Interaction Between Polymorphisms of IFN-γ and MICA Correlated with Hepatocellular Carcinoma

Machine learning-based disulfidptosis-related lncRNA signature predicts prognosis, immune infiltration and drug sensitivity in hepatocellular carcinoma

Disulfidptosis a new cell death mode, which can cause the death of Hepatocellular Carcinoma (HCC) cells. However, the significance of disulfidptosis-related Long non-coding RNAs (DRLs) in the prognosis and immunotherapy of HCC remains unclear. Based on The Cancer Genome Atlas (TCGA) database, we used Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression model to construct DRL Prognostic Signature (DRLPS)-based risk scores and performed Gene Expression Omnibus outside validation. Survival analysis was performed and a nomogram was constructed. Moreover, we performed functional enrichment annotation, immune infiltration and drug sensitivity analyses. Five DRLs (AL590705.3, AC072054.1, AC069307.1, AC107959.3 and ZNF232-AS1) were identified to construct prognostic signature. DRLPS-based risk scores exhibited better predictive efficacy of survival than conventional clinical features. The nomogram showed high congruence between the predicted survival and observed survival. Gene set were mainly enriched in cell proliferation, differentiation and growth function related pathways. Immune cell infiltration in the low-risk group was significantly higher than that in the high-risk group. Additionally, the high-risk group exhibited higher sensitivity to Afatinib, Fulvestrant, Gefitinib, Osimertinib, Sapitinib, and Taselisib. In conclusion, our study highlighted the potential utility of the constructed DRLPS in the prognosis prediction of HCC patients, which demonstrated promising clinical application value.

Study of the association between a MICA gene polymorphism and cholangiocarcinoma in Egyptian patients

Introduction

An inflammatory environment is the common pathway for the development of cholangiocarcinoma (CCA). The natural killer group 2D receptor (NKG2D), an activating receptor for NK cells, is a potent immune axis in the antitumor and antimicrobial immune response through its binding to NKG2D ligands (NKG2DLs). NKG2DLs are normally absent or poorly expressed in most cells; conversely, they are upregulated in stressed cells. We studied the rs2596542 polymorphism located upstream of the MICA gene, which encodes an NKG2DL, in patients with CCA as a marker for early disease detection and a possible therapeutic target.

Material and methods

A case-control study was conducted on 40 patients with CCA and 45 healthy individuals (as controls). After routine examination, the rs2596542 polymorphism of the MICA gene was investigated using real-time PCR.

Results

We found that a TT homozygous genotype was significantly predominant in patients with CCA (p = 0.039), with the T allele being dominantly distributed in CCA (p = 0.007). High levels of CA19-9 were significantly associated with the TT genotype in the patients. However, we did not detect significant differences in rs2596542C/T genotype and allele distribution between patients with CCA with cirrhosis and those without cirrhosis (p > 0.05).

Conclusions

The MICA rs2596542 polymorphism may affect the susceptibility to CCA, but not its progression. The TT genotype could be used as a potential diagnostic marker for CCA and triggering the MICA pathway could be a promising therapeutic target.

Diseases association with the polymorphic major histocompatibility complex class I related chain a: MICA gene

The Major Histocompatibility Complex class I chain-related molecule A (MICA) genes encode a highly polymorphic glycoprotein among the cell surface antigens that trigger an immune response after allograft transplantation. It is encoded by the MICA gene, a member of the glycosylated MIC genes. Discovered in 1994, the MICA gene is located within the MHC class I region. Moreover, its biological function is achieved through the interaction with the NKG2D receptor. Unlike the classical HLA molecules, MICA protein is not associated with β2- microglobulin nor binds peptides. MICA gene expression may result in a cytotoxic response and IFN-γ secretion through the up-regulation by heat shock proteins in response to infection (Human Cytomegalovirus HCMV), mediated by NKG2D-expressing cells. Anti-MICA antibodies were identified as significant risk factors for antibody mediated rejection after being detected in sera of patients with graft rejection. In addition, soluble MICA proteins (sMICA) has been detected in the serum of transplant recipients with cancers. Furthermore, the association of MICA polymorphisms with infectious diseases, various autoimmune diseases, cancer, and allograft rejection or graft-versus-host disease (GVHD) has been studied. Moreover, numerous advanced disease studies centered on MICA polymorphism are independent of HLA association. In this review, we discussed the up-to-date data about MICA and the association of MICA polymorphism with infections, autoimmune diseases, graft-versus-host disease, and cancer.

