A pilot genome-wide association study of breast cancer susceptibility loci in Indonesia

SNP-array profiling data from breast cancer patients and healthy women's blood DNA samples

Breast cancer is commonly acknowledged as the primary type of cancer on a global scale, exerting a substantial influence on death rates, particularly in developing countries. The aforementioned discovery provides evidence in favor of the concept that genetic factors may contribute to the onset of breast cancer. This paper presents the unprocessed idat data containing single nucleotide polymorphisms (SNPs) acquired from breast cancer patients and a control group comprising of healthy women. The DNA was obtained from stored blood samples that were collected from a total of 48 female patients diagnosed with breast cancer at Cipto Mangunkusumo National Hospital Jakarta and Dharmais National Cancer Center Hospital Jakarta. Additionally, 24 healthy women were included as control subjects. Subsequently, the DNA samples were subjected to hybridization onto Infinium Asian Screening Array (ASA)'s beadchips. The chip was then subjected to fluorescence intensity measurements using an iScan machine manufactured by Illumina. The data output is produced in the form of a .idat file for each sample. Subsequently, further quality control measures and population stratification analysis were conducted using PLINK (v1.9). After the conclusion of the quality control procedure, 72 individuals and a dataset consisting of 424,285 genetic variants were selected for further analysis. The idat raw data files have been added to the Gene Expression Omnibus (GEO) with accession number: GSE245794 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE245794).

Genome-wide and transcriptome-wide association studies of mammographic density phenotypes reveal novel loci

BACKGROUND

Mammographic density (MD) phenotypes, including percent density (PMD), area of dense tissue (DA), and area of non-dense tissue (NDA), are associated with breast cancer risk. Twin studies suggest that MD phenotypes are highly heritable. However, only a small proportion of their variance is explained by identified genetic variants.

METHODS

We conducted a genome-wide association study, as well as a transcriptome-wide association study (TWAS), of age- and BMI-adjusted DA, NDA, and PMD in up to 27,900 European-ancestry women from the MODE/BCAC consortia.

RESULTS

We identified 28 genome-wide significant loci for MD phenotypes, including nine novel signals (5q11.2, 5q14.1, 5q31.1, 5q33.3, 5q35.1, 7p11.2, 8q24.13, 12p11.2, 16q12.2). Further, 45% of all known breast cancer SNPs were associated with at least one MD phenotype at p < 0.05. TWAS further identified two novel genes (SHOX2 and CRISPLD2) whose genetically predicted expression was significantly associated with MD phenotypes.

CONCLUSIONS

Our findings provided novel insight into the genetic background of MD phenotypes, and further demonstrated their shared genetic basis with breast cancer.

Loss of Single-Stranded DNA Binding Protein 2 Expression Is Associated with Aggressiveness and Poor Overall Survival in Patients with Invasive Breast Carcinoma

Background: Single-stranded DNA binding protein 2 (SSBP2) is involved in the DNA damage response and the maintenance of genome stability. Previous studies have suggested that SSBP2 has a tumor suppressor function or oncogenic function. Loss of SSBP2 expression has been reported in various tumors. However, the role of SSBP2 expression in invasive breast carcinoma has not been reported. Methods: Immunohistochemical staining for SSBP2 was performed on tissue microarrays consisting of 491 invasive breast carcinoma cases. The result of nuclear SSBP2 staining was stratified as either negative or positive. Then, we investigated the correlations between SSBP2 expression and various clinicopathological parameters and patient outcomes. Results: Loss of nuclear SSBP2 expression was observed in 61 cases (12.4%) of 491 invasive breast carcinomas. Loss of nuclear SSBP2 expression was significantly correlated with larger tumor size (p < 0.001, chi-squared test), higher histological grade (p = 0.016, Cochran–Armitage trend test), higher pathological T stage (p < 0.001, Cochran–Armitage trend test), estrogen receptor status (p < 0.001, chi-squared test), and molecular subtype (p < 0.001, chi-squared test). Kaplan–Meier survival analysis revealed that patients with loss of nuclear SSBP2 expression had worse overall survival (p = 0.013, log-rank test). However, loss of nuclear SSBP2 expression was not correlated with recurrence-free survival (p = 0.175, log-rank test). Conclusions: Loss of nuclear SSBP2 expression was associated with adverse clinicopathological characteristics and poor patient outcomes. SSBP2 acts as a tumor suppressor in invasive breast carcinoma and may be used as a prognostic biomarker.

