A polymorphism at the miR-502 binding site in the 3'-untranslated region of the histone methyltransferase SET8 is associated with hepatocellular carcinoma outcome

Epi-miRNAs: Regulators of the Histone Modification Machinery in Human Cancer

Cancer is a leading cause of death and disability worldwide. Epigenetic deregulation is one of the most critical mechanisms in carcinogenesis and can be classified into effects on DNA methylation and histone modification. MicroRNAs are small noncoding RNAs involved in fine-tuning their target genes after transcription. Various microRNAs control the expression of histone modifiers and are involved in a variety of cancers. Therefore, overexpression or downregulation of microRNAs can alter cell fate and cause malignancies. In this review, we discuss the role of microRNAs in regulating the histone modification machinery in various cancers, with a focus on the histone-modifying enzymes such as acetylases, deacetylases, methyltransferases, demethylases, kinases, phosphatases, desumoylases, ubiquitinases, and deubiquitinases. Understanding of microRNA-related aberrations underlying histone modifiers in pathogenesis of different cancers can help identify novel therapeutic targets or early detection approaches that allow better management of patients or monitoring of treatment response.

A polymorphism in the 3'-untranslated region of the matrix metallopeptidase 9 gene is associated with susceptibility to idiopathic calcium nephrolithiasis in the Chinese population

Objective

To investigate whether single nucleotide polymorphisms (SNPs) in the 3′ untranslated region (UTR) of the matrix metallopeptidase 9 gene (MMP9) are associated with susceptibility to calcium oxalate stones.

Methods

A total of 428 patients with kidney stone disease (KSD) and 450 control individuals were enrolled. Three MMP9 SNPs (rs20544, rs9509, and rs1056628) were genotyped, and MMP9 mRNA and protein expression was determined in patients and controls. The dual luciferase reporter gene assay was conducted by transfecting HEK293 cells with miR-491-5p mimics and plasmids containing MMP9 with rs1056628 AA/CC genotypes.

Results

The rs1056628 CC genotype was significantly increased in KSD patients compared with controls (CC vs AA: odds ratio [OR] = 2.279, 95% confidence interval [CI] = 1.048–4.956). The rs1056628 C allele frequency was higher in KSD patients than controls. The increased KSD risks associated with rs1056628 were more evident in individuals aged <30 years (OR = 3.504, 95% CI = 1.102–11.139) and men (OR = 2.522, 95% CI = 1.004–6.334). mRNA and protein levels of MMP9 were significantly higher in KSD patients with the CC genotype than in those with the AA genotype.

Conclusion

This study demonstrates that MMP9 SNP rs1056628 is associated with a significant KSD risk in Chinese Han individuals.

Histone methyltransferase SET8 is regulated by miR-192/215 and induces oncogene-induced senescence via p53-dependent DNA damage in human gastric carcinoma cells

Gastric cancer (GC) is the most common cancer throughout the world. Despite advances of the treatments, detailed oncogenic mechanisms are largely unknown. In our previous study, we investigated microRNA (miR) expression profiles in human GC using miR microarrays. We found miR-192/215 were upregulated in GC tissues. Then gene microarray was implemented to discover the targets of miR-192/215. We compared the expression profile of BGC823 cells transfected with miR-192/215 inhibitors, and HFE145 cells transfected with miR-192/-215 mimics, respectively. SET8 was identified as a proposed target based on the expression change of more than twofold. SET8 belongs to the SET domain-containing methyltransferase family and specifically catalyzes monomethylation of H4K20me. It is involved in diverse functions in tumorigenesis and metastasis. Therefore, we focused on the contributions of miR-192/215/SET8 axis to the development of GC. In this study, we observe that functionally, SET8 regulated by miR-192/215 is involved in GC-related biological activities. SET8 is also found to trigger oncogene-induced senescence (OIS) in GC in vivo and in vitro, which is dependent on the DDR (DNA damage response) and p53. Our findings reveal that SET8 functions as a negative regulator of metastasis via the OIS-signaling pathway. Taken together, we investigated the functional significance, molecular mechanisms, and clinical impact of miR-192/215/SET8/p53 in GC.

SETD8 promotes stemness characteristics and is a potential prognostic biomarker of gastric adenocarcinoma

SETD8 is a lysine methyltransferase containing an SET domain, which is involved in the carcinogenesis of many cancer types through monomethylation of the histone H4 lysine 20. However, its prognostic value and underlying mechanisms in gastric adenocarcinoma (GA) have not been extensively studied. Here, we assessed SETD8 expression and its relationship with clinicopathological parameters, cancer stemness-related proteins, cell cycle-related proteins, and PI3K/Akt pathway proteins in GA. SETD8 expression in GA tissues was correlated with the primary tumor stage, lymph node metastasis, tumor size, gross type, and clinical stage. SETD8 was an independent predictor of poor overall survival of patients with GA. Cox regression analysis showed that SETD8 is a potential biomarker of unfavorable clinical outcomes in patients with GA. Moreover, SETD8 overexpression was associated with cancer stemness-related genes, cell cycle-related genes, and PI3K/Akt/NF-κB pathway genes in clinical GA tissue samples. SETD8 silencing downregulated the expression of cancer stemness-associated genes (LSD1 and SOX2) and inhibited GA cell proliferation, spheroid formation, invasion, and migration. Additionally, LY294002 significantly reduced the expression of SETD8, pAkt-Ser473, pPI3K-p85, and NFκB-p65 in MKN74 and MKN28 cells. SETD8 may be a novel cancer stemness-associated protein and potential prognostic biomarker in GA.

SETD8 is a prognostic biomarker that contributes to stem-like cell properties in non-small cell lung cancer

SETD8 is a lysine methyltransferase containing an SET domain and has been reported to regulate various biological processes, including carcinogenesis. However, its prognostic value and mechanisms of action in non-small cell lung cancer (NSCLC) have not been extensively studied. Here, we assessed SETD8 expression and its relationship with clinicopathological parameters, cancer stemness proteins, and cell cycle-regulating proteins in NSCLC. SETD8 expression in NSCLC tissues was correlated with primary tumor stage, lymph node metastases, and clinical stage. Moreover, SETD8 was an independent predictor of poor overall survival in NSCLC. A Cox regression analysis showed that SETD8 was a potential biomarker of unfavorable clinical outcomes in patients with NSCLC. SETD8 overexpression was associated with cancer stemness-related genes and cell cycle-related genes in NSCLC tissue samples. SETD8 silencing significantly reduced the expression of cancer stemness-associated genes (CD44, LGR5, and SOX2) and inhibited NSCLC cell proliferation, spheroid formation, invasion, and migration. Our findings demonstrate that SETD8 may be a novel cancer stemness-associated protein and a potential prognostic biomarker in NSCLC.

Downregulation of histone methyltransferase SET8 inhibits progression of hepatocellular carcinoma

The expression of lysine methyltransferase SET8, which is involved in carcinogenesis of many types of human cancers through monomethylation of histone H4 lysine 20 (H4K20), is associated with the prognosis of hepatocellular carcinoma (HCC). We performed a functional analysis for SET8 to assess its effect on HCC progression. SET8 knockdown inhibited proliferation, migration and invasion of HCC cells. SET8 knockdown also inhibited tumour growth in a human xenograft mouse model. Overexpression of SET8 displayed the reverse effect, while treatment with the SET8 inhibitor UNC0379 produced an effect similar to SET8 knockdown. In addition, drug sensitivity testing in SET8-siRNA transfected HCC cells indicated that docetaxel inhibited cell growth dramatically, as demonstrated by the Cell Counting Kit-8 (CCK-8) assay. Furthermore, gene expression microarray analysis showed that genes altered after SET8 knockdown were clustered in pathways related to tumorigenesis and metastasis. Our data suggests that targeting SET8 for HCC therapy can inhibit the proliferation and invasion of HCC cells as well as increase their sensitivity to chemotherapy.

