Polymorphism of Secretary PLA2G2A Gene Associated with Its Serum Level in Type2 Diabetes Mellitus Patients in Northern Iran

Bioinformatics and Next-Generation Data Analysis for Identification of Genes and Molecular Pathways Involved in Subjects with Diabetes and Obesity

Background and Objectives: A subject with diabetes and obesity is a class of the metabolic disorder. The current investigation aimed to elucidate the potential biomarker and prognostic targets in subjects with diabetes and obesity. Materials and Methods: The next-generation sequencing (NGS) data of GSE132831 was downloaded from Gene Expression Omnibus (GEO) database. Functional enrichment analysis of DEGs was conducted with ToppGene. The protein-protein interactions network, module analysis, target gene-miRNA regulatory network and target gene-TF regulatory network were constructed and analyzed. Furthermore, hub genes were validated by receiver operating characteristic (ROC) analysis. A total of 872 DEGs, including 439 up-regulated genes and 433 down-regulated genes were observed. Results: Second, functional enrichment analysis showed that these DEGs are mainly involved in the axon guidance, neutrophil degranulation, plasma membrane bounded cell projection organization and cell activation. The top ten hub genes (MYH9, FLNA, DCTN1, CLTC, ERBB2, TCF4, VIM, LRRK2, IFI16 and CAV1) could be utilized as potential diagnostic indicators for subjects with diabetes and obesity. The hub genes were validated in subjects with diabetes and obesity. Conclusion: This investigation found effective and reliable molecular biomarkers for diagnosis and prognosis by integrated bioinformatics analysis, suggesting new and key therapeutic targets for subjects with diabetes and obesity.

Effect of copy number variation of PLA2G2A gene to growth traits in Chinese cattle

SIMPLE SUMMARY

As a member of genetic polymorphism, copy number variation has been a commonly used method in the world for investigating effect of genetic polymorphism on gene expression. Effect of genetic polymorphism made on livestock development has been more and more important in beef cattle molecular breeding. The characteristics of Chinese cattle are excellent meat quality, tolerant to rough feeding, good environmental adaptability and so on. But there are some obvious weaknesses still exist in the process of cattle growth and development, such as weak hindquarters and growth slowly. To improve the growth performance and market competitiveness of Chinese cattle, a lot of studies have been made about finding and investigating effective molecular marker. In this study, Q-PCR and data association analysis were used for PLA2G2A gene copy number variation detection and related effect analysis in Chinese cattle. Results showed that PLA2G2A gene has a significant effect on two breeds of Chinese cattle on growth traits, which could be a basic materials and effective information of cattle molecular markers breeding. PLA2G2A, member of secreted phospholipases A2 (sPLA2) in superfamily of phospholipase A2, could catalyze the process of glycerophospholipids hydrolysis from position of sn-2 acyl with the release of free fatty acids and lysophospholipids. Researches about PLA2G2A gene are mostly focus on disease, including tumors and diabetes, the number of study occurred on animal breeding is weak. In this study, blood samples were collected from five breeds of Chinese cattle (Qingchuan cattle, Xianan cattle, Yunling cattle, Pinan cattle and Guyuan cattle) for PLA2G2A gene CNV type detection. SPSS 20.0 software and method of ANOVA were used to analyzed the association between types of CNV and growth traits. Results reveal that the distribution of different copy number types in different cattle breeds is different. In QC, XN and GY cattle, the frequencies of Deletion and Duplication are about 40%; in YL cattle, the frequency of Deletion type exceeds 60%; in PN cattle, the frequency of Duplication is closed to 80%. Association analysis indicate that CNV of PLA2G2A gene showed a positive effect in cattle growth: in QC cattle, Chest depth with Normal type copy number possess a increased trend (P < 0.05); individuals with Deletion type copy number have better performance on Height at sacrum, Heart girth and Body height in GY cattle (P < 0.05). The functional role and molecular mechanism of PLA2G2A gene in animal growth and development are still unclear, and it is necessary for processing a further research. This research aims to provide basic materials for molecular breeding of Chinese cattle.

Differential gene expression profile by RNA sequencing study of elderly osteoporotic hip fracture patients with sarcopenia

Background

The purpose of this study was to report the RNA sequencing profile according to the presence or absence of sarcopenia in elderly patients with osteoporotic hip fracture. Therefore, an important genetic factor candidate for sarcopenia causing hip fracture in elderly with osteoporosis has been identified.

Methods

The patient group involved subjects over 65 years who had undergone hip fracture surgery. Among 323 hip fracture (HF) patients identified from May 2017 to December 2019, 162 HF patients (90 non-sarcopenia and 72 sarcopenia groups), excluding subjects with high energy trauma and non-osteoporosis, were finally included in the analysis. For RNA sequencing, each patient with hand grip strength (HGS) values in the top 10% were enrolled in the control group and with the bottom 10% in the patient group. After excluding patients with poor tissue quality, 6 patients and 5 patients were selected for sarcopenia and non-sarcopenia groups, respectively. For qPCR validation, each patient with HGS values in the top 20% and bottom 20% was enrolled in the control and patient groups, respectively. After excluding patients with poor tissue quality, 12 patients and 12 patients were enrolled in the sarcopenia and non-sarcopenia groups, respectively. Sarcopenia was defined according to the Asia Working Group for Sarcopenia (AWGS) criteria for low muscle strength (hand grip strength below 18 ​kg in women and 28 ​kg in men) and low muscle mass (SMI below 5.4 ​kg/m² in women and 7.0 ​kg/m² in men). The libraries were prepared for 100 bp paired-end sequencing using TruSeq Stranded mRNA Sample Preparation Kit (Illumina, CA, USA). The gene expression counts were supplied to Deseq2 to extract possible gene sets as differentially expressed genes (DEG) that discriminate between sarcopenia and non-sarcopenia groups that were carefully assigned by clinical observation. For the classification of the candidate genes from DEG analysis, we used the public databases; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Quantitative real-time PCR was performed for validation.

Results

Samples collected were subjected to RNAseq using the Illumina platform. A total of 11 samples from both sarcopenia and non-sarcopenia groups were sequenced. Fifteen genes (RUNX 1, NGFR, CH3L1, BCL3, PLA2G2A, MYBPH, TEP1, SEMA6B, CSPG4, ACSL5, SLC25A3, NDUFB5, CYC1, ACAT1, and TCAP) were identified as differentially expressed genes (DEG) in both the groups.

In the qPCR results, the expression levels of SLC25A3 and TCAP gene in the OS group were significantly lower than in the non-OS groups whereas an increase in RUNX1 mRNA level was observed in the OS samples (p ​< ​0.05).

Conclusions

In summary, this study detected gene expression difference according to the presence or absence of sarcopenia in elderly osteoporosis female patients with hip fracture. We have also identified 15 important genes (RUNX 1, NGFR, CH3L1, BCL3, PLA2G2A, MYBPH, TEP1, SEMA6B, CSPG4, ACSL5, SLC25A3, NDUFB5, CYC1, ACAT1, TCAP), a few GO categories and biological pathways that may be associated with the osteosarcopenia. Our study may provide effective means for the prevention, diagnosis and treatment sarcopenia in elderly osteoporosis female patients.

The Translational potential of this article

These findings provide a novel insight into the effects of aging on the response in women with postmenopausal osteoporosis. Further studies are underway to identify the specific signalling pathways involved. These results reveal potential therapeutic targets that could aid the regenerative capacity of aging skeletal muscle.