Identification of hub genes, miRNAs and regulatory factors relevant for Duchenne muscular dystrophy by bioinformatics analysis

Transcriptomic characterization of tissues from patients and subsequent pathway analyses reveal biological pathways that are implicated in spastic ataxia

BACKGROUND

Spastic ataxias (SAs) encompass a group of rare and severe neurodegenerative diseases, characterized by an overlap between ataxia and spastic paraplegia clinical features. They have been associated with pathogenic variants in a number of genes, including GBA2. This gene codes for the non-lysososomal β-glucosylceramidase, which is involved in sphingolipid metabolism through its catalytic role in the degradation of glucosylceramide. However, the mechanism by which GBA2 variants lead to the development of SA is still unclear.

METHODS

In this work, we perform next-generation RNA-sequencing (RNA-seq), in an attempt to discover differentially expressed genes (DEGs) in lymphoblastoid, fibroblast cell lines and induced pluripotent stem cell-derived neurons derived from patients with SA, homozygous for the GBA2 c.1780G > C missense variant. We further exploit DEGs in pathway analyses in order to elucidate candidate molecular mechanisms that are implicated in the development of the GBA2 gene-associated SA.

RESULTS

Our data reveal a total of 5217 genes with significantly altered expression between patient and control tested tissues. Furthermore, the most significant extracted pathways are presented and discussed for their possible role in the pathogenesis of the disease. Among them are the oxidative stress, neuroinflammation, sphingolipid signaling and metabolism, PI3K-Akt and MAPK signaling pathways.

CONCLUSIONS

Overall, our work examines for the first time the transcriptome profiles of GBA2-associated SA patients and suggests pathways and pathway synergies that could possibly have a role in SA pathogenesis. Lastly, it provides a list of DEGs and pathways that could be further validated towards the discovery of disease biomarkers.

A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma

Even in the current age of advanced medicine, the prognosis of malignant peritoneal mesothelioma (MPM) remains abysmal. Molecular mechanisms responsible for the initiation and progression of MPM are still largely not understood. Adopting an integrated bioinformatics approach, this study aims to identify the key genes and pathways responsible for MPM. Genes that are differentially expressed in MPM in comparison with the peritoneum of healthy controls have been identified by analyzing a microarray gene expression dataset. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of these differentially expressed genes (DEG) were conducted to gain a better insight. A protein-protein interaction (PPI) network of the proteins encoded by the DEGs was constructed using STRING and hub genes were detected analyzing this network. Next, the transcription factors and miRNAs that have possible regulatory roles on the hub genes were detected. Finally, survival analyses based on the hub genes were conducted using the GEPIA2 web server. Six hundred six genes were found to be differentially expressed in MPM; 133 are upregulated and 473 are downregulated. Analyzing the STRING generated PPI network, six dense modules and 12 hub genes were identified. Fifteen transcription factors and 10 miRNAs were identified to have the most extensive regulatory functions on the DEGs. Through bioinformatics analyses, this work provides an insight into the potential genes and pathways involved in MPM.

Level and change in bone microarchitectural parameters and their relationship with previous fracture and established bone mineral density loci

BACKGROUND

Osteoporosis is characterised by a reduction of bone mineral density (BMD) and predisposition to fracture. Bone microarchitecture, measured by high resolution peripheral quantitative computed tomography (HR-pQCT), has been related to fragility fractures and BMD and has been the subject of large-scale genome-wide analysis. We investigated whether fracture was related to baseline values and longitudinal changes in bone microarchitecture and whether bone microarchitecture was associated with established BMD loci.

METHODS

115 males and 99 females (aged 72-81 at baseline) from the Hertfordshire Cohort Study (HCS) were analysed. Fracture history was determined in 2011-2012 by self-report and vertebral fracture assessment. Participants underwent HR-pQCT scans of the distal radius and tibia in 2011-2012 and 2017. Previous fracture in relation to baseline values and changes in tibial HR-pQCT parameters was examined using sex-adjusted logistic regression with and without adjustment for age, sociodemographic, lifestyle and clinical characteristics; baseline values and changes in parameters associated with previous fracture were then examined in relation to four established BMD loci after adjustment for sex and age.

RESULTS

Previous fracture was related to: higher trabecular area (fully-adjusted odds ratio [95% CI] per SD greater baseline value: 2.18 [1.27,3.73], p = 0.005); lower total volumetric BMD (0.53 [0.34,0.84], p = 0.007), cortical area (0.53 [0.30,0.95], p = 0.032), cortical BMD (0.56 [0.36,0.88], p = 0.011) and cortical thickness (0.45 [0.27,0.77], p = 0.004); and greater declines in trabecular BMD (p = 0.001). Associations were robust in sex- and fully-adjusted analysis. Relationships between BMD loci and these HR-pQCT parameters were weak: rs3801387 (WNT16) was related to decline in trabecular BMD (p = 0.011) but no other associations were significant (p > 0.05).

CONCLUSION

Baseline values of HR-pQCT parameters and greater decline in trabecular BMD were associated with fracture. Change in trabecular BMD was associated with WNT16 which has been demonstrated to influence bone health in murine models and human genome-wide association studies (GWAS).