The ubiquitin-specific protease USP17 prevents cellular senescence by stabilizing the methyltransferase SET8 and transcriptionally repressing p21

Su(var)3-9, Enhancer-of-zeste, and Trithorax (SET) domain-containing protein 8 (SET8) is the sole enzyme that monomethylates Lys-20 of histone H4 (H4K20). SET8 has been implicated in the regulation of multiple biological processes, such as gene transcription, the cell cycle, and senescence. SET8 quickly undergoes ubiquitination and degradation by several E3 ubiquitin ligases; however, the enzyme that deubiquitinates SET8 has not yet been identified. Here we demonstrated that ubiquitin-specific peptidase 17-like family member (USP17) deubiquitinates and therefore stabilizes the SET8 protein. We observed that USP17 interacts with SET8 and removes polyubiquitin chains from SET8. USP17 knockdown not only decreased SET8 protein levels and H4K20 monomethylation but also increased the levels of the cyclin-dependent kinase inhibitor p21. As a consequence, USP17 knockdown suppressed cell proliferation. We noted that USP17 was down-regulated in replicative senescence and that USP17 inhibition alone was sufficient to trigger cellular senescence. These results reveal a regulatory mechanism whereby USP17 prevents cellular senescence by removing ubiquitin marks from and stabilizing SET8 and transcriptionally repressing p21.

Monomethyltransferase SET8 facilitates hepatocellular carcinoma growth by enhancing aerobic glycolysis

Hepatocellular carcinoma (HCC) is one of the most aggressive cancers worldwide. Despite such a public health importance, efficient therapeutic agents are still lacking for this malignancy. Most tumor cells use aerobic glycolysis to sustain anabolic growth, including HCC, and the preference of glycolysis often leads to a close association with poorer clinical outcomes. The histone methyltransferase SET8 plays crucial roles in controlling cell-cycle progression, transcription regulation, and tumorigenesis. However, it remains largely undefined whether SET8 affects the glucose metabolism in HCC. Here, we report that upregulation of SET8 is positively correlated with a poor survival rate in HCC patients. Both in vitro and in vivo studies revealed that SET8 deficiency conferred an impaired glucose metabolism phenotype and thus inhibited the progression of HCC tumors. By contrast, SET8 overexpression aggravated the glycolytic alterations and tumor progression. Mechanistically, SET8 directly binds to and inactivates KLF4, resulting in suppression of its downstream SIRT4. We also provided further evidence that mutations in SET8 failed to restrain the transactivation of SIRT4 by KLF4. Our data collectively uncover a novel mechanism of SET8 in mediating glycolytic metabolism in HCC cells and may provide a basis for targeting SET8 as a therapeutic strategy in HCC.

Association of an miR-502-binding site polymorphism in the 3'-untranslated region of SET8 with colorectal cancer

The histone methyltransferase SET8 is regulated by microRNA-502 through the binding site in its 3'-untranslated region, and the rs16917496 polymorphism at the miR-502-binding site in the SET8 gene has been implicated in a number of cancer types. The rs16917496 polymorphism including CC, CT and TT genotypes was analyzed in patients with colorectal cancer; the CC genotype was identified to be independently associated with longer post-operative survival times using multivariate analysis (relative risk, 2.406; 95% confidence interval, 1.017-5.691; P=0.046). In addition, decreased SET8 expression was associated with the SET8 CC genotype and longer survival times for patients with colorectal cancer. The results of the present study indicated that miR-502 mediates SET8 expression at least partly by altering the binding affinity between miR-502 and SET8 so as to modify the colorectal cancer outcome. The results indicate that SET8 may be a novel target for colorectal cancer therapy.

KMT5A promotes metastasis of clear cell renal cell carcinoma through reducing cadherin-1 expression

Clear cell renal cell carcinoma (ccRCC) is one of the most common types of kidney cancer and is accompanied by a poor prognosis due to a high potential for metastasis and recurrence. The mechanism of ccRCC metastasis is not well known. N-lysine methyltransferase KMT5A serves a crucial role in the progression of human cancer; however, the function of KMT5A in the development of ccRCCs has not yet been investigated, which has triggered an interest in investigating the potential association between KMT5A and ccRCC. The present study demonstrates for the first time that KMT5A is a driving factor in ccRCC metastasis. The KMT5A expression level was revealed to be significantly higher in ccRCC tissues compared with adjacent normal tissues. Patients with ccRCC whose tumors expressed high levels of KMT5A were demonstrated to have significantly shorter postoperative survival times. In vitro knockdown of KMT5A expression in 786-O cells inhibited cell migration and invasion. KMT5A reduced cadherin-1 (CDH1) protein levels by directly inhibiting its transcription. The CDH1 mRNA levels were inversely correlated with KMT5A expression in ccRCC samples. Patients with high tumor KMT5A or low CDH1 levels had the poorest prognosis with the shortest overall survival (OS) time, and this combination was demonstrated to be an independent prognostic indicator for patient OS time in ccRCC, more accurate than monitoring KMT5A or CDH1 alone. Together, these results indicate that KMT5A serves a vital role in ccRCC development and progression, and it may be a novel target for ccRCC treatment and prevention.

The association between rs16917496 T/C polymorphism of SET8 gene and cancer risk in Asian populations: a meta-analysis

Epidemiological studies have demonstrated close associations between SET8 rs16917496 T/C polymorphism and cancer risk, but the results of published studies were not consistent. We therefore performed this meta-analysis to explore the associations between rs16917496 T/C polymorphism and cancer risk. Five online databases were searched. Odds ratios (ORs) with a 95% confidence interval (CI) were calculated to assess the association between rs16917496 T/C polymorphism and cancer risk. In addition, heterogeneity, accumulative, sensitivity analysis, and publication bias were conducted to check the statistical power. Overall, 13 publications involving 5878 subjects were identified according to included criteria. No significant cancer risk was observed in genetic model of SET8 rs16917496 T/C polymorphism in Asian populations (C vs. T: OR = 1.04, 95%CI = 0.88–1.23, P = 0.63%; TC vs. TT: OR = 1.17, 95%CI = 0.96–1.24, P = 0.11%; CC vs. TT: OR = 0.90, 95%CI = 0.60–1.37, P = 0.63; TC+CC vs. TT: OR = 1.11, 95%CI = 0.90–1.38, P = 0.33; CC vs. TT+TC: OR = 0.92, 95%CI = 0.65–1.30, P = 0.63). Furthermore, similar associations were found in the subgroup analysis of race diversity, control design, genotyping methods, and different cancer types. In summary, our meta-analysis indicated that the SET8 rs16917496 T/C polymorphism may not play a critical role in cancer development in Asian populations.

