KRAS Gene Polymorphisms and their Impact on Breast Cancer Risk in an Iranian Population

Genetic variations in tumor-suppressor miRNA-encoding genes and their target genes: focus on breast cancer development and possible therapeutic strategies

MicroRNAs (miRNAs) negatively affect gene expression by binding to their specific mRNAs resulting in either mRNA destruction or translational repression. The aberrant expression of various miRNAs has been associated with a number of human cancer. Oncogenic or tumor-suppressor miRNAs regulate a variety of pathways involved in the development of breast cancer (BC), including cell proliferation, apoptosis, metastasis, cancer recurrence, and chemoresistance. Variations in miRNA-encoding genes and their target genes lead to dysregulated gene expression resulting in the development and progression of BC. The various therapeutic approaches to treat the disease include chemotherapy, radiation therapy, surgical removal, hormone therapy, chemotherapy, and targeted biological therapy. The purpose of the current review is to explore the genetic variations in tumor-suppressor miRNA-encoding genes and their target genes in association with the disease development and prognosis. The therapeutic interventions targeting the variants for better disease outcomes have also been discussed.

Evaluation of the Role of the KRAS Gene Polymorphism LCS6 (rs61764370) in Iraqi Women with Ovarian Cancer

In carcinogenesis, KRAS is an essential oncogene that plays a key function. The polymorphism of rs61764370 is a candidate for cancer susceptibility in KRAS3' untranslated region. The current study aimed to determine the role and impact of the KRAS gene polymorphism (rs61764370 T>G) on the risk of ovarian cancer development in the Iraqi population. In total, 84 ovarian cancer patients and 28 ovarian benign tumors were involved in a case-control study. DNA extraction from the formalin-fixed/paraffin-embedded tissues, followed by the sequencing of PCR products was carried out in genetic analysis for the detection of the KRAS polymorphism (rs61764370 T>G). The results showed that the frequencies of the KRAS gene polymorphism (rs61764370) in ovarian cancer patients were 78 (92.85%) and 6 (7.15%) with genotypes homozygote TT and heterozygote TG, respectively. These corresponding values in patients with benign ovarian tumors were 25 (89.3%) and 3 (10.7%) with homozygote TT and heterozygote TG, respectively. None of the patients either with malignant or benign tumors have been detected with homozygote genotype GG. Genotype frequency of the TT and TG showed that the heterozygote TT genotype vs. TG and T allele vs. G allele were more frequent in malignant and benign tumors (P≤0.01). Statistically, there was no association between the KRAS polymorphism and the clinical characteristics of ovarian cancer patients, such as age, family history, menopause, histological type, tumor size, or tumor stage. In conclusion, a significant association was found between rs61764370 and the risk of ovarian cancer in the Iraqi population, particularly those with genotypes homozygote TT. On the other hand, genotypes had no relationship with any of the clinical characteristics of ovarian cancer patients. Additional well-designed studies with larger sample sizes are recommended to validate the precise role of KRAS LCS6 variations in ovarian cancer risk.

Classifying Breast Cancer Molecular Subtypes by Using Deep Clustering Approach

Cancer is a complex disease with a high rate of mortality. The characteristics of tumor masses are very heterogeneous; thus, the appropriate classification of tumors is a critical point in the effective treatment. A high level of heterogeneity has also been observed in breast cancer. Therefore, detecting the molecular subtypes of this disease is an essential issue for medicine that could be facilitated using bioinformatics. This study aims to discover the molecular subtypes of breast cancer using somatic mutation profiles of tumors. Nonetheless, the somatic mutation profiles are very sparse. Therefore, a network propagation method is used in the gene interaction network to make the mutation profiles dense. Afterward, the deep embedded clustering (DEC) method is used to classify the breast tumors into four subtypes. In the next step, gene signature of each subtype is obtained using Fisher's exact test. Besides the enrichment of gene signatures in numerous biological databases, clinical and molecular analyses verify that the proposed method using mutation profiles can efficiently detect the molecular subtypes of breast cancer. Finally, a supervised classifier is trained based on the discovered subtypes to predict the molecular subtype of a new patient. The code and material of the method are available at: https://github.com/nrohani/MolecularSubtypes.