Main insights of genome wide association studies into HCV-related HCC

Background

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-mortality globally. Hepatocarcinogenesis is a complex multifactorial process. Host genetic background appeared to play a crucial role in the progression of HCC among chronic hepatitis C patients, especially in the era of Genome Wide Association Studies (GWAS) which allowed us to study the association of millions of single nucleotide polymorphisms (SNPs) with different complex diseases. This article aimed to review the discovered SNPs associated with the risk of HCV-related HCC development which was reported in the published GWA studies and subsequent validation studies and also try to explain the possible functional pathways.

Main text

We reviewed the recent GWA studies which reported several new loci associated with the risk of HCV-related HCC, such as (SNPs) in MHC class I polypeptide-related sequence A (MICA), DEP domain-containing 5 (DEPDC5), Tolloid-like protein 1 (TLL1), and human leukocyte antigen (HLA) genes. We also explained the possible underlying biological mechanisms that affect the host immune response pathways. Additionally, we discussed the controversial results reported by the subsequent validation studies of different ethnicities.

Conclusions

Although GWA studies reported strong evidence of the association between the identified SNPs and the risk of HCV-related HCC development, more functional experiments are necessary to confirm the defined roles of these genetic mutations for the future clinical application in different populations.

SNP rs2240688 in CD133 gene on susceptibility and clinicopathological features of hepatocellular carcinoma

Background

CD133 is one of the important cancer stem cells (CSCs) markers of hepatocellular carcinoma (HCC). The aim of this study was to explore the relationship between CD133 single-nucleotide polymorphisms (SNPs) and risk factors associated with HCC susceptibility and clinicopathological features in HCC cases and healthy controls from the Guangxi region of southern China.

Methods

A case control study was conducted, including 565 HCC patients and 561 control subjects. The genotyping of rs2240688 was performed using the SNaPshot method. Unconditional logistic regression was used to correct for gender, age, and other confounding factors. Odds ratio (OR) and its 95% confidence interval (CI) were calculated to analyze the relationship between allele and genotype frequency and the risk of HCC.

Results

The distribution frequencies of CD133 alleles and genotypes in the HCC case group and the control group were statistically significant (P<0.05). The CA heterozygous (P=0.003, OR =1.463, 95% CI: 1.134–1.887) and CC homozygous genotypes (P=0.036, OR =1.910, 95% CI: 1.044–3.493), as well as C carrier status (P=0.004, OR =1.465, 95% CI: 1.136–1.889) and C alleles (P=0.004, OR =1.465, 95% CI: 1.136–1.889), were associated with an increased risk of HCC. Additionally, in the subgroup analysis of CD133 rs2240688 polymorphism and clinical characteristics, the results showed that the genotype distribution of CD133 rs2240688 was significantly different in genotype distribution of metastasis and alanine aminotransferase (ALT).

Conclusions

the expression of miRNA binding site rs2240688 of tumor stem cell marker gene CD133 in HCC may be a promising marker for the prediction of HCC, but larger studies are still needed.