Analysis of mutations in CDC27, CTBP2, HYDIN and KMT5A genes in carotid paragangliomas

Carotid paragangliomas (CPGLs) are rare neuroendocrine tumors that arise from paraganglionic tissue of the carotid body localizing at the bifurcation of carotid artery. These tumors are slowly growing, but occasionally they become aggressive and metastatic. Surgical treatment remains high-risk and extremely challenging; radiation and chemotherapy are poorly effective. The study of molecular pathogenesis of CPGLs will allow developing novel therapeutic approaches and revealing biomarkers. Previously, we performed the exome sequencing of 52 CPGLs and estimated mutational load (ML). Paired histologically normal tissues or blood were unavailable, so potentially germline mutations were excluded from the analysis with strong filtering conditions using 1000 Genomes Project and ExAC databases. In this work, ten genes (ZNF717, CDC27, FRG2C, FAM104B, CTBP2, HLA-DRB1, HYDIN, KMT5A, MUC3A, and PRSS3) characterized by the highest level of mutational load were analyzed. Using several prediction algorithms (SIFT, PolyPhen-2, MutationTaster, and LRT), potentially pathogenic mutations were identified in four genes (CDC27, CTBP2, HYDIN, and KMT5A). Many of these mutations occurred in the majority of cases, and their mutation type was checked using exome sequencing data of blood prepared with the same exome enrichment kit that was used for preparation of exome libraries from CPGLs. The majority of the mutations were germline that can apparently be associated with annotation errors in 1000 Genomes Pro ject and ExAC. However, part of the mutations identified in CDC27, CTBP2, HYDIN, and KMT5A remain potentially pathogenic, and there is a large body of data on the involvement of these genes in the formation and progression of other tumors. This allows considering CDC27, CTBP2, HYDIN, and KMT5A genes as potentially associated with CPGL pathogenesis and requires taking them into account in further investigations. Thus, there is a necessity to improve the methods for identification of cancer-asso ciated genes as well as pathogenic mutations. 

The SMYD3 VNTR 3/3 polymorphism confers an increased risk and poor prognosis of hepatocellular carcinoma in a Chinese population

OBJECTIVE

Hepatocellular carcinoma (HCC) is one of the most lethal human malignancies in China, and the genetic link of hepatocarcinogenesis remains to be defined. Thus, we explored the role of SET and myeloid translocation protein 8, Nervy, and DEAF1 (MYND) domain containing protein 3 (SMYD3) gene polymorphism on risk and prognosis of HCC.

METHODS

A total of 236 patients with HCC who received treatment in Affiliated Hospital of Jining Medical University for the first time and 230 healthy individuals were enrolled in the study. After DNA extraction for all the subjects, polymerase chain reaction (PCR) was used to amplify and sequence variable numbers of tandem repeat (VNTR) loci of SMYD3 gene. SMYD3 gene was genotyped and its frequency distribution was calculated. Age, education level, income, smoking and drinking history, HCC family history, tumor node metastasis (TNM) staging, maximum tumor diameter, lymph node metastasis (LNM) etc. were investigated. Correlation of SMYD3 gene polymorphism and other risk factors with the occurrence and prognosis of HCC was analyzed.

RESULTS

The family history of HCC, drinking history, cirrhosis, and HBV or/and HCV infection, SMYD3 VNTR 3/3 were more frequently observed in subjects with HCC. Patients with SMYD3 VNTR 3/3 genotype, drinking-history, family history of HCC, cirrhosis and hepatitis B virus (HBV), TNM staging, maximum tumor diameter, LNM were more vulnerable to HCC. Besides, patients with SMYD3 VNTR 3/3 genotype had lower 2- and 3-year survival rate. The COX regression analysis revealed that drinking history, family history of HCC, SMYD3 VNTR 3/3 genotype, TNM staging, and LNM were all related to the prognosis of HCC.

CONCLUSION

This study indicates that drinking history, family history of HCC and SMYD3 VNTR 3/3, TNM staging, maximum tumor diameter, LNM might be risk factors for HCC, and SMYD3 VNTR 3/3 might contribute to a lower 2- and 3-year survival rate of patients with HCC.

Gene Expression Analysis of Two Epithelial-mesenchymal Transition-related Genes: Long Noncoding RNA-ATB and SETD8 in Gastric Cancer Tissues

Background

Cancer is the second cause of death after cardiovascular diseases worldwide. Tumor metastasis is the main cause of death in patients with cancer; therefore, unraveling the molecular mechanisms involved in metastasis is critical. Epithelial-mesenchymal transition (EMT) is believed to promote tumor metastasis. Based on the critical roles of long noncoding RNA-ATB (lncRNA-ATB) and SETD8 genes in cancer pathogenesis and EMT, in this study, we aimed to assess expression profile and clinicopathological relevance of these two genes in human gastric cancer.

Materials and Methods

Quantitative real-time polymerase chain reaction was performed to assess these gene expressions in gastric cancer tissues and various cell lines. The associations between these gene expressions and clinicopathological characteristics were also analyzed.

Results

Insignificant downregulation of lncRNA-ATB and significant upregulation of SETD8 in cancerous versus noncancerous gastric tissues were observed. Among different examined cell lines, all displayed both genes expression. Except for a significant inverse correlation between the expression levels of lncRNA-ATB and depth of invasion (T) and a direct association between SETD8 levels and advanced tumor grades, no significant association was found with other clinicopathological characteristics.

Conclusion

lncRNA-ATB and SETD8 genes may play a critical role in gastric cancer progression and may serve as potential diagnostic/prognostic biomarkers in cancer patients.

Downregulation of SETD8 by miR-382 is involved in glioma progression

BACKGROUND

SETD8 (named PR-SET7 or KMT5a) has been reported to regulate various biological processes including carcinogenesis. However, the role of SETD8 in glioma progression has not been investigated.

METHOD

qPCR and western blot were used to detect the expression levels of miR-382 and SETD8. MTT and wound healing assay used to detect the cell proliferation and migratory capability. A predicted target of miR-382 (SETD8) was first validated using a luciferase assay.

RESULTS

In this study, we found that SETD8 expression was evidently upregulated in glioma tissues and glioma cells, compared with the adjacent normal tissues and normal human astrocytes (NHA). Next, we showed that SETD8 evidently induced cell proliferation and migration in vitro and in vivo. In addition,dual-luciferase assays revealed that miR-382 directly regulates oncogenic SETD8 expression in U87 and U251 cells. Finally a statistically significant inverse correlation of miR-382 and SETD8 expression was observed in 30 glioma patients.

CONCLUSION

These data indicated that oncogenic SETD8 was regulated by miR-382 and involved glioma progression, revealing new therapeutic targets for glioma cancer.

A functional single nucleotide polymorphism of SET8 is prognostic for breast cancer

A single-nucleotide polymorphism (SNP) locus rs16917496 (T > C) within the 3′-untranslated region (3′-UTR) of SET8 was associated with susceptibility in several malignancies including breast cancer. To further elucidate the prognostic relevance of this SNP in breast cancer, we conducted a clinical study as well as SET8 expression analysis in a cohort of 1,190 breast cancer patients. We demonstrated the expression levels of SET8 in TT genotype were higher than in CC genotypes, and high levels of SET8 were associated with poor survival. SET8 expression was significantly higher in breast tumor tissue than in paired adjacent normal tissue. In addition, survival analysis in 315 patients showed SNP rs16917496 was an independent prognostic factor of breast cancer outcome with TT genotype associated with poor survival compared with CC/CT genotypes. Thus, this SNP may serve as a genetic prognostic factor and a treatment target for breast cancer. Future studies are warranted.

Genetic polymorphisms of microRNA machinery genes predict overall survival of esophageal squamous carcinoma

BACKGROUND

MicroRNA (miRNA)-related single nucleotide polymorphisms (miR-SNPs) in miRNA processing machinery genes are implicated in carcinogenesis, as they change the expression profiles of miRNA. Six miR-SNPs in miRNA processing machinery genes, including Dicer (rs3742330), RAN (rs14035), XPO5 (rs11077), TNRC6B (rs9623117), GEMIN3 (rs197412), and GEMIN4 (rs2740348), were evaluated for their association with esophageal squamous cell carcinoma (ESCC).

METHODS

The miR-SNP of the miRNA processing genes were genotyped using the polymerase chain reaction-ligase detection reaction (PCR-LDR) assay, while the XPO5 expression levels in ESCC tissues were measured by immunochemistry methods.

