Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis

Impact of IRGM gene promoter polymorphisms on susceptibility to chronic HBV infection

The autophagy gene immunity-related GTPase M (IRGM) can affect the immune response against intracellular pathogens. The study was performed to determine any possible association between three IRGM single-nucleotide polymorphisms (SNPs) (rs4958842, rs4958843 and rs4958846) and chronic hepatitis B virus (HBV) infection. A total of 171 chronic HBV-infected individuals and 171 healthy controls were collected. Peripheral blood cells and Sanger sequencing were used to extract genomic DNA and determine the SNP genotypes, respectively. The C allele of rs4958843 is a risk factor for chronic HBV infection in various genetic models, including allelic, codominant and dominant models, with the following respective statistical data: allelic (T vs. C: OR = 1.371, 95% CI = 1.009-1.863, p = .043), codominant (TT vs. CC: OR = 2.137, 95% CI = 1.104-4.138, p = .024) and dominant (TT + TC vs. CC: OR = 1.976, 95% CI = 1.106-3.533, p = .021) models. The genotype and allele distributions of rs4958842 and rs4958846 showed no significant differences between chronic HBV infection patients and healthy controls. IRGM rs4958843 CC genotype carriers had significantly elevated values of alanine transaminase, aspartate transaminase alpha-fetoprotein and total bilirubin (OR = 3.467, 95%CI = 1.167-10.298), which was positively associated with the disease progression of HBV infection. Mutant allele C of IRGM rs4958843 polymorphism is associated with the risk of chronic HBV infection in the Han people in central China and contributes to the disease progression.

Autophagy related gene 5 polymorphism rs17587319 (C/G) in asthmatic patients in North Indian population

Objective: Genetic background and environmental stimuli play an important role in asthma, which is an individual's hyper-responsiveness to these stimuli leading to airway inflammation. Autophagy Related Gene 5 (ATG5) plays a critical role in the autophagy pathway and has been shown to be involved in asthma. The genetic polymorphisms in the ATG5 have been reported to predispose individuals to asthma. The role of single nucleotide polymorphism rs17587319 (C/G) of ATG5 in asthma has not been studied so far. Materials and methods: In this study, we in silico analysed rs17587319 (C/G) using web-based tools Human Splice Finder (HSF) and RegulomeDB and further a case-control study was conducted that included 187 blood samples (94 asthmatic and 93 healthy controls). Results: In silico analysis suggested alteration of splicing signals by this intronic variant. The samples were genotyped by applying the PCR-RFLP method. The MAF obtained was 0.022 and 0.043 in healthy controls and asthmatic individuals, respectively. The statistical analysis revealed no association (allelic model, OR = 2.02, 95%CI = 0.59-6.83, p = 0.25; co-dominant model, OR = 2.06, 95%CI = 0.6-7.12, p = 0.24) of rs17587319 (C/G) with the susceptibility to asthma in the north Indian population. Conclusions: In conclusion, rs17587319 (C/G) of ATG5 does not predispose individuals to asthma in our part of the world. Further studies are needed including more number of samples to ascertain the role of this polymorphism in asthma.

Autophagy-related 5 in acute ischemic stroke: Variation and linkage with neurofunction, and survival

OBJECTIVE

Autophagy-related 5 (ATG5) facilitates the pathologic process of acute ischemic stroke (AIS) via multiple ways. This study aimed to identify the association of serum ATG5 with clinical outcomes in AIS patients.

METHODS

Serum ATG5 from 280 AIS patients were detected at admission, Day (D)1, D3, D7, D30, and D90 after admission by enzyme-linked immunosorbent assay. The median (interquartile range) follow-up was 21.1 (5.9-43.9) months. Another 50 healthy controls (HCs) were also enrolled for serum ATG5 determination.

