Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14

Lack of significant associations between single nucleotide polymorphisms in LPAL2-LPA genetic region and all cancer incidence and mortality in Japanese population: The Japan public health center-based prospective study

BACKGROUND

High lipoprotein (a) level is an established cardiovascular risk, but its association with non-cardiovascular diseases, especially cancer, is controversial. Serum lipoprotein (a) levels vary widely by genetic backgrounds and are largely determined by the genetic variations of apolipoprotein (a) gene, LPA. In this study, we investigate the association between SNPs in LPA region and cancer incidence and mortality in Japanese.

METHODS

A genetic cohort study was conducted utilizing the data from 9923 participants in the Japan Public Health Center-based Prospective Study (JPHC Study). Twenty-five SNPs in the LPAL2-LPA region were selected from the genome-wide genotyped data. Cox regression analysis adjusted for the covariates and competing risks of death from other causes, were used to estimate the relative risk (hazard ratios (HR) with 95% confidence intervals (CI)) of overall and site-specific cancer incidence and mortality, for each SNP.

RESULTS

No significant association was found between SNPs in the LPAL2-LPA region and cancer incidence or mortality (overall/site-specific cancer). In men, however, HRs for stomach cancer incidence of 18SNPs were estimated higher than 1.5 (e.g., 2.15 for rs13202636, model free, 95%CI: 1.28-3.62) and those for stomach cancer mortality of 2SNPs (rs9365171, rs1367211) were estimated 2.13 (recessive, 95%CI:1.04-4.37) and 1.61 (additive, 95%CI: 1.00-2.59). Additionally, the minor allele for SNP rs3798220 showed increased death risk from colorectal cancer (CRC) in men (HR: 3.29, 95% CI:1.59 - 6.81) and decreased CRC incidence risk in women (HR: 0.46, 95%CI: 0.22-0.94). Minor allele carrier of any of 4SNPs could have risk of prostate cancer incidence (e.g., rs9365171 dominant, HR: 1.71, 95%CI: 1.06-2.77).

CONCLUSIONS

None of the 25 SNPs in the LPAL2-LPA region was found to be significantly associated with cancer incidence or mortality. Considering the possible association between SNPs in LPAL2-LPA region and colorectal, prostate and stomach cancer incidence or mortality, further analysis using different cohorts is warranted.

Examining the Factors That Affect the Diagnosis of Patients with Positive Fecal Occult Blood Test Results

Due to the threat of colorectal cancer (CRC) to health, Taiwan included the fecal occult blood test (FOBT) under preventive health services in 2010. We examined the factors that affect the diagnosis of people with positive FOBT results. Data were retrospectively collected from the CRC screening database. In the model predicting factors that affect the diagnosis of 89,046 people with positive FOBT results, the risks of disease in the CRC group were lower in medical institutions that conducted follow-up examinations in regions such as Northern Taiwan compared to that in Eastern Taiwan (p = 0.013); they were lower in the age group of 50 to 65 years than those in the age group of 71 to 75 years (p < 0.001, p = 0.016), and lower in the outpatient medical units that conducted follow-up examinations than those in the inpatient medical units by 0.565 times (p < 0.001, 95% CI: 0.493−0.647). Factors affecting the diagnosis of patients with positive FOBT results were gender, the region of the medical institution, medical unit for follow-up examinations, age, screening site, family history, type of follow-up examinations, and follow-up time. Therefore, the identification of characteristics of patients with positive FOBT results and the promotion of follow-up examination are important prevention strategies for CRC.