RESULTS

Patients carrying the rs11077 AA allele exhibited a significantly increased lifespan than AC+CC carriers, as determined by univariate and multivariate analyses (relative risk: 2.490; 95% confidence interval [CI]: 1.225-5.058; P=.012). Furthermore, the rs11077 AA genotype displayed a trend for high XPO5 expression in ESCC tissues by immunochemistry analysis, and these high XPO5 expression levels were also associated with high survival rates among ESCC patients.

CONCLUSION

Our results suggested that the miRNA machinery gene expression-associated miR-SNPs would modify cancer outcomes; in this light, XPO5 may be an important new target for ESCC therapy.

miR-502-mediated histone methyltransferase SET8 expression is associated with clear cell renal cell carcinoma risk

Genetic variants may affect the interactions between microRNAs (miRNAs/miRs) and their target genes by modulating their binding affinity or by creating, or destroying a miRNA-binding site. SET domain containing (lysine methyltransferase) 8 (SET8) is the sole lysine methyltransferase that catalyzes the monomethylation of histone H4 lysine 20, and is associated with tumor growth, invasion and metastasis. In the present study, the rs16917496 polymorphism within the miR-502 binding site of the SET8 mRNA 3' untranslated region (3'UTR) in patients with clear cell renal cell carcinoma (ccRCC) and healthy controls was genotyped. The SET8 CC genotype was associated with a decreased ccRCC risk compared with the CT [P=0.003; odds ratio (OR)=0.318; 95% confidence interval (CI), 0.146-0.691], TT (P=0.011; OR=0.402; 95% CI, 0.197-0.819) and CT+TT (P=0.004; OR=0.370; 95% CI, 0.186-0.736) genotypes. The SET8 CC genotype was associated with reduced SET8 expression based on immunostaining of ccRCC tissue. Low SET8 protein levels were negatively associated with tumor-node-metastasis staging in patients with ccRCC according to the size of tumor and lymph node metastases. SET8-knockdown inhibited renal carcinoma 786-O cell proliferation, migration and invasion. c-Myc and matrix metalloproteinase-7 mRNA expression were downregulated upon SET8-knockdown in renal carcinoma 786-O cells. These data indicated that SET8 may be a functional tumor promoter and that its activation, which is partially regulated by changing the miR-502 and SET8 3'UTR binding affinity, may serve an important role in ccRCC development.

Polymorphism (rs16917496) at the miR-502 Binding Site of the Lysine Methyltransferase 5A (SET8) and Its Correlation with Colorectal Cancer in Iranians

Background:

One of the gene expression regulatory mechanisms is mediated by small noncoding RNAs called microRNA (miRNA). They interact with a recognition sequence located mostly in 3’-untranslated regions (3’-UTRs) of mRNAs. Polymorphisms in miRNAs recognition sequences could affect gene expression which in turn may alter disease susceptibility. SET8, a member of the SET domain-containing methyltransferase, acts in a variety of biological processes such as genomic stability. Here, we report correlation of rs16917496 polymorphism, located in the recognition sequence of miR-502 within 3’-UTR of SET8, with colorectal cancer (CRC) in Iranians.

Materials and Methods:

One hundred and seventy CRC patients and 170 noncancer counterparts were recruited in this case–control study. Genotyping of rs16917496 was performed using polymerase chain reaction-restriction fragment length polymorphism method.

Results:

There was no significant association of rs16917496 with CRC in population under study (P value for genotype and allele distribution were >0.05). However, stratification analysis based on smoking status revealed that TT+TC genotypes of SET8 rs16917496 are strongly associated with increased risk of CRC (odds ratio: 5.8, 95% confidence interval: 1.37–24.34, P - 0.005) in smoker subgroup.

Conclusion:

Correlation of rs16917496 T allele with CRC in smokers is emphasizing the importance of individuals’ genotype in the recruitment of adverse health hazards of smoking more profoundly for certain people compared to others.

Functional polymorphism at the miR-502-binding site in the 3' untranslated region of the SETD8 gene increased the risk of prostate cancer in a sample of Iranian population

MicroRNAs (miRNAs), a class of non-coding RNAs, bind to the 3' untranslated regions (3'-UTRs) of target mRNAs and regulate gene expression. Genetic variations in miRNA binding domains influence the susceptibility to several diseases such as cancer. Several studies investigated the impact of single-nucleotide polymorphism (SNP) rs16917496 T>C within the 3'-UTR of SETD8 on cancer susceptibility, but the results were controversial. In addition, no study has been conducted to inspect the impact of this SNP in prostate cancer (PCa). Thus, the present study aimed to find out the possible association between rs16917496 polymorphism at the 3'UTR of SETD8 and PCa risk. This case-control study was done on 169 patients with pathologically confirmed PCa and 182 benign prostatic hyperplasia (BPH). Genotyping was done using PCR-RFLP method. The findings revealed that rs16917496 variant significantly increased the risk of PCa in codominant (OR=2.54, 95%CI=1.50-4.30, p<0.001, TC VS TT and OR=3.03, 95%CI=1.63-5.66, p<0.001, CC vs TT), dominant (OR=2.86, 95%CI=1.62-4.43, p<0.001, p<0.001). The C allele significantly increased the risk of PCa (OR=1.72, 95%CI=1.28-2.33, p<0.001) compared to T allele. In conclusion, the findings indicated that rs16917496 polymorphism may be a risk for predisposition to PCa in an Iranian population. Further studies with larger sample sizes and different ethnicities are required to confirm our findings.

MiRNAs and miRNA Polymorphisms Modify Drug Response

Differences in expression of drug response-related genes contribute to inter-individual variation in drugs’ biological effects. MicroRNAs (miRNAs) are small noncoding RNAs emerging as new players in epigenetic regulation of gene expression at post-transcriptional level. MiRNAs regulate the expression of genes involved in drug metabolism, drug transportation, drug targets and downstream signal molecules directly or indirectly. MiRNA polymorphisms, the genetic variations affecting miRNA expression and/or miRNA-mRNA interaction, provide a new insight into the understanding of inter-individual difference in drug response. Here, we provide an overview of the recent progress in miRNAs mediated regulation of biotransformation enzymes, drug transporters, and nuclear receptors. We also describe the implications of miRNA polymorphisms in cancer chemotherapy response.

The emerging role of lysine methyltransferase SETD8 in human diseases

SETD8/SET8/Pr-SET7/KMT5A is the only known lysine methyltransferase (KMT) that monomethylates lysine 20 of histone H4 (H4K20) in vivo. Lysine residues of non-histone proteins including proliferating cell nuclear antigen (PCNA) and p53 are also monomethylated. As a consequence, the methyltransferase activity of the enzyme is implicated in many essential cellular processes including DNA replication, DNA damage response, transcription modulation, and cell cycle regulation. This review aims to provide an overview of the roles of SETD8 in physiological and pathological pathways and to discuss the progress made to date in inhibiting the activity of SETD8 by small molecules, with an emphasis on their discovery, selectivity over other methyltransferases and cellular activity.