A Review of the Epidemiology of Breast Cancer in Asia: Focus on Risk Factors

Background and Aim:

Breast cancer is the most prevalent cancer in women. To date, regional differences in breast cancer risk factors have not been identified. The aim of our review was to gain a better understanding of the role of risk factors in women with breast cancer in Asia.

Methods:

We conducted a PubMed search on 15 March 2016, for journal articles published in English between 2011 and 2016, which reported data for human subjects in Asia with a diagnosis of breast cancer. Search terms included breast neoplasm, epidemiology, Asia, prevalence, incidence, risk and cost of illness. Studies of any design were included, except for review articles and meta-analyses, which were excluded to avoid duplication of data. No exclusions were made based on breast cancer treatment. We reported the results using the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines.

Results:

A total of 776 abstracts were retrieved. After screening against the eligibility criteria, 562 abstracts were excluded. The remaining 214 abstracts, which were published between 2013 and 2015, were included in this review. Results were summarized and reported under three categories: incidence, prevalence or outcomes for breast cancer in Asia; modifiable risk factors; and non-modifiable risk factors. We found that the increased risk of breast cancer among participants from Asia was associated with older age, family history of breast cancer, early menarche, late menopause, high body mass index, being obese or overweight, exposure to tobacco smoke, and high dietary intake of fats or fatty foods. In contrast, intake of dietary fruits, vegetables, and plant- and soy-based products was associated with a decreased breast cancer risk. While based on limited data, when compared to women from the United States, women from Asia had a decreased risk of breast cancer.

Conclusions:

This review of 214 abstracts of studies in Asia, published between 2013 and 2015, confirmed the relevance of known non-modifiable and modifiable risk factors for women with breast cancer.

SNHG1 Long Noncoding RNA is Potentially Up-Regulated in Colorectal Adenocarcinoma

Colorectal cancer (CRC) is one of the most common types of cancer worldwide. However, the molecular mechanisms involved in CRC initiation and progression is remained to be unknown. It seems that lncRNAs, as the main and lengthy functional transcripts of the genome, have important roles in different cancers such as CRC. CRC-related lncRNAs are reported to be involved in diverse molecular processes such as metastasis, invasion, cell proliferation, and apoptosis. This study was aimed to analyse the expression level of lncRNA SNHG1 in colorectal adenocarcinoma and normal tissues. We performed an in silico analysis on a large cohort and confirmed the results by experimental analysis of clinical samples through real-time PCR. Our findings demonstrated that that SNHG1 is potentially overexpressed in tumor tissues compared with adjacent normal tissues. The expression level of SNHG1 was shown to be potentially associated with clinicopathological features of tumors. The current study suggests the potential role of SNHG1 in colon cancer progression.

Systematic analysis of genetic variants in cancer-testis genes identified two novel lung cancer susceptibility loci in Chinese population