Association of IFN-γ polymorphisms with ankylosing spondylitis risk

The case‐control study was designed to investigate the genetic effects of interferon‐gamma (IFN‐γ) rs2069727 and rs1861494 polymorphisms on ankylosing spondylitis (AS) susceptibility in a Chinese Han population. Blood samples were collected from 108 AS patients and 110 healthy controls. IFN‐γ polymorphisms were genotyped by polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP). Hardy‐Weinberg equilibrium (HWE) test was performed in control group. Odds ratios (OR) with 95% confidence intervals (95% CI) were calculated using chi‐square test to evaluate the association between AS susceptibility and IFN‐γ polymorphisms, and the results were adjusted by logistic regressive analysis. The frequency of rs2069727 CC genotype was much higher in cases than that in controls, suggested its significant association with increased AS risk (adjusted OR = 5.899, 95% CI = 1.563‐22.261; P = .009). In addition, C allele also showed close association with increased risk of AS (adjusted OR = 2.052, 95% CI = 1.286‐1.704, P  = 0 .003). While the genotype and allele frequencies of IFN‐γ rs1861494 polymorphism were not significantly different between patients and controls (P  > 0.05 for all), IFN‐γ rs2069727 polymorphism is significantly associated with increased AS risk in a Chinese Han Population.

Association between MICA rs2596542 Polymorphism with the Risk of Hepatocellular Carcinoma in Chronic Hepatitis C Patients

In this study we investigated the impact of rs2596542A/G single nucleotide polymorphism (SNP) in the major histocompatibility complex class I chain-related sequence A (MICA) gene on HCV-induced hepatocellular carcinoma (HCC) susceptibility in a Brazilian population. In total, 252 HCV-infected patients (98 with HCV-induced HCC and 154 non-malignant HCV-induced liver cirrhosis) were enrolled and 98 healthy control subjects (negative anti-HCV). The MICA rs2596542 SNP genotypes were determined by real-time PCR assay. No differences in MICA genotype frequencies between HCV-induced cirrhosis patients and controls were observed. However, genotype frequencies of rs2596542A/G SNP were statistically different between HCV-induced HCC patients and controls (p = 0.048), and also between HCC and HCV-induced cirrhosis patients (p = 0.039). The highest frequency of the rs2596542AA genotype was observed in HCC patients (31.6%) when compared with HCV-induced cirrhosis patients (18.8%) and healthy controls (19.4%). Also, rs2596542AA genotype carriers have an increased risk for HCC when compared to HCV-induced cirrhosis status [odds ratio (OR) = 1.99; 95% confidence interval (CI) = 1.06-3.74, p = 0.020)] and healthy individuals (OR = 1.92, 95% CI = 1.00-3.70, p = 0.049). Taken together our study suggest that MICA rs2596542 SNP impacts HCV-induced HCC susceptibility suggesting that genetic variants in MICA are of clinical relevance to hepatocarcinogenesis by impacting host immune response in chronic HCV infection.

Clustered microRNAs hsa-miR-221-3p/hsa-miR-222-3p and their targeted genes might be prognostic predictors for hepatocellular carcinoma

Objective: MicroRNAs (miRNAs) have been explored in malignancies. We investigated the functions of clustered miRNAs hsa-miR-221/222-3p in hepatocellular carcinoma (HCC). Methods: Human miRNA tissue atlas website was determined expression levels in liver tissue. Four databases, TarBase, miRTarBase, miRecords and miRPathDB, were found experimentally validated target genes of clustered miRNAs. TargetScanHuman was predicted target genes. The STRING website was depicted protein-protein interaction (PPI) networks. The OncoLnc website analyzed prognostic values for hsa-miR-221/222-3p and their target genes. The MCODE plugin calculated modules of PPI networks. Receiver operating characteristic (ROC) curves were predicted 1, 3, and 5 years prognostic values. Results: Expression of clustered miRNAs was high in liver tissues. A total of 1577 target genes were identified. Enrichment analysis showed that target genes were enriched mainly in cancer, Wnt signaling and ErbB signaling pathways. Two modules were calculated using PPI networks. Has-miR-221-3p was not associated with prognosis (P = 0.401). Has-miR-222-3p and target genes ESR1, TMED7, CBFB, ETS2, UBE2J1 and UBE2N of the clustered miRNAs were associated with HCC survival (all P < 0.05). Has-miR-222-3p, CBFB, and UBE2N showed good performance of ROC in prognosis prediction at 1, 3, and 5 years (all area under curves > 0.600). Conclusion: Has-miR-222-3p and target genes, especially CBFB, UBE2N, may serve as prognostic predictors for HCC.