A new layer of degradation mechanism for PR-Set7/Set8 during cell cycle

Set8 is critically involved in transcription regulation, cell cycle progression and genomic stability. Emerging evidence has revealed that E3 ubiquitin ligases such as CRL4^cdt2 and SCF^Skp2 regulate Set8 protein abundance. However, it is unclear whether other E3 ligase(s) could govern Set8 level for proper cell cycle progression in response to genotoxic stress such as UV irradiation. Recently, we report that the SCF^β-TRCP complex regulates Set8 protein stability by targeting it for ubiquitination and subsequent degradation. Notably, Set8 interacts with the SCF^β-TRCP E3 ligase complex. We further revealed a critical role of CKI in SCF^β-TRCP-mediated degradation of Set8. Mechanistically, CKI-mediated phosphorylation of Set8 at the S253 site promotes its destruction by SCF^β-TRCP. Importantly, SCF^β-TRCP-dependent Set8 destruction also contributes to the tight control of cell proliferation and cell cycle progression, in response to UV irradiation. Here, we summarize our new findings regarding the crucial role of β-TRCP in CKI-mediated Set8 degradation, which could provide new evidence to support that dysregulation of a tight regulatory network of Set8 could lead to aberrant cell cycle process.

miR-502 medaited histone methyltransferase SET8 expression is associated with outcome of esophageal squamous cell carcinoma

The histone methyltransferase SET8, whose expression is regulated by miR-502 though the binding site in the 3′ UTR of SET8, implicated in cancer development. Single nucleotide polymorphism (SNP) of rs16917496 located in the miR-502 and SET8 binding site was analyzed in esophageal squamous cell carcinoma (ESCC) patients, the SET8 C/C genotype was independently associated with longer post-operative survival by multivariate analysis (relative risk, 2.250; 95% CI, 1.041–4.857; p = 0.039). Moreover, the reduced SET8 expression mediated by SET8 C/C genotype was associated with longer ESCC survival. Functional assay indicated that the SET8 knock down could inhibit proliferation and promote apoptosis of ESCC cells. The subsequent assay also showed the markedly inhibition of ESCC cell migration and invasion by SET8 knock down. Our data suggested that the altering SET8 expression, which is mediated at least partly by miR-502 through changing the binding affinity between miR-502 and SET8 3′ UTR, could modify the ESCC outcome by inhibiting the proliferation and invasion as well as promoting the apoptosis of ECSS cell. Our data indicated that SET8 was a new target for ESCC therapy.

Prognostic significance of Dicer expression in hepatocellular carcinoma

Dicer is a RNaseIII endonuclease of the microRNA processing pathway, which is implicated in carcinogenesis of various types of human cancer. The present study assessed the expression level of Dicer in hepatocellular carcinoma (HCC) tissue to evaluate its association with HCC tumorigenesis. A low expression of Dicer was significantly associated with a shorter postoperative survival time of patients with HCC, which was assessed using the log-rank test with Kaplan-Meier survival analysis. Multivariate analysis identified that Dicer expression was an independent predictor for HCC outcome (relative risk, 0.660; 95% confidence interval, 0.506–0.861; P=0.002). A functional assay demonstrated that Dicer overexpression inhibited the proliferation and promoted the apoptosis of HCC cells. In addition, a Transwell assay revealed that Dicer markedly inhibited the migration and invasion of HCC cells. The present findings indicate that Dicer expression modified the outcomes of HCC patients by inhibiting proliferation, promoting apoptosis and inhibiting metastasis of HCC cells.

MiR-502/SET8 regulatory circuit in pathobiology of breast cancer

Our previous research and extensive epidemiological studies reproducibly demonstrated that miR-502 potentially targeted the expression of H4K20 methyltransferase SET8 in a wide spectrum of cancer. Yet, the direct targeting of SET8 by miR-502 has not been definitively proven. The clinical significance of the miR-502/SET8 regulatory circuit is also not clear. Here, we conducted cell-based experiments and clinical studies in a cohort of 279 breast cancer samples. We provide evidence that SET8 is a direct target of miR-502. Treatment with miR-502 or downregulation of SET8 suppressed cell proliferation and cell cycle, and reduced cell migration, invasion and EMT. Clinical analyses showed the miR-502 expression was lower in tumor tissues than in adjacent non-tumor tissues and had a significant inverse correlation with that of SET8. Furthermore, high expression of SET8 was significantly associated with poor overall survival (OS) and disease free survival (DFS) of breast cancer. The low expression ratio of miR-502 to SET8 mRNA was also significantly associated with poor OS. Thus, the miR-502/SET8 regulatory circuit emerges as a key regulator of the pathobiology of cancer and a focal point for possible therapeutic intervention.

SCF(β-TRCP) promotes cell growth by targeting PR-Set7/Set8 for degradation

The Set8/PR-Set7/KMT5a methyltransferase plays critical roles in governing transcriptional regulation, cell cycle progression and tumorigenesis. Although CRL4(Cdt2) was reported to regulate Set8 stability, deleting the PIP motif only led to partial resistance to ultraviolet-induced degradation of Set8, indicating the existence of additional E3 ligase(s) controlling Set8 stability. Furthermore, it remains largely undefined how DNA damage-induced kinase cascades trigger the timely destruction of Set8 to govern tumorigenesis. Here, we report that SCF(β-TRCP) earmarks Set8 for ubiquitination and degradation in a casein kinase I-dependent manner, which is activated by DNA-damaging agents. Biologically, both CRL4(Cdt2) and SCF(β-TRCP)-mediated pathways contribute to ultraviolet-induced Set8 degradation to control cell cycle progression, governing the onset of DNA damage-induced checkpoints. Therefore, like many critical cell cycle regulators including p21 and Cdt1, we uncover a tight regulatory network to accurately control Set8 abundance. Our studies further suggest that aberrancies in this delicate degradation pathway might contribute to aberrant elevation of Set8 in human tumours.

MicroRNAs as biomarkers for hepatocellular carcinoma diagnosis and prognosis

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world, and it is the second leading cause of cancer-related deaths. Despite improvements in HCC therapy, the overall survival rate is still very low because of the late detection of the tumors. Thus, early detection of HCC offers the best chance of survival for patients. MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs involved in the regulation of gene expression and protein translation. Many studies have shown that they played a very important role in cancer progresses and outcomes. The aberrant expression of miRNAs is common in various human malignancies and it modulates cancer-associated genomic regions or fragile sites. As for the relationship between miRNAs and HCC, several studies have demonstrated that the aberrant expression of specific miRNAs can be detected in HCC patients' serum and plasma or HCC cells and tissues, and miRNAs have shown great promise as diagnostic and prognostic markers for HCC. In the present review, we discussed the applications of miRNAs as biomarkers for HCC diagnosis and prognosis, and the association between miRNAs polymorphisms and the risk of HCC as well.

A polymorphism at the microRNA binding site in the 3' untranslated region of RYR3 is associated with outcome in hepatocellular carcinoma

Objective

MicroRNAs can bind to the 3′ untranslated regions (UTRs) of messenger RNAs, where they interfere with the translation of targeting genes, thereby regulating cell differentiation, apoptosis, and tumorigenesis. In this study, three microRNA binding site single nucleotide polymorphisms (SNPs) located in the 3′ UTR of RYR3 (rs1044129), C14orf101 (rs4901706), and KIAA0423 (rs1053667) were genotyped to assess their relationships with the risks and outcomes of hepatocellular carcinoma (HCC).

Methods

The SNPs were genotyped with the ligation detection reaction method. Renilla luciferase reporter assays were used to measure the binding affinity between microRNA 367 and RYR3. Survival curves were calculated using the Kaplan–Meier method, and comparisons between the curves were made using the log-rank test. Multivariate survival analysis was performed using a Cox proportional hazards model.

Results

It was found that rs1044129 at the 3′ UTR of RYR3 was related to postoperative survival in HCC, with the AA type associated with longer survival times as per the log-rank test. After adjusting with the Cox model, rs104419 was identified as an independent predictor of HCC survival (relative risk: 1.812; 95% confidence interval: 1.026–3.201; P=0.041). Luciferase analysis also indicated the different binding affinities between the SNPs of rs1044129 and microRNA 367.

Conclusion

The SNP in the microRNA binding site of RYR3 can be used as a valuable biomarker when predicting HCC outcomes.