RESULTS

ATG5 was elevated (p < 0.001) (vs. HCs), and positively correlated with hyperlipidemia (p = 0.016), and the national institutes of health stroke scale score (p = 0.001) in AIS patients. Interestingly, ATG5 was increased from admission to D1, but gradually decreased until D90 (p < 0.001). Besides, 85 (30.4%) and 195 (69.6%) AIS patients were assessed as modified Rankin Scale (mRS) >2 and mRS ≤2 at D90, respectively. ATG5 at admission, D1, D3, D30, and D90 was elevated in AIS patients with mRS >2 versus those with mRS ≤2 (all p < 0.050). ATG5 at admission, D1, D3, D7, D30, or D90 was elevated in relapsed (vs. non-relapsed) or died (vs. survived) AIS patients (all p < 0.050). Recurrence-free survival was shortened in AIS patients with high (≥52.0 ng/mL) ATG5 versus those with low (<52.0 ng/mL) ATG5 at admission, D3, D7, and D30 (all p < 0.050); overall survival was shorter in AIS patients with high (vs. low) ATG5 at D7 and D30 (both p < 0.050).

INTERPRETATION

Serum ATG5 elevates at first, thereafter gradually declines, whose elevation associates with neurological dysfunction, recurrence, and death risk in AIS patients.

Brucine D restrains colorectal cancer tumorigenesis and autophagy by downregulating circ_0068464

Bruceine D (BD) from Brucea javanica (L) exerts an antitumor effect in several human cancers. At present, it has not been reported whether BD inhibits the malignancy of colorectal cancer (CRC) cells. Therefore, investigating the role and regulatory mechanisms of BD in CRC is the main thrust of this study. Effect of BD on CRC cell viability, proliferation, apoptosis, invasion, and autophagy was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide, 5-ethynyl-2'-deoxyuridine, flow cytometry, transwell invasion, and western blotting assays. Expression changes of has_circ_0068464 (circ_0068464) were detected using real time quantitative polymerase chain reaction. The molecular mechanisms related to circ_0068464 were predicted through online prediction websites Starbase 2.0, circinteractome, and CircBank and validated using dual-luciferase reporter and RNA pull-down assays. The tumorigenic ability of BD and circ_0068464 on CRC was confirmed by xenograft experiments. The results showed that BD lessened CRC cell proliferation, invasion, autophagy, and prompted cell apoptosis. Circ_0068464 was overexpressed in CRC samples and cells. BD led to a significant reduction in circ_0068464 levels in cells of this carcinoma, but circ_0068464 overexpression partially rescued these effects urged by BD. Also, the combination of BD and circ_0068464 silencing decreased xenograft tumor growth compared to BD alone. Importantly, circ_0068464 could regulate ATG5 expression by functioning as a miR-520h molecular sponge. In conclusion, BD might suppress CRC growth by inhibiting the circ_0068464/miR-520h/ATG5 axis, providing a new perspective for the molecular pathogenesis of CRC and preliminarily indicating that BD may be a promising drug for CRC treatment.

Increased expression of autophagy-related gene 5 indicates poor prognosis in patients with hepatocellular carcinoma

OBJECTIVES

As a critical component of the autophagic machinery, autophagy-related gene 5 (ATG5) is essential for autophagosome formation. Autophagy participates in the transformation and progression of various malignant tumors, but the role of ATG5 in hepatocellular carcinoma (HCC) remains to be illustrated. In this study we aimed to investigate the prognostic significance of ATG5 in HCC.

METHODS

ATG5 expression was evaluated in 89 pairs of HCC tissues and adjacent non-tumor tissues. The relationship between ATG5 expression and patients' clinicopathological characteristics and prognosis were evaluated. Moreover, subgroup analyses were performed regarding patients' age and number of tumors. Nomograms estimating overall survival (OS) and disease-free survival (DFS) were conducted.

RESULTS

ATG5 expression was increased in HCC specimens rather than adjacent non-tumor tissues. The upregulated ATG5 expression was positively associated with serum α-fetoprotein (AFP) level. Moreover, cases with a strong ATG5 expression had a poorer disease-free survival (DFS) and overall survival (OS) than those with a weak ATG5 expression. Multivariate analysis showed that a strong expression of ATG5 was related to a poor OS and DFS in patients with HCC. Further analysis indicated that cases with a higher ATG5 expression had a poorer OS and DFS in the young patients (≤55 years) and those with solitary tumor. The nomogram suggested that there was a coherence between nomogram prediction and the actual situation of patient survival related to ATG5.

CONCLUSION

ATG5 promotes tumor progression in HCC, making it a potential biomarker in the diagnosis and a therapeutic target of HCC.

