Non-synonymous single nucleotide polymorphisms of ATG5 destabilize ATG12–ATG5/ATG16L1 complex: An enzyme with E3 like activity of ubiquitin conjugation system

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.

Apoptosis and autophagy of muscle cell during pork postmortem aging

OBJECTIVE

Pork is an important source of animal protein in many countries. Subtle physiochemical changes occur during pork postmortem aging. The changes of apoptosis and autophagy in pork at 6 h to 72 h after slaughter were studied to provide evidence for pork quality.

METHODS

In this article, morphological changes of postmortem pork was observed through Hematoxylin-eosin staining, apoptotic nuclei were observed by TdT-mediated dUTP nick end labeling assay, protein related to apoptosis and autophagy expressions were tested by western blot and LC3 level were expressed according to immunofluorescence assay.

RESULTS

In this study, we found the occurrence of apoptosis in postmortem pork, and the process was characterized by nucleus condensation and fragmentation, formation of apoptotic bodies, increase in apoptosis-related Bax/Bcl-2 levels, and activation of caspases. Autophagy reached its peak between 24 and 48 h after slaughter, accompanied by the formation of autophagosomes on the cell membrane and expression of autophagy-related proteins beclin-1, P62, LC3-I, LC3-II, and ATG5.

CONCLUSION

Obvious apoptosis was observed at 12 h and autophagy reached its peak at 48 h. The present work provides the evidence for the occurrence of apoptosis and autophagy during postmortem aging of pork. In conclusion, the apoptosis and autophagy of muscle cells discovered in this study have important implications for pork in the meat industry.

Autophagy-related genes polymorphism in hepatitis B virus-associated hepatocellular carcinoma: A systematic review

BACKGROUND

Chronic hepatitis B (CHB) virus is the most common risk factor for developing liver malignancy. Autophagy is an essential element in human cell maintenance. Several studies have demonstrated that autophagy plays a vital role in liver cancer at different stages. In this systematic review, we intend to investigate the role of polymorphism and mutations of autophagy-related genes (ATGs) in the pathogenesis and carcinogenesis of the hepatitis B virus (HBV).

MATERIALS AND METHODS

The search was conducted in online databases (Web of Science, PubMed, and Scopus) using Viruses, Infections, Polymorphism, Autophagy, and ATG. The study was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria.

RESULTS

The primary search results led to 422 studies. By screening and eligibility evaluation, only four studies were relevant. The most important polymorphisms in hepatocellular carcinoma were rs2241880 in ATG16L1, rs77859116, rs510432, and rs548234 in ATG5. Furthermore, some polymorphisms are associated with an increased risk of HBV infection including, rs2241880 in ATG16L1 and rs6568431 in ATG5.

CONCLUSION

The current study highlights the importance of rs2241880 in ATG16L1 and rs77859116, rs510432, and rs548234 in ATG5 for HBV-induced HCC. Additionally, some mutations in ATG16L1 and ATG5 were important in risk of HBV infection. The study highlights the gap of knowledge in the field of ATG polymorphisms in HBV infection and HBV-induced 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.

κ-Carrageenan oligosaccharides induce microglia autophagy through AMPK/ULK1 pathway to regulate their immune response

Microglia are the main effector cells of immune response in central nervous system and are important targets for disease prevention and treatment. Κ-carrageenan Oligosaccharide (KOS), obtained by enzymatic hydrolysis from carrageenan of marine red algae, can inhibit the release of inflammatory factors from the over-activated microglia. The mechanism of microglia autophagy induced by KOS and its relationship with inflammation were studied to explore the development prospect of KOS in the research and treatment of inflammatory related diseases. The effect of KOS on inducing autophagy was detected by the secretion of cytokines by lipopolysaccharide (LPS)-activated microglia, respectively. The protein expression of autophagy-related signaling pathways were detected by Western Blot. The results showed that KOS could significantly protect the microglia from over-activated inflammatory by inducing the autophagy and inhibiting the release of inflammatory cytokines. And KOS could reduce the expression of the protein that related to the AMPK/ULK1 pathways in microglia, so as to regulate the autophagy pathway, and inhibit the inflammatory response of over-activated microglia. The study on the effect of KOS on microglia autophagy and excessive inflammatory response will provide a theoretical basis for further studies on the inhibition of nerve injury by regulating microglia autophagy and inflammatory response.

Computational and artificial neural network based study of functional SNPs of human LEPR protein associated with reproductive function

Genetic polymorphisms are mostly associated with inherited diseases, detecting and analyzing the biological significance of functional single-nucleotide polymorphisms (SNPs) using wet laboratory experiments is an arduous task hence the computational analysis of putative SNPs is essential before conducting a study on a large population. SNP in the leptin receptor (LEPR) could result in the retention of intracellular signalling due to the structural and functional instability of the receptor causing abnormal reproductive function in human. In this first comprehensive computational analysis of LEPR gene mutation, we have identified and analyzed the functional consequence and structural significance of the SNPs in LEPR using recently developed several computational algorithms. Thirteen deleterious mutations such as W13C, S93G, I232R, Q307H, Y354C, E497A, Q571H, R612H, K656N, T690A, T699M V741M, and L760R were identified in the LEPR gene coding region. Backpropagation algorithm has been developed to forestall the deleterious nature of SNP and to validate the outcome of the tested computational tools. From ConSurf prediction three SNPs (Q571H, R612H, and T699M) were highly conserved on LEPR protein and the most deleterious variant R612H had one hydrogen bond abolished and severely reduced protein stability. Molecular docking suggested that the mutant (R612H) LEPR had lowest binding energy than native LEPR with the ligand molecule. Thus the energetically destructive changeover of ARG to HIS in R612H could possibly affect the LEPR protein structural stability and functional constancy due to interruption in the amino acid interactions and could result in reproductive disorders in human and increases the complication in obstetric and pregnancy outcome.

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.