Association of four genetic variants with colorectal cancer in Kazakhstan population

The study was conducted to search for polymorphisms located in the 10th chromosome associated with colorectal adenocarcinoma in representatives of the Kazakhstan population. Study was performed with 282 colorectal cancer (CRC) patients and 159 controls. Genotyping of SNPs was performed by QuantStudio 12K Flex PCR. For four significant SNPs inheritance model analysis was performed. Increasing risk of CRC was noted for rs10795668 in log-additive model (OR = 1.45, 95% CI: 1.05–1.99, p = 0.023); for rs1035209 in log-additive model (OR = 1.79, 95% CI: 1.18–2.72, p = 0.003); for rs11190164 in log-additive model (OR = 1.67, 95% CI: 1.17–2.38, p = 0.004). Decreasing risk of CRC was noted for rs10506868 in log-additive model (OR = 0.56, 95% CI: 0.37–0.85, p = 0.006). We detected SNPs that are associated with CRC risk in the Kazakhstan population.

Factors affecting the follow-up time after a positive result in the fecal occult blood test

In 2010, Taiwan included the fecal occult blood test (FOBT) under preventive health insurance services. For patients whose test positive, receiving follow-ups is paramount. This study investigated factors affecting the follow-up time of these patients. This retrospective study used data from the colorectal cancer screening archives. The study period was from 2010 to 2013, and the subjects were 50-75-year-old persons who tested positive for FOBT. The t test, one-way ANOVA, and multiple regression were performed to address the differences in the mean tracking period between variables such as the population's demographic characteristics. The mean follow-up time for the 98,482 participants whose screening results were positive exhibited significant differences (p < 0.001) according to medical unit region and classification, age, screening location, family history, examination method, and diagnosis. The model predicting the mean follow-up time predicted a period of 10.079 days longer for those whose hospital was on an offshore island than that of those whose hospital was in the eastern regions. The follow-up time was 1.257 days shorter for people who were inpatients than those who were outpatients and was 8.902 days longer for people who underwent double contrast barium enema plus flexible sigmoidoscopy than those who underwent other examination methods. Patients with a family history of colorectal cancer and those whose examination results indicated cancer had a follow-up time of 2.562 and 2.476 days shorter than those who did not know their family history and those with other results, respectively. Factors affecting the follow-up time of people whose FOBT results were positive consisted of the location and classification of the follow-up institution, age, screening location, family history, examination method, and diagnosis. This provides valuable references for improving the cancer screening program.

Repurposing non-invasive prenatal testing data: Population study of single nucleotide variants associated with colorectal cancer and Lynch syndrome

In our previous work, genomic data generated through non-invasive prenatal testing (NIPT) based on low-coverage massively parallel whole-genome sequencing of total plasma DNA of pregnant women in Slovakia was described as a valuable source of population specific data. In the present study, these data were used to determine the population allele frequency of common risk variants located in genes associated with colorectal cancer (CRC) and Lynch syndrome (LS). Allele frequencies of identified variants were compared with six world populations to detect significant differences between populations. Finally, variants were interpreted, functional consequences were searched for and clinical significance of variants was investigated using publicly available databases. Although the present study did not identify any pathogenic variants associated with CRC or LS in the Slovak population using NIPT data, significant differences were observed in the allelic frequency of risk CRC variants previously reported in genome-wide association studies and common variants located in genes associated with LS. As Slovakia is one of the leading countries with the highest incidence of CRC among male patients in the world, there is a need for studies dedicated to investigating the cause of such a high incidence of CRC in Slovakia. The present study also assumed that extensive cross-country data aggregation of NIPT results would represent an unprecedented source of information concerning human genome variation in cancer research.

Evaluation of common genetic variants in vitamin E-related pathway genes and colorectal cancer susceptibility