Cancer-testis (CT) genes played important roles in the progression of malignant tumors and were recognized as promising therapeutic targets. However, the roles of genetic variants in CT genes in lung cancer susceptibility have not been well depicted. This study aimed to evaluate the associations between genetic variants in CT genes and lung cancer risk in Chinese population. A total of 22,556 qualified SNPs from 268 lung cancer associated CT genes were initially evaluated based on our previous lung cancer GWAS (Genome-wide association studies) with 2,331 cases and 3,077 controls. As a result, 17 candidate SNPs were further genotyped in 1,056 cases and 1,053 controls using Sequenom platform. Two variants (rs6941653, OPRM1, T > C, screening: OR = 1.24, 95%CI: 1.12-1.38, P = 2.40×10^-5; validation: OR = 1.18, 95%CI: 1.01-1.37, P = 0.039 and rs402969, NLRP8, C > T, screening: OR = 1.15, 95%CI: 1.04-1.26, P = 0.006; validation: OR = 1.16, 95%CI: 1.02-1.33, P = 0.028) were identified as novel lung cancer susceptibility variants. Stratification analysis indicated that the effect of rs6941653 was stronger in lung squamous cell carcinoma (OR = 1.36) than that in lung adenocarcinoma (OR = 1.15, I² = 77%, P = 0.04). Finally, functional annotations, differential gene expression analysis, pathway and gene ontology analyses were performed to suggest the potential functions of our identified variants and genes. In conclusion, this study identified two novel lung cancer risk variants in Chinese population and provided deeper insight into the roles of CT genes in lung tumorigenesis.

Germline variants and somatic mutation signatures of breast cancer across populations of African and European ancestry in the US and Nigeria

Somatic mutation signatures may represent footprints of genetic and environmental exposures that cause different cancer. Few studies have comprehensively examined their association with germline variants, and none in an indigenous African population. SomaticSignatures was employed to extract mutation signatures based on whole-genome or whole-exome sequencing data from female patients with breast cancer (TCGA, training set, n = 1,011; Nigerian samples, validation set, n = 170), and to estimate contributions of signatures in each sample. Association between somatic signatures and common single nucleotide polymorphisms (SNPs) or rare deleterious variants were examined using linear regression. Nine stable signatures were inferred, and four signatures (APOBEC C>T, APOBEC C>G, aging and homologous recombination deficiency) were highly similar to known COSMIC signatures and explained the majority (60-85%) of signature contributions. There were significant heritable components associated with APOBEC C>T signature (h² = 0.575, p = 0.010) and the combined APOBEC signatures (h² = 0.432, p = 0.042). In TCGA dataset, seven common SNPs within or near GNB5 were significantly associated with an increased proportion (beta = 0.33, 95% CI = 0.21-0.45) of APOBEC signature contribution at genome-wide significance, while rare germline mutations in MTCL1 was also significantly associated with a higher contribution of this signature (p = 6.1 × 10^-6 ). This is the first study to identify associations between germline variants and mutational patterns in breast cancer across diverse populations and geography. The findings provide evidence to substantiate causal links between germline genetic risk variants and carcinogenesis.

Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks

Genome-wide association studies (GWAS) have successfully identified single variants associated with diseases. To increase the power of GWAS, gene-based and pathway-based tests are commonly employed to detect more risk factors. However, the gene- and pathway-based association tests may be biased towards genes or pathways containing a large number of single-nucleotide polymorphisms (SNPs) with small P-values caused by high linkage disequilibrium (LD) correlations. To address such bias, numerous pathway-based methods have been developed. Here we propose a novel method, DGAT-path, to divide all SNPs assigned to genes in each pathway into LD blocks, and to sum the chi-square statistics of LD blocks for assessing the significance of the pathway by permutation tests. The method was proven robust with the type I error rate >1.6 times lower than other methods. Meanwhile, the method displays a higher power and is not biased by the pathway size. The applications to the GWAS summary statistics for schizophrenia and breast cancer indicate that the detected top pathways contain more genes close to associated SNPs than other methods. As a result, the method identified 17 and 12 significant pathways containing 20 and 21 novel associated genes, respectively for two diseases. The method is available online by http://sparks-lab.org/server/DGAT-path.