ATG5: A central autophagy regulator implicated in various human diseases

Autophagy, an intracellular conserved degradative process, plays a central role in the renewal/recycling of a cell to maintain the homeostasis of nutrients and energy within the cell. ATG5, a key component of autophagy, regulates the formation of the autophagosome, a hallmark of autophagy. ATG5 binds with ATG12 and ATG16L1 resulting in E3 like ligase complex, which is necessary for autophagosome expansion. Available data suggest that ATG5 is indispensable for autophagy and has an imperative role in several essential biological processes. Moreover, ATG5 has also been demonstrated to possess autophagy-independent functions that magnify its significance and therapeutic potential. ATG5 interacts with various molecules for the execution of different processes implicated during physiological and pathological conditions. Furthermore, ATG5 genetic variants are associated with various ailments. This review discusses various autophagy-dependent and autophagy-independent roles of ATG5, highlights its various deleterious genetic variants reported until now, and various studies supporting it as a potential drug target.

Association of IRGM gene promoter polymorphisms with Hepatitis B Virus infection

BACKGROUND

In response to intracellular pathogens the autophagy gene IRGM plays an essential role in the innate immune response. Various identified IRGM gene risk loci are associated with several diseases, but so far no study is available which shows the association of IRGM with HBV infection.

METHODS

We genotyped promoter variants (rs4958842, rs4958843, and rs4958846) of IRGM in HBV infected patients (551) and healthy controls (247) for their role in HBV infection. The genotyping was done applying methods developed in our laboratory and various biochemical parameters were assessed applying commercially available kits.

RESULTS

Data analysis has shown that the mutant allele A of rs4958842 plays a role in the protection from HBV infection in various genetic models that includes allelic, co-dominant and dominant models with the respective statistical data (OR=0.61; 95%CI=0.48-0.78; p=0.0003), (OR=0.52; 95%CI=0.38-0.71; p=0.0008) and (OR=0.51; 95%CI=0.38-0.70, p=0.0004). In CHB, protective association was observed in allelic (OR=0.48; 95%CI=0.35-0.65, p=0.0004), co-dominant (OR=0.38; 95%CI=0.26-0.54, p=0.0004) and dominant models (OR=0.38; 95%CI=0.26-0.54, p=0.0002). Mutant allele C of rs49598843 was associated with the risk of CHB in co-dominant (OR=1.52; 95%CI=1.07-2.16, p=0.04) and dominant models (OR=1.41; 95%CI=1.00-2.00, p=0.04). The mutant allele C of rs4958846 decreased the risk of HBV infection in allelic (OR=0.74; 95%CI=0.59-0.92, p=0.01), dominant (OR=0.72; 95%CI=0.53-0.98, p=0.05), homozygous (OR=0.42; 95%CI=0.24-0.74, p=0.01) and recessive (OR=0.42; 95%CI=0.24-0.74, p=0.0004) models. However, in asymptomatic group it was associated with the increased chance of HBV infection. Haplotypes, ATT (OR=0.47; 95%CI=0.33-0.68, p=0.001), GTC (OR=0.68; 95%CI=0.51-0.92, p=0.01) protect while GTT (OR=2.01; 95%CI=(1.55-2.60), p<0.0001) predisposes the individuals to HBV infection. All of these p-values mentioned here were obtained after performing Bonferroni correction.

CONCLUSION

In conclusion, our findings revealed that mutant allele A of rs4958842, mutant allele C of rs4958843 and rs4958846 were associated with hepatitis B virus infection in the North Indian population.

Increased ATG5 Expression Predicts Poor Prognosis and Promotes EMT in Cervical Carcinoma