Single nucleotide polymorphisms of microRNA processing genes and outcome of non-Hodgkin's lymphoma

Objective

microRNA (miRNA)-related single nucleotide polymorphisms (miR-SNPs) in miRNA-processing machinery genes can affect cancer risk, treatment efficacy, and patients’ prognosis by mediating the expression of targeted genes. Five miR-SNPs in miRNA processing machinery genes, including XPO5 (rs11077), RAN (rs14035), TNRC6B (rs9623117), GEMIN3 (rs197412), and GEMIN4 (rs2740348), in 168 non-Hodgkin’s lymphoma (NHL) patients were evaluated for their association with the cancer risk and outcomes associated with NHL.

Materials and methods

miR-SNPs were genotyped using polymerase chain reaction–ligase detection reaction. The survival curves were calculated using the Kaplan–Meier method, and comparisons between the curves were made using the log-rank test. Multivariate survival analysis was performed using a Cox proportional hazards model.

Results

Among the five SNPs, only rs197412 located in the coding region of the GEMIN3 gene was identified; it was independently associated with overall survival in NHL patients, as determined by multivariate analysis (relative risk: 1.649; 95% confidence interval: 1.110–2.449; P=0.013). The prognostic value of this miR-SNP in patient outcomes was also observed in the diffuse large B-cell lymphoma and T-cell lymphoma NHL subtypes.

Conclusion

Our results suggested that the specific genetic variants observed in the miRNA machinery genes may affect NHL survival.

miR-502 inhibits cell proliferation and tumor growth in hepatocellular carcinoma through suppressing phosphoinositide 3-kinase catalytic subunit gamma

MicroRNAs (miRNAs) play a key role in carcinogenesis and tumor progression in hepatocellular carcinoma (HCC). In the present study, we demonstrated that miR-502 significantly inhibits HCC cell proliferation in vitro and tumor growth in vivo. G1/S cell cycle arrest and apoptosis of HCC cells were induced by miR-502. Phosphoinositide 3-kinase catalytic subunit gamma (PIK3CG) was identified as a direct downstream target of miR-502 in HCC cells. Notably, overexpression of PIK3CG reversed the inhibitory effects of miR-502 in HCC cells. Our findings suggest that miR-502 functions as a tumor suppressor in HCC via inhibition of PI3KCG, supporting its utility as a promising therapeutic gene target for this tumor type.

A functional variant at miRNA-122 binding site in IL-1α 3' UTR predicts risk and HPV-positive tumours of oropharyngeal cancer

BACKGROUND

Genetic polymorphisms in the 3' untranslated regions (3' UTRs) targeted by miRNAs alter the strength of miRNA binding in a manner that affects the behaviour of individual miRNAs. An insertion (Ins)/deletion (Del) polymorphism (rs3783553) in the 3' UTR of IL-1α may disrupt a binding site for miRNA-122. IL-1α plays an important role in inflammation, immunity and defense against infection. Thus, we hypothesised that the rs3783553 polymorphism affects individual susceptibility to human papillomavirus (HPV)-associated oral squamous cell carcinoma (OSCC).

METHODS

We genotyped the rs3783553 polymorphism; and determined HPV16 L1 serology, tumour HPV16 DNA and serum IL-1α expression. Univariate/multivariable logistic regression models were used to calculate associations.

RESULTS

We found that HPV16 L1 seropositivity alone was associated with an increased risk of OSCC (Odds ratio (OR), 3.1; 95% confidence interval (CI), 2.1-4.6), and the risk of HPV16-associated OSCC was modified by the rs3783553 polymorphism. Patients with both HPV16 L1 seropositivity and Del/Del genotype for the rs3783553 had the highest risk of OSCC when using patients with HPV16 L1 seronegativity and Ins/Del+Ins/Ins genotypes as a comparison group. Notably, that effect modification was particularly pronounced in several subgroups (e.g. SCCOP, never-smokers and never-drinkers). The patients with Del/Del genotype were approximately 3.0 times more likely to have HPV16-positive squamous cell carcinoma of the oropharynx (SCCOP) tumours compared to those patients with Ins/Del+Ins/Ins genotypes. Additionally, functional relevance of this variant was characterised to explore the genotype-phenotype correlation.

CONCLUSION

These results suggest that IL-1α 3' UTR rs3783553 polymorphism may be functional and influence susceptibility to HPV16-associated OSCC, particularly for SCCOP. Validation of our findings is warranted.

Association of a miR-502-binding site single nucleotide polymorphism in the 3'-untranslated region of SET8 and the TP53 codon 72 polymorphism with cervical cancer in the Chinese population

OBJECTIVE

This study was conducted to identify whether polymorphic variants of set domain-containing protein 8 (SET8) and tumor protein p53 (TP53) codon 72, either independently or jointly, might be associated with increased risk for cervical cancer.

METHODS

We genotyped SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA from 114 cervical cancer patients and 200 controls using the polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing.

RESULTS

The frequency of SET8 CC (odds ratios (OR) = 2.717, 95% CI=1.436-5.141) or TP53 GG (OR=2.168, 95% CI=1.149-4.089) genotype was associated with an increased risk of cervical cancer on comparison with the SET8 TT or TP53 CC genotypes, respectively. In additional, interaction between the SET8 and TP53 polymorphisms increased the risk of cervical cancer in a synergistic manner, with the OR being 9.913 (95% CI=2.028-48.459) for subjects carrying both SET8 CC and TP53 GG genotypes.

CONCLUSION

These data suggest that there are significant associations between the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism with cervical cancer in Chinese, and there is a gene-gene interaction.

Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation

Setd8 is the sole histone methyltransferase in mammals capable of monomethylating histone H4 lysine 20 (H4K20me1). Setd8 is expressed at significantly higher levels in erythroid cells than any other cell or tissue type, suggesting that Setd8 has an erythroid-cell-specific function. To test this hypothesis, stable Setd8 knockdown was established in extensively self-renewing erythroblasts (ESREs), a well-characterized, nontransformed model of erythroid maturation. Knockdown of Setd8 resulted in impaired erythroid maturation characterized by a delay in hemoglobin accumulation, larger mean cell area, persistent ckit expression, incomplete nuclear condensation, and lower rates of enucleation. Setd8 knockdown did not alter ESRE proliferation or viability or result in accumulation of DNA damage. Global gene expression analyses following Setd8 knockdown demonstrated that in erythroid cells, Setd8 functions primarily as a repressor. Most notably, Gata2 expression was significantly higher in knockdown cells than in control cells and Gata2 knockdown rescued some of the maturation impairments associated with Setd8 disruption. Setd8 occupies critical regulatory elements in the Gata2 locus, and knockdown of Setd8 resulted in loss of H4K20me1 and gain of H4 acetylation at the Gata2 1S promoter. These results suggest that Setd8 is an important regulator of erythroid maturation that works in part through repression of Gata2 expression.

Complex interactions between microRNAs and hepatitis B/C viruses

MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate the expression of many target genes via mRNA degradation or translation inhibition. Many studies have shown that miRNAs are involved in the modulation of gene expression and replication of hepatitis B virus (HBV) and hepatitis C virus (HCV) and play a pivotal role in host-virus interactions. Increasing evidence also demonstrates that viral infection leads to alteration of the miRNA expression profile in hepatic tissues or circulation. The deregulated miRNAs participate in hepatocellular carcinoma (HCC) initiation and progression by functioning as oncogenes or tumor suppressor genes by targeting various genes involved in cancer-related signaling pathways. The distinct expression pattern of miRNAs may be a useful marker for the diagnosis and prognosis of virus-related diseases considering the limitation of currently used biomarkers. Moreover, the role of deregulated miRNA in host-virus interactions and HCC development suggested that miRNAs may serve as therapeutic targets or as tools. In this review, we summarize the recent findings about the deregulation and the role of miRNAs during HBV/HCV infection and HCC development, and we discuss the possible mechanism of action of miRNAs in the pathogenesis of virus-related diseases. Furthermore, we discuss the potential of using miRNAs as markers for diagnosis and prognosis as well as therapeutic targets and drugs.

