Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains

BACKGROUND

In the post-GWAS era, there is an unmet need to decode the underpinning genetic etiologies of late-onset Alzheimer's disease (LOAD) and translate the associations to causation.

METHODS

We conducted ATAC-seq profiling using NeuN sorted-nuclei from 40 frozen brain tissues to determine LOAD-specific changes in chromatin accessibility landscape in a cell-type specific manner.

RESULTS

We identified 211 LOAD-specific differential chromatin accessibility sites in neuronal-nuclei, four of which overlapped with LOAD-GWAS regions (±100 kb of SNP). While the non-neuronal nuclei did not show LOAD-specific differences, stratification by sex identified 842 LOAD-specific chromatin accessibility sites in females. Seven of these sex-dependent sites in the non-neuronal samples overlapped LOAD-GWAS regions including APOE. LOAD loci were functionally validated using single-nuclei RNA-seq datasets.

CONCLUSIONS

Using brain sorted-nuclei enabled the identification of sex-dependent cell type-specific LOAD alterations in chromatin structure. These findings enhance the interpretation of LOAD-GWAS discoveries, provide potential pathomechanisms, and suggest novel LOAD-loci.

Expression and survival analysis of the STAT gene family in diffuse gliomas using integrated bioinformatics

Signal Transducer and Activator of Transcription (STAT) belongs to the acyltransferase family and participates in cell viability response to different cell stimuli and pathogens. By mediating the expression of a variety of genes, the STAT family plays a prominent part in mammal immunity, proliferation and differentiation. Dysregulations and mutations of STAT factors have been revealed in many kinds of cancers including diffuse gliomas; however, expression characteristic and prognostic value of STAT in diffuse gliomas remain to be elucidated. In this study, we analyzed the transcriptional and survival data of gliomas using ONCOMINE, cBioPortal, GEPIA, COXPRESDB and WEBGESTALTR databases. The results demonstrated that the transcriptional level of STAT1, STAT3 and STAT5A in gliomas was significantly higher than that in normal tissue. Furthermore, dysregulations of STAT1, STAT3, STAT4, STAT5B and STAT6 were referred to as the potential biomarkers to sub-group analysis of gliomas. Survival analysis by the Kaplan-Meier Plotter suggested that glioma patients with high expression of STAT1, STAT3 and STAT5B tended to have poor survival. These data revealed that the STAT family may be an essential aspect of glioma progression and prognosis.

Global profiling of alternative RNA splicing events provides insights into molecular differences between various types of hepatocellular carcinoma

Background

Dysregulations in alternative splicing (AS) patterns have been associated with many human diseases including cancer. In the present study, alterations to the global RNA splicing landscape of cellular genes were investigated in a large-scale screen from 377 liver tissue samples using high-throughput RNA sequencing data.

Results

Our study identifies modifications in the AS patterns of transcripts encoded by more than 2500 genes such as tumor suppressor genes, transcription factors, and kinases. These findings provide insights into the molecular differences between various types of hepatocellular carcinoma (HCC). Our analysis allowed the identification of 761 unique transcripts for which AS is misregulated in HBV-associated HCC, while 68 are unique to HCV-associated HCC, 54 to HBV&HCV-associated HCC, and 299 to virus-free HCC. Moreover, we demonstrate that the expression pattern of the RNA splicing factor hnRNPC in HCC tissues significantly correlates with patient survival. We also show that the expression of the HBx protein from HBV leads to modifications in the AS profiles of cellular genes. Finally, using RNA interference and a reverse transcription-PCR screening platform, we examined the implications of cellular proteins involved in the splicing of transcripts involved in apoptosis and demonstrate the potential contribution of these proteins in AS control.

Conclusions

This study provides the first comprehensive portrait of global changes in the RNA splicing signatures that occur in hepatocellular carcinoma. Moreover, these data allowed us to identify unique signatures of genes for which AS is misregulated in the different types of HCC.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3029-z) contains supplementary material, which is available to authorized users.