Transcriptomic Changes of Murine Visceral Fat Exposed to Intermittent Hypoxia at Single Cell Resolution

Intermittent hypoxia (IH) is a hallmark of obstructive sleep apnea (OSA) and induces metabolic dysfunction manifesting as inflammation, increased lipolysis and insulin resistance in visceral white adipose tissues (vWAT). However, the cell types and their corresponding transcriptional pathways underlying these functional perturbations are unknown. Here, we applied single nucleus RNA sequencing (snRNA-seq) coupled with aggregate RNA-seq methods to evaluate the cellular heterogeneity in vWAT following IH exposures mimicking OSA. C57BL/6 male mice were exposed to IH and room air (RA) for 6 weeks, and nuclei from vWAT were isolated and processed for snRNA-seq followed by differential expressed gene (DEGs) analyses by cell type, along with gene ontology and canonical pathways enrichment tests of significance. IH induced significant transcriptional changes compared to RA across 14 different cell types identified in vWAT. We identified cell-specific signature markers, transcriptional networks, metabolic signaling pathways, and cellular subpopulation enrichment in vWAT. Globally, we also identify 298 common regulated genes across multiple cellular types that are associated with metabolic pathways. Deconvolution of cell types in vWAT using global RNA-seq revealed that distinct adipocytes appear to be differentially implicated in key aspects of metabolic dysfunction. Thus, the heterogeneity of vWAT and its response to IH at the cellular level provides important insights into the metabolic morbidity of OSA and may possibly translate into therapeutic targets.

RNA-Seq profiling revealed PBMC RNA as potential biomarker for hepatocellular carcinoma

Background Hepatocellular carcinoma is one of the most common malignancies with extremely high incidence and mortality rates. Although there have been many studies focus on biomarkers study, few have been reported on PBMC RNA profiles of hepatocellular carcinoma. Methods In this study, we attempted to profile the expression of Peripheral Blood Mononuclear Cells (PBMCs) RNA by using RNA-seq technology and compared the transcriptome between hepatocellular carcinoma patients and the healthy controls. 17 patients and 17 healthy controls involved in this study, PBMCs RNA were sequenced. The sequencing data were analyzed with bioinformatics tools and qRT-PCR was used for selected differential expressed gene validation. Results It is showed that 1578 dysregulated genes found including 1334 upregulated genes and 244 downregulated genes. GO enrichment and KEGG analysis denoted most of the differential expressed genes (DEGs) involved in immune response are closely related to hepatocellular carcinoma. Expression of the 6 selected genes (DEGs, SELENBP1, SLC4A1, SLC26A8, HSPA8P4, CALM1, and RPL7p24) were confirmed by qRT-PCR, and higher sensitivity and specificity obtained by ROC analysis of the 6 genes. CALM1 was found gradually decreasing along with the tumor enlarged. Conclusions It is suggested potential biomarker for diagnosis, classification and therapeutic target of hepatocellular carcinomas. This study provided new visions into development of liver cancer and potential efficient clinical diagnosis in the future.

Transcriptome Profile of the Variegated Ficus microcarpa c.v. Milky Stripe Fig Leaf

Photosynthetic properties and transcriptomic profiles of green and white sectors of Ficus microcarpa (c.v. milky stripe fig) leaves were examined in naturally variegated plants. An anatomic analysis indicated that chloroplasts of the white sectors contained a higher abundance of starch granules and lacked stacked thylakoids. Moreover, no photosynthetic rate was detected in the white sectors. Transcriptome profile and differential expressed gene (DEG) analysis showed that genes encoding PSII core proteins were down-regulated in the white sectors. In genes related to chlorophyll metabolism, no DEGs were identified in the biosynthesis pathway of chlorophyll. However, genes encoding the first step of chlorophyll breakdown were up-regulated. The repression of genes involved in N-assimilation suggests that the white sectors were deprived of N. The mutation in the transcription factor mitochondrial transcription termination factor (mTERF) suggests that it induces colorlessness in leaves of the milky stripe fig.