MicroRNA binding site polymorphisms as biomarkers in cancer management and research

MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression. They have been implicated in a broad range of biological processes, and miRNA-related genetic alterations probably underlie several human diseases. Single nucleotide polymorphisms of transcripts may modulate the posttranscriptional regulation of gene expression by miRNAs and explain interindividual variability in cancer risk and in chemotherapy response. On the basis of recent association studies published in the literature, the present review mainly summarizes the potential role of miRNAs as molecular biomarkers for disease susceptibility, diagnosis, prognosis, and drug-response prediction in tumors. Many clues suggest a role for polymorphisms within the 3' untranslated regions of KRAS rs61764370, SET8 rs16917496, and MDM4 rs4245739 as SNPs in miRNA binding sites highly promising in the biology of human cancer. However, more studies are needed to better characterize the composite spectrum of genetic determinants for future use of markers in risk prediction and clinical management of diseases, heading toward personalized medicine.

Association of functional polymorphism at the miR-502-binding site in the 3' untranslated region of the SETD8 gene with risk of childhood acute lymphoblastic leukemia, a preliminary report

MicroRNAs (miRNAs), a class of non-coding RNAs, bind to the 3' untranslated regions (UTRs) of mRNAs, where they interfere with translation of genes and are implicated in the pathogenesis of diverse diseases. In the present study, we evaluate the impact of rs16917496 polymorphism within the miR-502 miRNA seed region at the 3'UTR of SEDT8 on childhood acute lymphoblastic leukemia (ALL). This case-control study was done on 75 ALL and 115 healthy children. Genotyping of rs16917496 C/T polymorphism was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The results showed that CT as well as CT + TT decreased the risk of ALL in comparison with CC genotype (odds ratio (OR) = 0.29, 95 % confidence intervals (95 % CI) = 0.11-0.78, P = 0.014 and OR = 0.31, 95 % CI = 0.12-0.82, P = 0.016, respectively). Our results demonstrated that SETD8 rs16917496 C/T polymorphism was associated with decreased risk of developing pediatric ALL in Zahedan, southeast Iran. Larger studies with different ethnicities are desired to validate our findings.

Interferon alpha-inducible protein 27 promotes epithelial-mesenchymal transition and induces ovarian tumorigenicity and stemness

BACKGROUND

Interferon alpha-inducible protein 27 (IFI27) is an interferon alpha-inducible protein, which was found to be upregulated in some cancers, such as breast cancer, squamous cell carcinoma, hepatocellular carcinoma, and serous ovarian carcinoma. However, the role of IFI27 in ovarian cancer remains to be elucidated. This study was designed to investigate the role of IFI27 in ovarian cancer tumorigenicity.

MATERIALS AND METHODS

The expression of IFI27 was examined in ovarian cancer tissues and cell lines by real time quantitative reverse transcription polymerase chain reaction and immunohistochemistry. The cell migration and invasion was investigated by wound healing and transwell invasion assay. The epithelial-mesenchymal transition markers were detected by Western blotting and the stemness was evaluated by sphere formation. The tumor growth was examined in the athymic mice model.

RESULTS

We found that IFI27 is overexpressed in ovarian cancer and associated with patients' survival. Interestingly, we further observed that the expression of IFI27 was associated with the expression of mesenchymal marker vimentin in ovarian cancer. Overexpression of IFI27 induces epithelial-mesenchymal transition and promotes epithelial ovarian cancer cells migration and invasion, tumorigenicity, stemness, and drug resistance. Moreover, overexpression of IFI27 is associated with loss of miR-502 in ovarian cancer. Reexpression of miR-502 inhibits IFI27-induced tumorigenicity, migration, and drug resistance.

CONCLUSIONS

These data suggested that IFI27 may be a potential target for developing novel diagnosis strategies and therapeutic interventions.

Single nucleotide polymorphisms of microRNA processing machinery genes and outcome of hepatocellular carcinoma

MicroRNA (miRNA)-related single nucleotide polymorphisms (miR-SNPs) can affect cancer development, treatment efficacy and patients prognosis. We examined 6 miR-SNPs in miRNA processing machinery genes including exportin 5 (XPO5) (rs11077), Ran-GTPase (RAN) (rs14035), Dicer (rs3742330), Trinucleotide Repeat Containing 6B (TNRC6B) (rs9623117), GEMIN3 (rs197412), GEMIN4 (rs2740348) in 108 surgically resected HCC patients and evaluated the impact of these miR-SNPs on HCC outcome. Among the 6 SNPs, only the A/A genotype of rs11077 located in XPO5 3'UTR was identified to associated independently with worse survival in HCC patients by multivariate analysis with relative risk, 0.395; 95% CI, 0.167-0.933; p = 0.034. This is the first study reporting that polymorphisms related to miRSNPs have prognostic value in hepatocellular carcinoma and identify the A/A genotype of rs11077 SNP site located in XPO5 3'UTR can help to predict worse prognosis in patients.

Association of miR-502-binding site single nucleotide polymorphism in the 3'-untranslated region of SET8 and TP53 codon 72 polymorphism with non-small cell lung cancer in Chinese population

The objective of this study was to identify whether the miR-502-binding site single nucleotide polymorphism (SNP) in the 3'-untranslated region (3'-UTR) of set domain-containing protein 8 (SET8) and the tumor protein p53 (TP53) codon 72 polymorphism were associated with the risk for non-small cell lung cancer (NSCLC), either independently or jointly, among Chinese people from southern Han. The genotypes of SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA were detected using polymerase chain reaction-restriction fragment length polymorphism and direct DNA sequencing in a case-control study on 164 NSCLC cases and 199 controls. The SET8 TT (odds ratio, OR = 2.173, 95% confidence interval, CI = 1.0454.517) or TP53 GG (OR = 2.579, 95% CI = 1.366-4.870) genotype was associated with an increased risk of NSCLC by comparing with the SET8 CC or TP53 CC genotype, respectively. Similar results were obtained in SET8 recessive model (OR = 2.074, 95% CI = 1.019-4.221, P < 0.05), and the dominant and recessive model of TP53 codon 72 were performed, respectively (OR = 1.809, 95% CI = 1.159-2.825, P < 0.05; OR = 1.933, 95% CI = 1.096-3.409, P < 0.05). In addition, interaction between the SET8 and TP53 polymorphisms increased the risk of NSCLC in a multiply manner, with the OR being 3.032 (95%CI = 1.580-5.816) for subjects carrying both SET8 TT and TP53 GG genotypes. Therefore, the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism may be markers of genetic susceptibility to NSCLC in Chinese population, and there is a possible gene-gene interaction in the incidence of NSCLC.

A genetic polymorphism in pre-miR-27a confers clinical outcome of non-small cell lung cancer in a Chinese population

Background

Recent evidence indicates that microRNAs (miRNAs) can function as tumor suppressors and oncogenes. Single nucleotide polymorphisms (SNPs) at miRNA genes can influence the maturation of miRNAs or miRNA-mediated transcriptional regulation. Our objective was to investigate the association of SNPs in deregulated miRNAs with clinical outcome in patients with non-small cell lung cancer (NSCLC) in a Chinese population.

Methods

Deregulated miRNAs in NSCLC and their SNPs were identified through public databases. A single SNP, rs895819 in pre-miR-27a, was found suitable for selection. TaqMan assays were performed for genotyping and to assess the effect on the overall survival (OS) and chemotherapy response in 576 NSCLC patients.