SNP rs2596542G>A in MICA is associated with risk of hepatocellular carcinoma: a meta-analysis

The association of major histocompatibility complex class I chain-related gene A (MICA) single nucleotide polymorphism (SNP) rs2596542G>A and hepatocellular carcinoma (HCC) has been broadly studied, with inconsistent results. Therefore, we conducted the current meta-analysis to better elucidate the roles of SNP rs2596542G>A in HCC. Eligible articles were searched in PubMed, CNKI, Wanfang, Embase, VIP, Web of Science, and CBM databases up to November 2018. Odds ratios (ORs) and 95% CIs were applied. A total of 11 articles, including 4528 HCC patients and 16,625 control subjects, were analyzed. Results revealed that rs2596542G>A was significantly associated with HCC in the heterozygote (G/A versus A/A, P=0.006, OR = 0.854; 95% CI: 0.763–0.956); and dominant (G/G + G/A versus A/A; P=0.021; OR = 0.796; 95% CI: 0.655–0.967) genetic models. Nevertheless, we also detected significant associations between rs2596542G>A and HCV-induced HCC. Additionally, according to our analyses, SNP rs2596542G>A was not correlated with HBV-induced HCC. In conclusion, our findings suggest that MICA SNP rs2596542G>A is associated with HCC susceptibility amongst the Asian, Caucasian, and African ethnicity in certain genetic models. Specifically, MICA SNP rs2396542G>A is associated with risk of HCV-induced HCC, not HBV-induced HCC.

Single nucleotide polymorphism of rs2596542 and the risk of hepatocellular carcinoma development: A meta-analysis

BACKGROUND

Major histocompatibility complex class I-related chain A (MICA) is considered as a tumor antigen, and its expression is affected by its genetic polymorphisms. However, the relationship between rs2596542 polymorphisms in MICA promoter region and hepatocellular carcinoma (HCC) is not fully elucidated so far. This study aims to explore the relationship between single nucleotide polymorphism of rs2596542 and the risk of HCC development through meta-analysis.

METHODS

MEDLINE, Web of Science, and EMBASE databases were systematically searched to identify relevant studies. A meta-analysis was performed to examine the association between MICA rs2596542 polymorphism and susceptibility to HCC. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated.

RESULTS

Fourteen case-control studies involving 4,900 HCC cases and 19,519 controls were included. The MICA rs2596542C allele was significantly associated with decreased risk of HCC based on allelic contrast (OR = 0.76, 95% CI = 0.69-0.83, P < .001), homozygote comparison (OR = 0.57, 95% CI = 0.48-0.69, P < .001), and a recessive genetic model (OR = 0.77, 95% CI = 0.65-0.91, P < .001), whereas patients carrying the MICA rs2596542TT genotype had significantly higher risk of HCC than those with the CT or CC genotype (TT vs CT + CC, OR = 1.57, 95% CI = 1.36-1.81, P < .001). Subgroups analyses based on the ethnic or the source of control groups found very similar findings.

CONCLUSION

The C allele in MICA rs2596542 is a protective factor for hepatocarcinogenesis, whereas the T allele is a risk factor. Further large and well-designed studies are needed to confirm this conclusion.

Association of IFNGR1 and IFNG genetic polymorphisms with the risk for pulmonary tuberculosis in the Chinese Tibetan population

