No clinical utility of KRAS variant rs61764370 for ovarian or breast cancer

Functional pri-miR-34b/c rs4938723 and KRAS 3'UTR rs61764370 SNPs: Novel phenotype modifiers in Li-Fraumeni Syndrome?

PURPOSE

Li-Fraumeni Syndrome (LFS) is a rare cancer predisposing condition caused by germline pathogenic TP53 variants, in which core tumors comprise sarcomas, breast, brain and adrenocortical neoplasms. Clinical manifestations are highly variable in carriers of the Brazilian germline founder variant TP53 p.R337H, possibly due to the influence of modifier genes such as miRNA genes involved in the regulation of the p53 pathway. Herein, we investigated the potential phenotypic effects of two miRNA-related functional SNPs, pri-miR-34b/c rs4938723 and 3'UTR KRAS rs61764370, in a cohort of 273 LFS patients from Southern and Southeastern Brazil.

METHODS

The genotyping of selected SNPs was performed by TaqMan® allelic discrimination and subsequently custom TaqMan® genotyping results were confirmed by Sanger sequencing in all SNP-positive LFS patients.

RESULTS

Although the KRAS SNP showed no effect as a phenotype modulator, the rs4938723 CC genotype was significantly associated with development of LFS non-core tumors (first tumor diagnosis) in p.R337H carriers (p = 0.039). Non-core tumors were also more frequently diagnosed in carriers of germline TP53 DNA binding domain variants harboring the rs4938723 C variant allele. Previous studies described pri-miR-34b/c rs4938723 C as a risk allele for sporadic occurrence of thyroid and prostate cancers (non-core tumors of the LFS spectrum).

CONCLUSION

With this study, we presented additional evidence about the importance of analyzing miRNA genes that could indirectly regulate p53 expression, and, therefore, may modulate the LFS phenotype, such as those of the miR-34 family.

Genetic Variability in the microRNA Binding Sites of BMPR1B, TGFBR1, IQGAP1, KRAS, SETD8 and RYR3 and Risk of Breast Cancer in Colombian Women

Background

Genetic variants in microRNA (miR) binding sites affect the regulation of miR-dependent gene expression and have been linked to the risk of a variety of cancers including breast cancer (BC). Most BC risk variants had been identified in women of European and Asian ancestry, but genetic data for Hispanic women are scarce. Here, we investigate the association between six variants in miR binding sites and BC risk in Colombian women.

Methods

We genotyped miR binding site variants in the BMPR1B, TGFBR1, IQGAP1, KRAS, SETD8 and RYR3 genes in 1022 BC cases and 1023 controls from the Colombian breast cancer case–control (Col-BCCC) study using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Multiple logistic regression and permutation techniques were applied to assess the association between genetic variants and BC risk.

Results

We found no evidence of association between any of the six miR binding site variants and overall or estrogen receptor subtype-specific BC risk in Colombian women.

Conclusion

Our findings may point to ethnic differences in the association between genetic variability in miR binding sites and breast cancer risk.

Prognostic Role of KRAS mRNA Expression in Breast Cancer

Purpose

We investigated the prognostic role of KRAS mRNA expression in breast cancer using The Cancer Genome Atlas (TCGA) and Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) databases.

Methods

Clinical and biological data of 1,093 breast cancers from TCGA database and 1,904 breast cancers from METABRIC database were analyzed. Overall survival (OS) and breast cancer-specific survival (BCSS) were determined.

Results

The group with high KRAS mRNA expression showed worse survival than the group with low KRAS mRNA expression regarding both OS (p = 0.012 in TCGA, p < 0.001 in METABRIC) and BCSS (p = 0.001 in METABRIC). According to multivariate analysis, the level of KRAS mRNA expression was an independent prognostic factor in both TCGA (hazard ratio [HR], 1.570; 95% confidence interval [CI], 1.026–2.403; p = 0.038) and METABRIC (HR, 1.254; 95% CI, 1.087–1.446; p = 0.002) databases. The prognostic impact of mRNA expression was effective only for luminal A subtype (p < 0.001 in METABRIC). Positive correlation was observed between mRNA expression and copy number alteration (CNA) (r = 0.577, p < 0.001 in TCGA; ρ = 0.343, p < 0.001 in METABRIC). Methylation showed negative correlations with both mRNA expression and CNA (r = −0.272, p < 0.001 in TCGA). The expression of mRNA had little association with the mutation status in breast cancers, having a mutation frequency of approximately 0.6%.