Cervical cancer has the second-highest incidence and mortality of female malignancy. The major causes of mortality in patients with cervical cancer are invasion and metastasis. The epithelial–mesenchymal transition (EMT) process plays a major role in the acquisition of metastatic potential and motility. Autophagy-related genes (ARGs) are implicated in the EMT process, and autophagy exerts a dual function in EMT management at different phases of tumor progression. However, the role of specific ARGs during the EMT process has not yet been reported in cervical cancer. Based on the data from the Cancer Genome Atlas (TCGA) cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) sequencing database, we performed the prognosis analysis for those ARGs obtained from the Human Autophagy database. ATG5 was identified as the only important harmful marker influencing survival of cervical cancer patients by univariate Cox regression (HR 1.7; 95% CI: 1.0–2.8, p = 0.047), and the 5-years survival rate for the high- and low-ATG5 expression groups was 0.486 (0.375–0.631) and 0.782 (0.708–0.863), respectively. TCGA CESC methylation data showed that eight methylation sites of ATG5 could also be significantly associated with the overall survival (OS) of cervical cancer patients. Single-sample gene-set enrichment and gene functional enrichment results showed that ATG5 was correlated with some cancer-related pathways, such as phagocytosis-related genes, endocytosis-related genes, immune-related genes, EMT score, and some EMT signature-related genes. Next, cell migration and invasion assay and Western blot were applied to detect the function of ATG5 in EMT of cervical cancer. In cervical cancer cells, ATG5 knockdown resulted in attenuation of migration and invasion. The functional study showed that knockdown of ATG5 could reverse EMT process by P-ERK, P-NFκBp65, P-mTOR pathways, and so on. In conclusion, the present study implies that ATG5 was a major contributor to EMT regulation and poor prognosis in cervical cancer.

The autophagy gene ATG16L1 (T300A) variant is associated with the risk and progression of HBV infection

Autophagy pathway genes variants that play crucial roles in immune responses are involved in many diseases but their role in viral diseases is ill-defined. ATG16L1 gene plays a crucial role in the autophagy process. In this study, we have investigated the role of ATG16L1 variant T300A in the risk of HBV infection. rs2241880 (T300A) variant in 551 HBV infected patients (at various stages of infection) and 247 healthy controls were genotyped applying PCR-RFLP. Data analysis revealed that mutant allele G contributes to the risk of hepatitis B infection. Mutant alleles were significantly associated the HBV risk in allelic (OR = 1.31; 95%CI = 1.06-1.63, p = .01) and homozygous (OR = 1.87; 95%CI = 1.17-2.99, p = .009) models. On stratifying HBV infected individuals according to the stage of infection, a significant association was observed in asymptomatic (allelic; OR = 1.52; 95%CI = 1.10-2.09, p = .01 and homozygous; OR = 2.30; 95%CI = 1.22-4.36, p = .01) and chronic (allelic; OR = 1.36; 95%CI = 1.07-1.73, p = .01 and homozygous; OR = 2.07; 95%CI = 1.22-3.53, p = .008) stages of infection. High HBV DNA levels were associated with mutant genotype GG in asymptomatic and chronic carriers. Significantly higher ALT levels were observed in the liver cirrhosis patients with mutant genotypes. In conclusion, our data suggest that rs2241880 mutant allele carriers (allelic and homozygous models) were associated with increased risk of hepatitis B virus infection in North Indian population.

Transcriptome analysis and histopathological observations of Geloina erosa gills upon Cr(VI) exposure

The heavy metal contamination like Cr(VI) has been increased by human activities and that threats the ecosystem health of mangrove areas. Bioindicator is an emerging tool in the environmental contamination assessment. The objective of this study was to investigate the Geloina erosa response mechanisms and sensitivities of several biomarkers in the Cr(VI) exposure and identify the G. erosa capability of being used as heavy metals bioindicator. In this study, G. erosa was exposed to 100 μmol·L^-1 Cr(VI) for 48 h. After transcriptome sequencing, a total of 134,817 unigenes were obtained, including 12,555 up-regulated and 18,829 down-regulated differentially expressed genes and were validated through quantitative real-time PCR. In addition, a total of 12,185 SSRs and 1,428,214 candidate SNPs were identified from all the G. erosa transcriptome libraries. Histopathology of the gill indicated the Cr(VI) exposure induced damage of the organ leading to its immunization, detoxification or apoptosis reactions. Among eight genes of the selected biomarkers, Calm, HSP70, CYP450, ATG5, TLR2, MYD88 and CASP8 were up-regulated, while TLR4 was down-regulated in response to the Cr(VI) exposure.