Genetic and molecular biology of breast cancer among Iranian patients

Abstract

Background, Breast cancer (BC) is one of the leading causes of cancer related deaths in Iran. This high ratio of mortality had a rising trend during the recent years which is probably associated with late diagnosis.

Main body

Therefore it is critical to define a unique panel of genetic markers for the early detection among our population. In present review we summarized all of the reported significant genetic markers among Iranian BC patients for the first time, which are categorized based on their cellular functions.

Conclusions

This review paves the way of introducing a unique ethnic specific panel of diagnostic markers among Iranian BC patients. Indeed, this review can also clarify the genetic and molecular bases of BC progression among Iranians.

Breast Cancer and miR-SNPs: The Importance of miR Germ-Line Genetics

Recent studies in cancer diagnostics have identified microRNAs (miRNAs) as promising cancer biomarkers. Single nucleotide polymorphisms (SNPs) in miRNA binding sites, seed regions, and coding sequences can help predict breast cancer risk, aggressiveness, response to stimuli, and prognosis. This review also documents significant known miR-SNPs in miRNA biogenesis genes and their effects on gene regulation in breast cancer, taking into account the genetic background and ethnicity of the sampled populations. When applicable, miR-SNPs are evaluated in the context of other patient factors, including mutations, hormonal status, and demographics. Given the power of miR-SNPs to predict patient cancer risk, prognosis, and outcomes, further study of miR-SNPs is warranted to improve efforts towards personalized medicine.

Association of rs712 polymorphism in a let-7 microRNA-binding site of KRAS gene with colorectal cancer in a Mexican population

OBJECTIVES

The rs712 polymorphism in a let-7 microRNA-binding site at KRAS gene has been associated with cancer. To examine its association with rs712 polymorphism, we analyzed Mexican individuals with colorectal cancer (CRC) and healthy subjects.

MATERIALS AND METHODS

Genotyping of the rs712 polymorphism was performed by polymerase chain reaction in 281 controls and 336 CRC patients.

RESULTS

The observed frequencies of rs712 polymorphism indicated an associated protective factor for CRC (P=0.032). An association between genotype and the disease was evident in: colon localization (allele T, odds ratio (OR) 3.82, 95% confidence Intervals (CI) 2.77-5.28, P=0.0001), node metastasis (genotype TT, OR 2.49, 95% CI 1.45-4.28, P=0.0009), poor differentiation (genotype GT, OR 2.35, 95% CI 1.35-4.1, P=0.0033), and poor chemotherapy response (genotype GT, OR 2.6, 95% CI 1.7-4.24, P=0.0001).

CONCLUSION

Comparison of the data from patients with control group showed that polymorphism of rs712 in KRAS gene was protective factor, which was associated with susceptibility for CRC. However, the genotypes TT and GT of rs712 polymorphism in KRAS could contribute significantly to colon localization, node metastasis, poor differentiation and poor chemotherapy response in CRC patients in this sample population.

Detection of a 4-bp Insertion/deletion Polymorphism within the Promoter of EGLN2 Using Mismatch PCR-RFLP and Its Association with Susceptibility to Breast Cancer

It has been shown that a 4-bp insertion/deletion (ins/del) polymorphism of EGLN2 influences the risk of several cancers. However, to date, no study has inspected the impact of the 4-bp ins/del polymorphism on breast cancer (BC) risk. A case-control study, including 134 breast cancer patients and 154 healthy women, was here conducted to examine the possible association between EGLN2 4-bp ins/del polymorphism and BC risk in a southeast Iranian population. A mismatched polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was designed for genotyping of the variant. Our findings did not support any association between the 4-bp ins/del polymorphism and the risk of BC in the codominant, dominant, recessive and allele inheritance models tested. When links between the EGLN2 4-bp ins/del polymorphism and clinicopathological characteristics of the patients were evaluate the variant was only associated with HER2 status. More studies with larger sample sizes and diverse ethnicities are warranted to verify our finding.