Interferon-gamma (IFNG) and its receptor (IFNGR1) are principal genes that associated with tuberculosis. In the current study we aimed to explore the genetic association of polymorphisms of IFNG and IFNGR1 with the risk of pulmonary tuberculosis (PTB) in the Chinese Tibetan population. We selected 467 PTB patients and 503 healthy controls to genotype 9 single nucleotide polymorphisms (SNPs). The unconditional logistic regression analysis was applied for assessing the associations, and the risk of PTB were evaluated by calculating the odds ratio (OR) and 95% confidence interval (CI). The results showed that mutants of rs9376268, rs1327475 and rs1327474 in IFNGR1 played a protective role in the PTB risk under genotype, dominant and additive model (P<0.05). On the contrary, minor allele “A” of rs2069705 in IFNG significantly increased the risk of PTB under genotype, dominant and additive model (P<0.05). However, after Bonferroni's multiple adjustment was applied to our data, which level of significant was set at P<0.0011 (0.05/45). Only variant of rs9376268 was significantly associated decrease the PTB susceptibility under additive model (OR=0.73, 95%CI=0.61-0.88, P<0.001). Furthermore, in the haplotype analysis, we found that the haplotypes “C-G-G-A-C”, “C-G-A-G-T” and “T-A-G-G-T” of rs9376267-rs9376268-rs1327475-rs7749390-rs1327474 block were extremely decreased the PTB risk (P<0.01), however, the haplotypes “C-G-G-A-T”, “T-G-G-G-T” and “C-G-G-G-T” of the block were extremely increased the PTB risk (P<0.01). These results suggested that variants of IFNGR1 may have a close relation with the PTB risk in Chinese Tibetan population.

The association between MICA/MICB polymorphism and respiratory syncytial virus infection in children

MICA/MICB gene polymorphisms are related to several cancers and infectious diseases, but there are no reports on the association between MICA/MICB gene polymorphisms and respiratory syncytial virus (RSV) infection. To clarify the association between MICA/MICB gene polymorphisms and infection of RSV in children, we collected fresh blood samples from paediatric patients with and without pneumonia after RSV infection. The MICA/MICB alleles were characterized by PCR sequence-specific primers (PCR-SSP) and PCR sequence-based genotyping (PCR-SBT), and then, the frequency of the MICA/MICB alleles and haplotypes was calculated. The results showed that the frequencies of MICA*002:01 and MICA-A9 in RSV-infected patients were significantly lower than in controls (9% vs. 20%, pc = 0.04). The allele frequency of MICA*002:01 in pneumonia patients (8%) and nonpneumonia patients (9%) was significantly lower than in controls (20%, pc = 0.02). MICA*002:01-MICB*008(Δrel = 0.616), MICA*009-MICB*016 (Δrel = 0.506), and MICA*045-MICB*014 (Δrel = 0.700) showed linkage disequilibrium in patients infected with RSV. The haplotype frequency of MICA*002:01-MICB*005:02 in RSV-infected patients was significantly lower than in controls (10% vs. 16%, pc = 0.033). In conclusion, allele MICA*002:01/A9 and haplotype MICA*002:01-MICB*005:02 were negatively associated with RSV respiratory tract infections.

Clinical significance of SNP (rs2596542) in histocompatibility complex class I-related gene A promoter region among hepatitis C virus related hepatocellular carcinoma cases

The major histocompatibility complex class I-related gene A (MICA) is an antigen induced by stress and performs an integral role in immune responses as an anti-infectious and antitumor agent. This work was designed to investigate whether (SNP) rs2596542C/T in MICA promoter region is predictive of liver cirrhosis (LC) and hepatocellular carcinoma (HCC) or not. Forty-seven healthy controls and 94 HCV-infected patients, subdivided into 47 LC and 47 HCC subjects were enrolled in this study. SNP association was studied using real time PCR and soluble serum MICA concentration was measured using ELISA. Results showed that heterozygous genotype rs2596542CT was significantly (P = 0.022) distributed between HCC and LC related CHC patients. The sMICA was significantly higher (P = 0.0001) among HCC and LC. No significant association (P = 0.56) between rs2596542CT genotypes and sMICA levels was observed. Studying SNP rs2596542C/T association with HCC and LC susceptibility revealed that statistical significant differences (P = 0.013, P = 0.027) were only observed between SNP rs2596542C/T and each of HCC and LC, respectively, versus healthy controls, indicating that the rs2596542C/T genetic variation is not a significant contributor to HCC development in LC patients. Moreover, the T allele was considered a risk factor for HCC and LC vulnerability in HCV patients (OR = 1.93 and 2.1, respectively), while the C allele contributes to decreasing HCC risk. Therefore, SNP (rs2596542C/T) in MICA promoter region and sMICA levels might be potential useful markers in the assessment of liver disease progression to LC and HCC.