Genetic association of polymorphisms at the intergenic region between PRDM1 and ATG5 with hepatitis B virus infection in Han Chinese patients

Chronic hepatitis B virus (HBV) infection is related to chronic hepatitis, cirrhosis, and hepatocellular carcinoma (HCC), and the interplay between the virus and host immune response leads to different outcomes of the infection. PR domain zinc finger protein 1 (PRDM1) and autophagy-related protein 5 (ATG5) are involved in immune response and HBV infection. An intergenic region between PRDM1 and ATG5 (PRDM1-ATG5 region) has been identified, and single-nucleotide polymorphisms (SNPs) in this region were shown to be involved in immune regulation. This study investigated the functionally relevant rs548234, rs6937876, and rs6568431 polymorphisms at the PRDM1-ATG5 region in a Han Chinese population (403 patients with chronic HBV infection [171 chronic hepatitis, 119 cirrhosis, and 113 HCC], 70 infection resolvers, and 196 healthy controls). The frequencies of the rs6568431 allele A in HBV patients (P = .005) and genotype CA in infection resolvers (P = .005) were significantly higher than in healthy controls. In the dominant model, HCC patients had significantly higher frequencies of rs548234 genotypes CC + TC than cirrhosis patients (P = .009). Rs548234 was an independent factor for HCC in comparison with either cirrhosis (P = .005) or all chronic HBV infection without HCC (P = .018). Functional annotation showed evidence of the role of the SNPs in gene regulation. In conclusion, through this study it is revealed for the first time that rs6568431 may be associated with susceptibility to HBV infection and that rs548234 may be associated with HCC risk in chronic HBV infection, supporting the presence of HBV-related disease-causing regulatory polymorphisms in the PRDM1-ATG5 intergenic region.

Autophagy-Related 5 Gene rs510432 Polymorphism Is Associated with Hepatocellular Carcinoma in Patients with Chronic Hepatitis B Virus Infection

BACKGROUND

Despite the identification of autophagy-related protein 5 (ATG5) as a molecule involved in the activated autophagy machinery during hepatitis B virus (HBV) infection and hepatocarcinogenesis, the consequences of ATG5 mutation carriage for patients with chronic HBV infection remain unclear. This study examined the association of ATG5 polymorphisms with HBV-related diseases including hepatocellular carcinoma (HCC).

PATIENTS AND METHODS

Two functionally relevant polymorphisms ATG5 rs573775 and rs510432 were genotyped by ligase detection reaction-polymerase chain reaction in 403 patients with chronic HBV infection (171 chronic hepatitis, 119 cirrhosis and 113 HCC) and 196 healthy controls. Univariate and multivariate logistic regression was performed to evaluate factors associated with HCC.

RESULTS

The rs573775 genotype and allele frequencies had no significant differences between patients with different clinical diseases. However, HCC patients had significantly higher frequency of rs510432 genotype AA (odds ratio [OR] 2.185, 95% confidence interval [CI] 1.042-4.581, P = 0.037, P value by Bonferroni correction [P_c] = 0.074) and allele A (OR 1.435, 95% CI 1.023-2.013, P_c = 0.036) than chronic hepatitis patients. In multivariate analyses, rs510432 allele A-containing genotypes (AA+GA) were independently associated with cirrhosis in comparison to chronic hepatitis (OR 1.927, 95%CI 1.011-3.017, P = 0.032). The rs510432 genotypes AA+GA were also independently associated with HCC in comparison to chronic hepatitis (OR 2.583, 95% CI 1.025-3.911, P = 0.006) or chronic HBV infection without HCC (OR 2.632, 95% CI 1.067-3.482, P = 0.032).

CONCLUSION

These results indicate that rs510432 genotypes AA+GA are associated with disease progression and HCC risk in chronic HBV infection, providing novel evidence for a role of ATG5 in the pathogenesis of HBV-related HCC.

ABBREVIATIONS

HBV: hepatitis B virus; HCC hepatocellular carcinoma; TNFSF10: tumor necrosis factor superfamily member 10; ATG5: autophagy-related protein 5; DNA: deoxyribonucleic acid; LDR-PCR: ligase detection reactions-polymerase chain reaction; PCR: polymerase chain reaction; SLE: systemic lupus erythematosus; BD: Behçet's disease; IL-10: interlukin-10; LPS: lipopolysaccharide; PBMC: peripheral blood mononuclear cells; CWP: coal workers' pneumoconiosis; TNF-α: tumor necrosis factor-α.