Vitamin E is effective for preventing the risk of cancer. However, few studies have elucidated the mechanism of vitamin E in cancer occurrence. Herein, we aimed to identify the genetic variants in vitamin E-related pathway genes associated with colorectal cancer risk. We applied logistic regression models to assess the association between single-nucleotide polymorphisms (SNPs) in vitamin E-related pathway genes and colorectal cancer risk in the Chinese and European population. The false discovery rate (FDR) method was used to correct multiple comparisons. The mRNA and protein expression analysis were evaluated in public database and in-house RNA-Seq data. SCARB1 rs73227586 was identified significantly increased risk of colorectal cancer in the Chinese population (odd ratio (OR) = 1.46, 95% confidence interval (CI) = 1.22-1.75, P = 2.99 × 10^-5). This finding was further validated in the European population (OR = 1.11, 95% CI = 1.02-1.20, P = 1.44 × 10^-2). Additionally, the mRNA and protein expression of SCARB1 were markedly up-regulated in colorectal tumor tissues. Moreover, rs73227586 T allele could increase the minimum free energy (MFE) and weaken binding ability to transcription factor ELL2. Our findings indicated that SCARB1 may play a carcinogenic role in colorectal cancer. Genetic variants in vitamin E-related pathway genes may concern to be predictors of colorectal cancer risk.

GTF2IRD1 on chromosome 7 is a novel oncogene regulating the tumor-suppressor gene TGFβR2 in colorectal cancer

Chromosome 7q (Ch.7q) is clonally amplified in colorectal cancer (CRC). We aimed to identify oncogenes on Ch.7q that are overexpressed through DNA copy number amplification and determine the biological and clinical significance of these oncogenes in CRC. We identified general transcription factor 2I repeat domain‐containing protein 1 (GTF2IRD1) as a potential oncogene using a CRC dataset from The Cancer Genome Atlas with a bioinformatics approach. We measured the expression of GTF2IRD1 in 98 patients with CRC using immunohistochemistry and RT‐quantitative PCR (RT‐qPCR). The biological effects of GTF2IRD1 expression were explored by gene set enrichment analysis (GSEA). Next, we undertook in vitro cell proliferation and cell cycle assays using siGTF2IRD1‐transfected CRC cells. We further investigated the oncogenic mechanisms through which GTF2IRD1 promoted CRC progression. Finally, we assessed the clinical significance of GTF2IRD1 expression by RT‐qPCR. GTF2IRD1 was overexpressed in tumor cells and liver metastatic lesions. The GSEA revealed a positive correlation between GTF2IRD1 expression and cell cycle progression‐related genes. GTF2IRD1 knockdown inhibited cell proliferation and induced cell cycle arrest in Smad4‐mutated CRC. GTF2IRD1 downregulated the expression of the gene encoding transforming growth factor β receptor 2 (TGFβR2), a tumor‐suppressor gene in Smad4‐mutated CRC. On multivariate analysis, high GTF2IRD1 expression was an independent poor prognostic factor. Clinicopathological analysis showed that GTF2IRD1 expression was positively correlated with liver metastasis. In conclusion, GTF2IRD1 promoted CRC progression by downregulating TGFβR2 and could be a prognostic biomarker on Ch.7q in CRC. GTF2IRD1 could also be a novel oncogene in CRC.

Interactions among lncRNAs, miRNAs and mRNA in colorectal cancer

Long non-coding RNAs (lncRNAs) are longer than 200 nts non-coding transcripts and have recently emerged as one of the largest and significantly diverse RNA families whereas microRNAs (miRNAs) are highly conserved short single-stranded ncRNAs (∼18-22 nucleotides). As families of small and long evolutionarily conserved ncRNAs, lncRNAs activate and repress genes via a variety of mechanisms at both transcriptional and translational levels, while miRNAs regulate protein-coding gene expression mainly through mRNA degradation or silencing, These ncRNAs have been proved to be involved in multiple biological functions, such as proliferation, differentiation, migration, angiogenesis and apoptosis. Today, while majority of studies have focused on defining the regulatory functions of lncRNAs and miRNAs, limited information have now available for the mutual regulations of lncRNAs, miRNAs and mRNA. Thus, the underlying molecular mechanisms, in particularly the interactions among lncRNAs, miRNAs and mRNA in development, growth, metastasis and therapeutic potential of cancer still remain obscure. Colorectal cancer (CRC) is known as the third most common and fourth leading cancer death worldwide. Increasing evidence showed the close correlations among aberrant expressions of lncRNAs, miRNAs and the occurrence, development of CRC. This review summarize the potential links among these RNAs in following three areas: 1, The biogenesis and roles of miRNAs in CRC; 2, The biogenesis and functions of lncRNAs in CRC; 3, The interactions among lncRNAs, miRNAs and mRNA in tumorigensis, growth, progression, EMT formation, chemoradiotherapy resistance, and therapeutic potential in CRC. We believe that identifying diverging lncRNAs, miRNAs and relevant genes, their interactions and complex molecular regulatory networks will provide important clues for understanding the mechanism and developing novel diagnostic and therapeutic strategies for CRC. Further efforts are warranted to bring the promise of regulating their activities into clinical utilities.