Conclusion

KRAS mRNA expression was significantly associated with breast cancer prognosis. It was found to be an independent prognostic factor for breast cancer. Prognostic role of KRAS mRNA expression was effective only in luminal A subtype. Further studies are needed to validate the prognostic role of KRAS mRNA expression in breast cancer, thus paving a way for clinical application of KRAS in practice.

KRAS SNPs are related to colorectal cancer susceptibility and survival in Chinese people

Aim: KRAS SNPs may increase KRAS transcription and KRAS levels. SNPs of KRAS 3'UTR can affect carcinoma risk and prognosis. Materials & methods: The rs8720 and rs7960917 in KRAS 3'UTR for colorectal carcinoma (CRC) risk and survival were investigated in a case-control study. Association between SNPs and CRC risk, survival analysis were analyzed by an unconditional logistic regression model, log-rank test, Kaplan-Meier estimation, Cox regression model and one-way analysis of variance. Results & conclusion: The genotype CT of rs8720 was significantly increased risk of CRC, decreased overall survival and event-free survival, and KRAS mRNA and protein expressions were significantly increased in individuals with rs8720 CT, TT genotype. rs8720 may be an important factor in CRC development and prognosis.

Tissue-specific microRNA expression alters cancer susceptibility conferred by a TP53 noncoding variant

A noncoding polymorphism (rs78378222) in TP53, carried by scores of millions of people, was previously associated with moderate risk of brain tumors and other neoplasms. We find a positive association between this variant and soft tissue sarcoma. In sharp contrast, it is protective against breast cancer. We generated a mouse line carrying this variant and found that it accelerates spontaneous tumorigenesis and glioma development, but strikingly, delays mammary tumorigenesis. The variant creates a miR-382-5p targeting site and compromises a miR-325-3p site. Their differential expression results in p53 downregulation in the brain, but p53 upregulation in the mammary gland of polymorphic mice compared to that of wild-type littermates. Thus, this variant is at odds with Li-Fraumeni Syndrome mutants in breast cancer predisposition yet consistent in glioma predisposition. Our findings elucidate an underlying mechanism of cancer susceptibility that is conferred by genetic variation and yet altered by microRNA expression.

Statistical genomics in rare cancer

Rare cancers make of more than 20% of cancer cases. Due to the rare nature, less research has been conducted on rare cancers resulting in worse outcomes for patients with rare cancers compared to common cancers. The ability to study rare cancers is impaired by the ability to collect a large enough set of patients to complete an adequately powered genomic study. In this manuscript we outline analytical approaches and public genomic datasets that have been used in genomic studies of rare cancers. These statistical analysis approaches and study designs include: gene set / pathway analyses, pedigree and consortium studies, meta-analysis or horizontal integration, and integration of multiple types of genomic information or vertical integration. We also discuss some of the publicly available resources that can be leveraged in rare cancer genomic studies.

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.

Benefit of cetuximab addition to a platinum-fluorouracil-based chemotherapy according to KRAS-LCS6 variant in an unselected population of recurrent and/or metastatic head and neck cancers

OBJECTIVES

To evaluate the benefit of cetuximab (Cx) addition to platinum-based and 5-fluorouracil chemotherapy (PFU) in unselected recurrent and/or metastatic head and neck cancer patients (R/MHNC) according to KRAS-LCS6 variant status.

METHODS

All patients who received at least two PFU ± Cx cycles from 2004 to 2014 were retrospectively included into to two distinct study periods according to Cx implementation: patients treated by PFU alone before 2009 and those treated by PFU + Cx from 2009. Primary objective was to evaluate the progression-free survival (PFS) between the two groups. Secondary objectives were to analyze the overall survival (OS) between the two groups and the prognostic impact of KRAS-LCS6 variant. Factors associated with survival were determined by a Cox multivariate analysis including age, WHO performance status (PS), type of treatment, KRAS-LCS6 variant, Charlson's score and p16 status.

RESULTS

Overall, 134 patients were included: 59 (44%) in PFU group and 75 (56%) in PFU + Cx group. Baseline characteristics were well balanced including 30% of patients with 2-3 PS. Median PFS was significantly improved in PFU + Cx group compared to PFU group (6.1 vs 4.4 months, respectively, HR 0.68, p = 0.02) and with a trend for better OS. A KRAS-LCS6 variant was found in 27 (25%) of samples without prognostic impact neither in whole population nor according to treatment. In multivariate analysis, addition of Cx to PFU was the only factor significantly associated with a better PFS (p = 0.01, HR 0.6).

CONCLUSION

Our results suggest that PFU + Cx combination may be effective in unselected population of R/MHNC regardless the KRAS-LCS6 variant status.