The Nonsynonymous Polymorphisms Val276Met and Gly393Ser of E2F1 Gene are Strongly Associated with Lung, and Head and Neck Cancers

AIM

The early gene factor-2 (E2F), a family of transcription factors, is involved in cell cycle regulation. Deregulated expression of most of the members of the E2F family is associated with various human cancers. In this study, we investigated the association between the E2F1 genetic variants rs3213173 (C/T) (Val276Met) and rs3213176 (G/A) (Gly393Ser) with the risk of lung cancer (LC) and head and neck cancer (HNC) in 190 patients and 230 control samples.

MATERIALS AND METHODS

We used polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and mutagenic primer-based PCR-RFLP methods to genotype all target polymorphisms.

RESULTS

The rs3213173 (C/T) polymorphism was associated with LC risk in the homozygous model (odds ratio [OR] = 2.954, 95% confidence interval [CI] 1.366-6.386; p = 0.004) as well as in heterozygous model (OR = 2.314; 95% CI = 1.369-3.912; p = 0.001). A significant association was also observed for the rs3213176 (G/A) polymorphism with LC risk in homozygous model, GG versus AA (OR = 2.750; 95% CI = 1.236-6.118; p = 0.01); in heterozygous model, GG versus GA (OR = 2.111; 95% CI = 1.256-3.549; p = 0.004); and in combined mutant GG versus GA+AA (OR = 2.214; 95% CI = 1.343-3.650; p = 0.001). The rs3213176 (G/A) marker was also associated with HNC risk.

CONCLUSIONS

Our findings reveal that the rs3213173 (C/T) and rs3213176 (G/A) polymorphisms of the E2F1 gene are genetic risk factors for susceptibility to LC and HNC in the North Indian Population.

E2F1 genetic variants and risk of cervical cancer in Indian women

Introduction:

Altered expression of many E2F family members have been reported in various human cancers. In this study, we investigated the role of non-synonymous single nucleotide polymorphisms (rs3213172 C/T, rs3213173 C/T, and rs3213176 G/A) of the gene E2F1 with cervical cancer.

Methods:

A total of 181 samples including 90 cervical cancer patients and 91 healthy controls were genotyped. The genotype frequencies of these polymorphisms in collected samples were determined by either PCR-RFLP or PCR-ARFLP methods. SHEsis software was used to analyze the haplotypes.

Results:

Statistically significant differences in the alleles and the genotypes frequencies were observed in rs3213172 (C/T) and rs3213173 (C/T) polymorphisms. The rs3213172 (C/T) polymorphism was a risk factor for cervical cancer in dominant model (odds ratio (OR) 1.96; 95% confidence interval (CI) 1.07, 3.60; P = 0.02) and heterozygous model (OR 1.90; 95% CI 1.01, 3.57; P = 0.04). The rs3213173 (C/T) polymorphism increased the risk of cervical cancer in the homozygous model (OR 2.71; 95% CI 1.11, 6.58; P = 0.02). The rs3213176 (G/A) polymorphism was not associated with cervical cancer risk in any of the genotypic models. In the haplotypes analysis, three haplotypes (CTG, TCG, and TTA) were associated with the cervical cancer risk.

Conclusions:

These findings revealed that rs3213172 (C/T) and rs3213173 (C/T) polymorphisms and haplotypes (CTG, TCG, and TTA) of the E2F1 gene might play role in the susceptibility of cervical cancer. This is the first report showing an association of these polymorphisms with the cervical cancer risk.

Effects of Mycobacterium tuberculosis Mutant Strain Hsp16.3 Gene on Murine RAW 264.7 Macrophage Autophagy

Heat shock protein Hsp16.3 is closely related to latent Mycobacterium tuberculosis (MTB) infection and plays an important role in sustained survival when MTB is dormant. In this study, the Hsp16.3 gene mutant MTB H37Rv strain (Hsp16.3ΔMTB) was obtained through gene recombination and infected into murine RAW 264.7 macrophages. Western blotting and immunofluorescence showed increased expression of the autophagy-related protein LC3, and transmission electron microscopy showed significantly increased macrophage autophagosomes, suggesting that Hsp16.3ΔMTB facilitates murine macrophage autophagy. These findings have implications for preventing and controlling tuberculosis.