the small intestine. These were defined as Mom (Modifier of Min) radiation-induced polyposis (Mrip1-5) on chromosome 2 (log of odds, LOD 2.8, p = 0.0003), two regions within chromosome 5 (LOD 5.2, p<0.00001, 6.2, p<0.00001) and two regions within chromosome 16 respectively (LOD 4.1, p  = 4×10−5, 4.8, p<0.00001). Suggestive QTLs were found for sham-irradiated mice on chromosomes 3, 6 and 13 (LOD 1.7, 1.5 and 2.0 respectively; p<0.005). Genes containing BALB/c specific non-synonymous polymorphisms were identified within Mrip regions and prediction programming used to locate potentially functional polymorphisms. Our study locates the QTL regions responsible for increased radiation-induced intestinal tumorigenesis in ApcMin/+ mice and identifies candidate genes with predicted functional polymorphisms that are involved in spindle checkpoint and chromosomal stability (Bub1b, Casc5, and Bub1), DNA repair (Recc1 and Prkdc) or inflammation (Duox2, Itgb2l and Cxcl5). Our study demonstrates use of in silico analysis in candidate gene identification as a way of reducing large-scale backcross breeding programmes

CCAT2, a novel noncoding RNA mapping to 8q24, underlies metastatic progression and chromosomal instability in colon cancer

The functional roles of SNPs within the 8q24 gene desert in the cancer phenotype are not yet well understood. Here, we report that CCAT2, a novel long noncoding RNA transcript (lncRNA) encompassing the rs6983267 SNP, is highly overexpressed in microsatellite-stable colorectal cancer and promotes tumor growth, metastasis, and chromosomal instability. We demonstrate that MYC, miR-17-5p, and miR-20a are up-regulated by CCAT2 through TCF7L2-mediated transcriptional regulation. We further identify the physical interaction between CCAT2 and TCF7L2 resulting in an enhancement of WNT signaling activity. We show that CCAT2 is itself a WNT downstream target, which suggests the existence of a feedback loop. Finally, we demonstrate that the SNP status affects CCAT2 expression and the risk allele G produces more CCAT2 transcript. Our results support a new mechanism of MYC and WNT regulation by the novel lncRNA CCAT2 in colorectal cancer pathogenesis, and provide an alternative explanation of the SNP-conferred cancer risk

Comprehensive assessment of variation at the transforming growth factor β type 1 receptor locus and colorectal cancer predisposition

The role of transforming growth factor β receptor type 1 (TGFBR1) polymorphisms, particularly a coding CGC insertion (rs11466445, TGFBR1*6A/9A) in exon 1, has been extensively investigated in regard to colorectal cancer (CRC) risk. These investigations have generated conflicting results. More recently, allele-specific expression (ASE) of TGFBR1 mRNA has been suggested as predisposing to CRC, with a relative risk of nearly 10-fold and a population attributable risk of ∼10%. Owing to the potential importance of TGFBR1 variants in CRC, we performed a comprehensive examination of tagging SNPs at and around the gene in 3,101 CRC cases and 3,334 controls of northern European ancestry. To test whether rare or subpolymorphic TGFBR1 variants were associated with CRC risk, we sequenced the gene's exons in a subset of patients. We also evaluated TGFBR1 ASE in a panel of CRC cases and controls. Overall, we found no association between TGFBR1 polymorphisms and CRC risk. The rare variant screen did not identify any changes of potentially pathogenic effects. No evidence of greater ASE in cases than controls was detected, and no haplotype around TGFBR1 could account for the ASE reported in other studies. We conclude that neither genetic variation nor ASE at TGFBR1 is likely to be a major CRC risk factor

A genome wide scan to show the LOD profiles of chromosomes 1–19 with adenoma multiplicity in the USI of the 2 Gy cohort.

<p>The horizontal line above the <i>y</i> axis represents a significant threshold score. Significant QTLs are detected on chromosomes 2, 5 and 16 and are defined as <i>Mom</i> radiation-induced polyposis (<i>Mrip</i>1–5; arrowed).</p

The LRS profile of <i>Mrip4</i> and <i>Mrip5</i> against markers distributed along chromosome 16 is determined using CIM (composite interval mapping) and compared with IM (interval mapping).

<p>The horizontal bar represents genome wide significance at p = 0.05. <i>Mrip4</i> and <i>Mrip5</i> are confirmed as separate non-linked QTLs associated with adenoma multiplicity in the USI of the 2 Gy mice.</p

The function of candidate genes and their role in radiation response and tumorigenesis.

<p>The function of candidate genes and their role in radiation response and tumorigenesis.</p

Main effect QTLs for tumour multiplicity in the small intestine of mice identified using a panel of 112 N2 sham-irradiated mice.

<p>The first column shows the chromosome (Chr.) number with the traits; USI (upper small intestine) and LSI (lower small intestine) in column 2. The marker name and position (cM) are determined by MIT; (<a href="http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease" target="_blank">http://www.broad.mit.edu/cgi-bin/mouse/sts_info?databasemouserelease</a>) and shown in column 3. Also given are the p-values with LRS (Likelihood Ratio Statistic), the percentage trait variance (%) and confidence intervals (CI). The level of significance attained was suggestive (Su) for all QTLS of the 0 Gy cohort.</p

Predictive assessment of <i>BALB</i> specific amino acid polymorphisms for potentially damaging alterations.

<p>We list the polymorphisms using MPD (Mouse Phenome Database) and known functional domains using STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) within the <i>Mrip</i> regions. Polyphen predictions are based on position specific independent count (PSIC) and if >1.5 then potentially damaging and shown in bold. SIFT predicts the substitution to be tolerated (T) or not tolerated (N), if intolerant then the substitution effect is stated. The conservation of sequence alignment at and around the amino acid substitution is compared using EMBL-EBI.</p

Summary of the process used in selecting genes from QTL regions.

<p>Summary of the process used in selecting genes from QTL regions.</p