Dataset Information

Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes.

ABSTRACT:

Background

Diabetes causes the dysregulation of several organs, and these effects are often closely associated with changes in the expression of long non-coding RNAs (lncRNAs), a group of non-coding RNAs, within these tissues. Previous studies have described a variety of changes in the expression profile of several lncRNAs from different organs in response to the pathogenesis of diabetes. However, none of these studies compared the expression profiles of these lncRNAs between these organs. This study was designed to identify common and specific lncRNAs involved in the progression of diabetes in the skeletal muscles and kidneys.

Methods

Publicly available RNA sequencing data of diabetic patients was obtained from the Gene Expression Omnibus database. By analyzing the expression of lncRNAs in these datasets, differentially expressed lncRNAs in each tissue between non-diabetic and diabetic patients were identified. To identify any lncRNAs changed in common in both kidney and muscle tissues, those lncRNAs that are significantly dysregulated in both datasets were selected.

Results

These evaluations identified a series of novel lncRNAs unique to each organ and several transcripts that were common to both skeletal muscle and kidney tissues in these patients. Interestingly, the genomic location of these lncRNAs suggests that they reside in close proximity to several protein-coding genes known to be related to diabetes suggesting that these lncRNAs may have a regulatory relationship with their neighboring genes.

Conclusion

These results offer valuable insights into the role of lncRNAs during the pathogenesis of diabetes.

SUBMITTER: Kim YK

PROVIDER: S-EPMC9512191 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Publications

Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes.

Kim Young-Kook YK

PloS one 20220926 9

<h4>Background</h4>Diabetes causes the dysregulation of several organs, and these effects are often closely associated with changes in the expression of long non-coding RNAs (lncRNAs), a group of non-coding RNAs, within these tissues. Previous studies have described a variety of changes in the expression profile of several lncRNAs from different organs in response to the pathogenesis of diabetes. However, none of these studies compared the expression profiles of these lncRNAs between these organ ...[more]

PMID: 36155986

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Project description:BackgroundRecovering high quality intact RNA from post-mortem tissue is of major concern for gene expression studies in animals and humans. Since the availability of post-mortem tissue is often associated with substantial delay, it is important that we understand the temporal variation in the stability of total RNA and of individual gene transcripts so as to be able to appropriately interpret the data generated from such studies. Hence, the objective of this experiment was to qualitatively and quantitatively assess the integrity of total and messenger RNA extracted from bovine skeletal muscle, subcutaneous adipose tissue and liver stored at 4 degrees C at a range of time points up to 22 days post-mortem. These conditions were designed to mimic the environment prevailing during the transport of beef from the abattoir to retail outlets.ResultsThe 28S and 18S rRNA molecules of total RNA were intact for up to 24 h post-mortem in liver and adipose tissues and up to 8 days post-mortem in skeletal muscle. The mRNA of housekeeping genes (GAPDH and ACTB) and two diet-related genes (RBP5 and SCD) were detectable up to 22 days post-mortem in skeletal muscle. While the mRNA stability of the two housekeeping genes was different in skeletal muscle and liver, they were similar to each other in adipose tissue. After 22 days post-mortem, the relative abundance of RBP5 gene was increased in skeletal muscle and in adipose tissue and decreased in liver. During this period, the relative abundance of SCD gene also increased in skeletal muscle whereas it decreased in both adipose tissue and liver.ConclusionStability of RNA in three tissues (skeletal muscle, subcutaneous adipose tissue and liver) subjected to long-term post-mortem storage at refrigeration temperature indicated that skeletal muscle can be a suitable tissue for recovering biologically useful RNA for gene expression studies even if the tissue is subjected to post-mortem storage for weeks, whereas adipose tissue and liver should be processed within 24 hours post-mortem.

Project description:BackgroundAlthough Helicobacter pylori (H.pylori) is the dominant gastrointestinal pathogen, the genetic and molecular mechanisms underlying H.pylori-related diseases have not been fully elucidated. Long non-coding RNAs (lncRNAs) have been identified in eukaryotic cells, many of which play important roles in regulating biological processes and pathogenesis. However, the expression changes of lncRNAs in human infected by H.pylori have been rarely reported. This study aimed to identify the dysregulated lncRNAs in human gastric epithelial cells and tissues infected with H.pylori.MethodsThe aberrant expression profiles of lncRNAs and mRNAs in GES-1 cells with or without H.pylori infection were explored by microarray analysis. LncRNA-mRNA co-expression network was constructed based on Pearson correlation analysis. Gene Ontology (GO) and KEGG Pathway analyses of aberrantly expressed mRNAs were performed to identify the related biological functions and pathologic pathways. The expression changes of target lncRNAs were validated by qRT-PCR to confirm the microarray data in both cells and clinical specimens.ResultsThree hundred three lncRNAs and 565 mRNAs were identified as aberrantly expressed transcripts (≥2 or ≤0.5-fold change, P < 0.05) in cells with H.pylori infection compared to controls. LncRNA-mRNA co-expression network showed the core lncRNAs/mRNAs which might play important roles in H.pylori-related pathogenesis. GO and KEGG analyses have indicated that the functions of aberrantly expressed mRNAs in H.pylori infection were related closely with inflammation and carcinogenesis. QRT-PCR data confirmed the expression pattern of 8 (n345630, XLOC_004787, n378726, LINC00473, XLOC_005517, LINC00152, XLOC_13370, and n408024) lncRNAs in infected cells. Additionally, four down-regulated (n345630, XLOC_004787, n378726, and LINC00473) lncRNAs were verified in H.pylori-positive gastric samples.ConclusionOur study provided a preliminary exploration of lncRNAs expression profiles in H.pylori-infected cells by microarray. These dysregulated lncRNAs might contribute to the pathological processes during H.pylori infection.

Dataset Information

Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes.

Background

Methods

Results

Conclusion

Publications

Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes.

Similar Datasets

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