The precision relationships between eight GWAS-identified genetic variants and breast cancer in a Chinese population

Some of the new breast cancer susceptibility loci discovered in recent Genome-wide association studies (GWASs) have not been confirmed in Chinese populations. To determine whether eight novel Single-Nucleotide Polymorphisms (SNPs) have associations with breast cancer risk in women from southeast China, we conducted a case-control study of 1,156 breast cancer patients and 1,256 healthy controls. We first validated that the SNPs rs12922061, rs2290203, and rs2981578 were associated with overall breast cancer risk in southeast Chinese women, with the per-allele OR of 1.209 (95%CI: 1.064-1.372), 1.176 (95%CI: 1.048-1.320), and 0.852 (95%CI: 0.759-0.956), respectively. Rs12922061 and rs2290203 even passed the threshold for Bonferroni correction (P value: 0.00625). In stratified analysis, we found another three SNPs were significantly associated within different subgroups. However, after Bonferroni correction (P value: 0.000446), there were no statistically significant was observed. In gene-environment interaction analysis, we observed gene-environment interactions played a potential role of in the risk of breast cancer. These findings provide new insight into the associations between the genetic susceptibility and fine classifications of breast cancer. Based on these results, we encourage further large series studies and functional research to confirm these finding.

BRCA1 Gene Mutation Screening for the Hereditary Breast and/or Ovarian Cancer Syndrome in Breast Cancer Cases: a First High Resolution DNA Melting Analysis in Indonesia

Specific patterns of the hereditary breast and ovarian cancer (HBOC) syndrome are related to mutations in the BRCA1 gene. One hundred unrelated breast cancer patients were interviewed to obtain clinical symptoms and signs, pedigree and familial history of HBOC syndrome related cancer. Subsequently, data were calculated using the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) risk prediction model. Patients with high score of BOADICEA were offered genetic testing. Eleven patients with high score of BOADICEA, 2 patients with low score of BOADICEA, 2 patient's family members and 15 controls underwent BRCA1 genetic testing. Mutation screening using PCR-HRM was carried out in 22 exons (41 amplicons) of BRCA1 gene. Sanger sequencing was subjected in all samples with aberrant graph. This study identified 10 variants in the BRCA1 gene, consisting of 6 missense mutations (c.1480C>A, c.2612C>T, c.2566T>C, c.3113A>G, c.3548 A>G, c.4837 A>G), 3 synonymous mutations (c.2082 C> T, c.2311 T> C and c.4308T>C) and one intronic mutation (c.134+35 G>T). All variants tend to be polymorphisms and unclassified variants. However, no known pathogenic mutations were found.

Genome-Wide Study of Response to Platinum, Taxane, and Combination Therapy in Ovarian Cancer: In vitro Phenotypes, Inherited Variation, and Disease Recurrence

Background: The standard treatment for epithelial ovarian cancer (EOC) patients with advanced disease is carboplatin-paclitaxel combination therapy following initial debulking surgery, yet there is wide inter-patient variation in clinical response. We sought to identify pharmacogenomic markers related to carboplatin-paclitaxel therapy.

Methods: The lymphoblastoid cell lines, derived from 74 invasive EOC patients seen at the Mayo Clinic, were treated with increasing concentrations of carboplatin and/or paclitaxel and assessed for in vitro drug response using MTT viability and caspase3/7 apoptosis assays. Drug response phenotypes IC50 (effective dose at which 50% of cells are viable) and EC50 (dose resulting in 50% induction of caspase 3/7 activity) were estimated for each patient to paclitaxel and carboplatin (alone and in combination). For each of the six drug response phenotypes, a genome-wide association study was conducted.

Results: Statistical analysis found paclitaxel in vitro drug response phenotypes to be moderately associated with time to EOC recurrence (p = 0.008 IC50; p = 0.058 EC50). Although no pharmacogenomic associations were significant at p < 5 × 10⁻⁸, seven genomic loci were associated with drug response at p < 10⁻⁶, including at 4q21.21 for carboplatin, 4p16.1 and 5q23.2 for paclitaxel, and 3q24, 10q, 1q44, and 13q21 for combination therapy. Nearby genes of interest include FRAS1, MGC32805, SNCAIP, SLC9A9, TIAL1, ZNF731P, and PCDH20.

Conclusions: These results suggest the existence of genetic loci associated with response to platinum-taxane therapies. Further research is needed to understand the mechanism by which these loci may impact EOC clinical response to this commonly used regimen.