Molecular Docking Analysis of Caspase-3 Activators as Potential Anticancer Agents

Introduction:

Caspase-3 plays a leading role in apoptosis and on activation, it cleaves many protein substrates in cells and causes cell death. Since many chemotherapeutics are known to induce apoptosis in cancer cells, promotion or activation of apoptosis via targeting apoptosis regulators has been suggested as a promising strategy for anticancer drug discovery. In this paper, we studied the interaction of 1,2,4-Oxadiazoles derivatives with anticancer drug target enzymes (PDB ID 3SRC).

Methods:

Molecular docking studies were performed on a series of 1,2,4-Oxadiazoles derivatives to find out molecular arrangement and spatial requirements for their binding potential for caspase-3 enzyme agonistic affinity to treat cancer. The Autodock 4.2 and GOLD 5.2 molecular modeling suites were used for the molecular docking analysis to provide information regarding important drug receptor interaction.

Results and Conclusion:

Both suites explained the spatial disposition of the drug with the active amino acid in the ligand binding domain of the enzyme. The amino acid asparagine 273 (ASN 273) of target has shown hydrogen bond interaction with the top ranked ligand.

A single nucleotide polymorphism in the 3'-untranslated region of the KRAS gene disrupts the interaction with let-7a and enhances the metastatic potential of osteosarcoma cells

The objective of the present study was to explore the molecular mechanism with which a single nucleotide polymorphism (rs61764370) interferes with the interaction between the 3'-untranslated region (3'-UTR) of Kirsten rat sarcoma viral oncogene homolog (KRAS) and let-7a, and its association with the metastasis of osteosarcoma (OS). In this study, we confirmed that KRAS is a target of let-7a in OS cells, and the introduction of rs61764370 minor allele into KRAS 3'-UTR significantly compromised the microRNA (miRNA)/mRNA interaction using a luciferase reporter system. Additionally, a total of 36 OS tissue samples of three different genotypes (TT,22; TG,10; GG,4) were obtained, and the expression of let-7a and KRAS was determined. We showed that let-7a mRNA expression was similar between each group whereas the mRNA and protein expression of KRAS in the TT genotype group was significantly lower than that in the GT or GG genotype groups. Moreover, we identified a negative regulatory relationship between let-7a and KRAS. Furthermore, we demonstrated that let-7a and KRAS interfered with the viability, invasiveness and migration of OS cells genotyped as TT. In the OS cells genotyped as TG, let-7a exerted minimal effects, and the effect of KRAS siRNA remained. Taken together, the findings of the present study demonstrated that the KRAS 3'-UTR rs61764370 polymorphism interfered with miRNA/mRNA interaction, and showed that the minor allele was associated with an elevated risk of developing metastatic disease in OS.

rs712 polymorphism within let-7 microRNA-binding site might be involved in the initiation and progression of colorectal cancer in Chinese population

rs712 within 3'-untranslated region of KRAS can affect the specific binding between the mRNA and its targeted microRNAs, leading to the activation of KRAS oncogene. However, the possible association between the locus and susceptibility to colorectal cancer (CRC) remains unclear. We investigated genotypes of the locus in 586 cases and 476 controls to explore the possible association between them. Results of our case-control study showed that genotypes TT (6.5% vs 2.5%, P=0.002, adjusted odds ratio [OR] =2.810, 95% confidence interval [CI] =1.342-5.488) and GT/TT (36.5% vs 30.5%, P=0.038, adjusted OR =1.342, 95% CI =1.030-1.712) and allele T (21.5% vs 6.5%, P=0.004, adjusted OR =1.328, 95% CI =1.105-1.722) of rs712 were significantly associated with an increased risk of CRC, and the significant association was also observed in the recessive model (TT vs GG/GT, 6.5% vs 2.5%, P=0.003, adjusted OR =0.372, 95% CI =0.191-0.725). However, there was no association between genotype GT and risk of CRC (30.0% vs 28.0%, P=0.235, adjusted OR =1.210, 95% CI =0.903-1.548). Furthermore, genotype GT (P=0.003) and allele T (P=0.003) were significantly associated with poor differentiation, and genotypes GT and TT and allele T were significantly associated with tumor-node-metastases stage III (P=0.001 for GT vs GG, P<0.001 for TT vs GG, and P<0.001 for T vs G) and node metastasis (P<0.001 for GT vs GG, P=0.001 for TT vs GG, and P<0.001 for T vs G), respectively. These findings indicated that allele T and genotypes TT and GT/TT of rs712 might be susceptible factors for CRC, and mutated allele and genotypes of the locus might predict a poor clinical outcome in Chinese population.