C3orf21 ablation promotes the proliferation of lung adenocarcinoma, and its mutation at the rs2131877 locus may serve as a susceptibility marker

Non-synonymous SNPs variants of PRKCG and its association with oncogenes predispose to hepatocellular carcinoma

BACKGROUND

PRKCG encodes PKC γ, which is categorized under the classical protein kinase C family. No studies have specifically established the relationship between PRKCG nsSNPs with structural and functional variations in PKC γ in the context of hepatocellular carcinoma (HCC). The present study aims to uncover this link through in-silico and experimental studies.

METHODS

The 3D structure of PKC γ was predicted. Molecular Dynamic (MD) Simulations were run and estimates were made for interactions, stability, conservation and post-translational alterations between wild and mutant structures. The association of PRKCG levels with HCC survival rate was determined. Genotyping analyses were conducted to investigate the deleterious PRKCG nsSNP association with HCC. mRNA expression of PKC γ, HIF-1 alpha, AKT, SOCS3 and VEGF in the blood of controls and HCC patients was analyzed and a genetic cascade was constructed depicting these interactions.

RESULTS

The expression level of studied oncogenes was compared to tumour suppressor genes. Through Alphafold, the 3D structure of PKC γ was explored. Fifteen SNPs were narrowed down for in-silico analyses that were identified in exons 5, 10 and 18 and the regulatory and kinase domain of PKC γ. Root mean square deviation and fluctuation along with the radius of gyration unveiled potential changes between the wild and mutated variant structures. Mutant genotype AA (homozygous) corresponding to nsSNP, rs386134171 had more frequency in patients with OR (2.446), RR (1.564) and P-values (< 0.0029) that highlights its significant association with HCC compared to controls in which the wild genotype GG was found more prevalent.

CONCLUSION

nsSNP rs386134171 can be a genetic marker for HCC diagnosis and therapeutic studies. This study has laid down a road map for future studies to be conducted on HCC.

Beta-Elemene Reduces the Malignancy of Non-Small Cell Lung Cancer by Enhancing C3orf21 Expression

Background

Beta-elemene has potent anti-tumor effect, but its anti-tumor mechanism remains unclear. Chromosome 3 open reading frame 21 (C3orf21) acts as a tumor suppressor. This study tested whether the anti-tumor effect of beta-elemene was associated with modulating C3orf21 expression in non-small cell lung cancer (NSCLC).

Materials and Methods

The impact of beta-elemene on C3orf21 expression in NSCLC cells was quantified. The stable C3orf21 silencing A549 and over-expressing PC-9 cells were established and their effects on the beta-elemene-attenuated proliferation, wound healing and invasion of NSCLC cells as well as the expression of key regulators and signal events were determined.

Results

Beta-elemene significantly up-regulated C3orf21 expression in NSCLC cells. Beta-elemene treatment significantly attenuated the proliferation, wound healing and invasion of NSCLC cells, which were significantly mitigated by C3orf21 silencing, but enhanced by C3orf21 over-expression. Similar patterns of beta-elemene-modulated cyclinD1, c-Myc, COX2, MMP2, MMP9, VEGF, PTEN and Notch1 expression were detected in NSCLC cells.

Conclusions

Such data indicated that beta-elemene treatment attenuated the malignancy of NSCLC cells by up-regulating C3orf21 expression. Our findings may provide new mechanisms underlying the pharmacological action of beta-elemene.

A Density Peak-Based Method to Detect Copy Number Variations From Next-Generation Sequencing Data

Copy number variation (CNV) is a common type of structural variations in human genome and confers biological meanings to human complex diseases. Detection of CNVs is an important step for a systematic analysis of CNVs in medical research of complex diseases. The recent development of next-generation sequencing (NGS) platforms provides unprecedented opportunities for the detection of CNVs at a base-level resolution. However, due to the intrinsic characteristics behind NGS data, accurate detection of CNVs is still a challenging task. In this article, we propose a new density peak-based method, called dpCNV, for the detection of CNVs from NGS data. The algorithm of dpCNV is designed based on density peak clustering algorithm. It extracts two features, i.e., local density and minimum distance, from sequencing read depth (RD) profile and generates a two-dimensional data. Based on the generated data, a two-dimensional null distribution is constructed to test the significance of each genome bin and then the significant genome bins are declared as CNVs. We test the performance of the dpCNV method on a number of simulated datasets and make comparison with several existing methods. The experimental results demonstrate that our proposed method outperforms others in terms of sensitivity and F1-score. We further apply it to a set of real sequencing samples and the results demonstrate the validity of dpCNV. Therefore, we expect that dpCNV can be used as a supplementary to existing methods and may become a routine tool in the field of genome mutation analysis.

XXYLT1 methylation contributes to the occurrence of lung adenocarcinoma: Methylation and lung adenocarcinoma

BACKGROUND

There is evidence that DNA methylation play major roles in lung cancer. In our previously study, C3 or f21 , also referred to as XXYLT1, rs2131877 polymorphism is associated with a reduced risk of lung adenocarcinoma. So, we explored the role of XXYLT1 methylation in lung adenocarcinoma.

METHODS

This study was conducted in 2 steps. In the first step, we recruited 15 patients with lung adenocarcinoma. Cancer tissues and para-carcinoma tissues were obtained from each of the patients. In the second step, 150 patients with lung adenocarcinom were enrolled, and cancer and normal lung tissue were obtained from each patients, respectively. The expression levels of XXYLT1 mRNA were determined, the deoxyribonucleic acid methylation status was analyzed by MassARRAY Spectrometry. The methylation data of individual units were generated by EpiTyper v1.0.5 software.

RESULTS

The XXYLT1 mRNA expression was significantly lower in cancer tissues than in para-carcinoma and normal lung tissues. Meanwhile, the methylation rates of three CpG units (CpG_23, CpG_25, and CpG_60.61.62.63.64.65) within the XXYLT1 gene were higher in cancer tissues compared to the para-carcinoma and the normal lung tissues. This difference was particularly significant in male patients.

CONCLUSIONS

Our results suggested that methylation of XXYLT1 may have significance in the pathogenesis of lung adenocarcinoma.

Glycogene expression profiles based on microarray data from cervical carcinoma HeLa cells with partially silenced E6 and E7 HPV oncogenes

Background

Aberrant glycosylation is a characteristic of tumour cells. The expression of certain glycan structures has been associated with poor prognosis. In cervical carcinoma, changes in the expression levels of some glycogenes have been associated with lymph invasion. Human papillomavirus (HPV) infection is one of the most important factors underlying the development of cervical cancer. The HPV oncoproteins E6 and E7 have been implicated in cervical carcinogenesis and can modify the host gene expression profile. The roles of these oncoproteins in glycosylation changes have not been previously reported.

Methods

To determine the effect of the E6 and E7 oncoproteins on glycogene expression we partially silenced the E6 and E7 oncogenes in HeLa cells, we performed a microarray expression assay to identify altered glycogenes and quantified the mRNA levels of glycogenes by RT-qPCR. A protein-protein interaction network was constructed to identify potentially altered glycosylation pathways.

Results

The microarray analysis showed 9 glycogenes that were upregulated and 7 glycogenes that were downregulated in HeLa shE6/E7 cells. Some of these genes participate in glycosylation related to Notch proteins and O-glycans antigens.

Conclusions

Our results support that E6 and E7 oncoproteins could modify glycogene expression the products of which participate in the synthesis of structures implicated in proliferation, adhesion and apoptosis.