Trends in and Predictions of Colorectal Cancer Incidence and Mortality in China From 1990 to 2025

Colorectal cancer (CRC) has emerged as a major public health concern in China during the last decade. In this study, we investigated the disease burden posed by CRC and analyzed temporal trends in CRC incidence and mortality rates in this country. We collected CRC incidence data from the Cancer Incidence in Five Continents, Volume XI dataset and the age-standardized incidence rate (ASIR) and age-standardized mortality rate (ASMR) of CRC by sex and age, from the 2016 Global Burden of Diseases Study. We used the average annual percentage change (AAPC) to quantify temporal trends in CRC incidence and mortality from 1990 to 2016 and found the ASIR of CRC increased from 14.25 per 100,000 in 1990 to 25.27 per 100,000 in 2016 (AAPC = 2.34, 95% confidence interval [CI] 2.29, 2.39). Cancer cases increased from 104.3 thousand to 392.8 thousand during the same period. The ASIR increased by 2.76% (95% CI 2.66%, 2.85%) and 1.70% (95% CI 1.64%, 1.76%) per year in males and females, respectively. The highest AAPC was found in people aged 15–49 years (2.76, 95% CI 2.59, 2.94). Cancer deaths increased from 81.1 thousand in 1990 to 167.1 thousand in 2016, while the ASMR remained stable (−0.04, 95% CI −0.13, 0.05), A mild increase (AAPC = 0.42, 95% CI 0.34, 0.51) was found among males and a significant decrease (AAPC = −0.75, 95% CI −0.90, −0.60) was found among females. Between 2016 and 2025, cancer cases and deaths are expected to increase from 392.8 and 167.1 thousand in 2016 to 642.3 (95% CI 498.4, 732.1) and 221.1 thousand (95% CI 122.5, 314.8) in 2025, respectively. Our study showed a steady increase in the CRC incidence in China over the past three decades and predicted a further increase in the near future. To combat this health concern, the prevention and management of known risk factors should be promoted through national polices. Greater priority should be given to CRC prevention in younger adults, and CRC screening should be widely adopted for this population.

Japanese genome-wide association study identifies a significant colorectal cancer susceptibility locus at chromosome 10p14

Genome‐wide association studies are a powerful tool for searching for disease susceptibility loci. Several studies identifying single nucleotide polymorphisms (SNP) connected intimately to the onset of colorectal cancer (CRC) have been published, but there are few reports of genome‐wide association studies in Japan. To identify genetic variants that modify the risk of CRC oncogenesis, especially in the Japanese population, we performed a multi‐stage genome‐wide association study using a large number of samples: 1846 CRC cases and 2675 controls. We identified 4 SNP (rs7912831, rs4749812, rs7898455 and rs10905453) in chromosome region 10p14 associated with CRC; however, there are no coding or non‐coding genes within this region of fairly extensive linkage disequilibrium (a 500‐kb block) on 10p14. Our study revealed that the 10p14 locus is significantly correlated with susceptibility to CRC in the Japanese population, in accordance with the results of multiple studies in other races.