Results

Log-rank test and Cox regression analysis indicated that the G allele of rs895819 was associated with shorter survival and increased risk of death in NSCLC [dominant model: 22.0 vs. 46.0 months, P<0.001; adjusted hazard ratio (HR) = 1.71, 95% confidential interval (CI): 1.12–2.26]. Further stepwise regression analysis suggested that this SNP was an independently unfavorable factor for the prognosis of NSCLC and the effect remained significant in subgroup analysis stratified by clinical parameters and treatment status. Moreover, multivariate logistic regression analysis showed that the subjects with AG/GG genotypes of rs895819 had significantly decreased response rate to platinum-based chemotherapy compared to those with the AA genotype.

Conclusion

Our results suggest that the pre-miR-27a rs895819 polymorphism may influence NSCLC patients’ clinical outcome. Further large sample studies should be used to validate our findings.

Genetic variation in a microRNA-502 minding site in SET8 gene confers clinical outcome of non-small cell lung cancer in a Chinese population

Background

Genetic variants may influence microRNA-target interaction through modulate their binding affinity, creating or destroying miRNA-binding sites. SET8, a member of the SET domain-containing methyltransferase, has been implicated in a variety array of biological processes.

Methods

Using Taqman assay, we genotyped a polymorphism rs16917496 T>C within the miR-502 binding site in the 3′-untranslated region of the SET8 gene in 576 non-small cell lung cancer (NSCLC) patients. Functions of rs16917496 were investigated using luciferase activity assay and validated by immunostaining.

Results

Log-rank test and cox regression indicated that the CC genotype was associated with a longer survival and a reduced risk of death for NSCLC [58.0 vs. 41.0 months, P = 0.031; hazard ratio = 0.44, 95% confidential interval: 0.26–0.74]. Further stepwise regression analysis suggested rs16917496 was an independently favorable factor for prognosis and the protective effect more prominent in never smokers, patients without diabetes and patients who received chemotherapy. A significant interaction was observed between rs16917496 and smoking status in relation to NSCLC survival (P<0.001). Luciferase activity assay showed a lower expression level for C allele as compared with T allele, and the miR-502 had an effect on modulation of SET8 gene in vitro. The CC genotype was associated with reduced SET8 protein expression based on immunostaining of 192 NSCLC tissue sample (P = 0.007). Lower levels of SET8 were associated with a non-significantly longer survival (55.0 vs. 43.1 months).

Conclusion

Our data suggested that the rs16917496 T>C located at miR-502 binding site contributes to NSCLC survival by altering SET8 expression through modulating miRNA-target interaction.

Sirtuin-3 (SIRT3) expression is associated with overall survival in esophageal cancer

Sirtuin-3 (SIRT3) was immunostained in 94 samples of esophageal cancer tissues and semiquantified using the HSCORE method to evaluate the predictive value of SIRT3 expression levels on esophageal cancer outcome. The relationship between SIRT3 expression and the 5-year survival rate of postoperational esophageal cancer patients was assessed with the Kaplan-Meier method. High expression of SIRT3 is associated with a shorter survival time in esophageal cancer patients, as shown by the log-rank test (P = .007), and the level of SIRT3 expression was identified as an independent predictor for esophageal cancer outcome using Cox proportional hazards model analysis (relative risk, 2.061; 95% confidence interval, 1.050-4.046; P = .036). SIRT3 expression was associated with esophageal cancer outcome. The analysis of SIRT3 levels can help in the identification of patient subgroups that are at high risk for poor disease outcomes.

A miR-SNP of the XPO5 gene is associated with advanced non-small-cell lung cancer

Objectives

MicroRNA (miRNA)-related single-nucleotide polymorphisms (SNPs) in miRNA processing machinery genes can affect cancer risk, treatment efficacy, and patient prognosis. A miR-SNP of rs11077 located in the 3′ untranslated region (3′ UTR) of the miRNA processing machinery gene XPO5 was examined in 112 advanced non-small-cell lung cancer (NSCLC) patients to evaluate its association with cancer outcome.

Materials and methods

The miR-SNP was genotyped with ligase detection reaction method. Survival curves were calculated using the Kaplan-Meier method, and multivariate survival analysis was performed using a Cox proportional hazards model.

Results

The AC genotype of rs11077, which carries C or A allele, was significantly associated with a better chemotherapy response (P = 0.001). In addition, rs11077 was independently associated with overall survival in advanced NSCLC patients through multivariate analysis (relative risk 0.457; 95% confidence interval: 0.251–0.831; P = 0.010).

Conclusion

rs11077 was associated with chemotherapy response and survival of advanced NSCLC patients. The analysis of miR-SNPs in miRNA processing machinery genes can help identify patient subgroups that are at high risk for poor disease outcomes.

A microRNA-related single nucleotide polymorphism of the XPO5 gene is associated with survival of small cell lung cancer patients

MicroRNA (miRNA)-related single nucleotide polymorphisms (miR-SNPs) in miRNA processing machinery genes affect cancer risk, treatment efficacy and patient prognosis. A miR-SNP of rs11077 located in the 3'UTR of miRNA processing machinery gene XPO5 was examined in small cell lung cancer (SCLC) patients to evaluate its association with cancer survival. A total of 42 patients were enrolled in the present study and genotyped for rs11077 and survival was assessed using the Kaplan-Meier method, as well as univariate and multivariate analyses. The AA genotype of rs11077 was identified for its significant association with better survival time (P=0.023). In addition, rs11077 was found to associate independently with overall survival in SCLC patients by multivariate analysis (relative risk 2.469; 95% CI, 1.088-5.603; P=0.031). The findings of this study suggest that although miR-SNP studies for miRNA processing machinery genes are still at an early age, miR-SNPs have an impact on cancer survival. In conclusion, a miR-SNP in the 3'UTR region of the XPO5 gene was identified as an independent prognostic marker for survival of advanced SCLC patients.

The role of microRNAs in cancer susceptibility

Single nucleotide polymorphisms (SNPs) are germline variations interspersed in the human genome. These subtle changes of DNA sequence can influence the susceptibility to various pathologies including cancer. The functional meaning of SNPs is not always clear, being, the majority of them, localized in noncoding regions. The discovery of microRNAs, tiny noncoding RNAs able to bind the 3′ untranslated region (UTR) of target genes and to consequently downregulate their expression, has provided a functional explanation of how some SNPs positioned in noncoding regions contribute to cancer susceptibility. In this paper we summarize the current knowledge of the effect on cancer susceptibility of SNPs included in regions related with miRNA-dependent pathways. Hereditary cancer comes up from mutations that occur in high-penetrant predisposing tumor genes. However, a considerable part of inherited cancers arises from multiple low-penetrant predisposing gene variants that influence the behavior of cancer insurgence. Despite the established significance of such polymorphic variants in cancer predisposition, sometimes their functional role remains unknown. The discovery of a new group of genes called microRNAs (miRNAs) opened an avenue for the functional interpretation of polymorphisms involved in cancer predisposition.

A polymorphism at the miR-502 binding site in the 3' untranslated region of the SET8 gene is associated with the outcome of small-cell lung cancer

microRNAs (miRNAs) bind to the 3' untranslated regions (UTRs) of messenger RNAs, where they interfere with translation of genes that regulate cell differentiation, apoptosis and tumourigenesis. The histone methyltransferase SET8 has been reported to methylate TP53 and regulate genomic stability. We analysed a single nucleotide polymorphism (rs16917496) within the miR-502 miRNA seed region at the 3' UTR of SET8 in small-cell lung cancer (SCLC) patients. The SET8 CC+CT genotype was identified to be independently associated with longer survival in SCLC patients by multivariate analysis (relative risk, 0.453; 95% CI 0.217-0.944; p=0.035). The analysis of genetic polymorphisms in miRNA binding sites may help to identify patient subgroups at high risk of poor outcome.