7 research outputs found
Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome.
Turner syndrome is a chromosomal abnormality characterized by the absence of whole or part of the X chromosome in females. This X aneuploidy condition is associated with a diverse set of clinical phenotypes such as gonadal dysfunction, short stature, osteoporosis and Type II diabetes mellitus, among others. These phenotypes differ in their severity and penetrance among the affected individuals. Haploinsufficiency for a few X linked genes has been associated with some of these disease phenotypes. RNA sequencing can provide valuable insights to understand molecular mechanism of disease process. In the current study, we have analysed the transcriptome profiles of human untransformed 45,X and 46,XX fibroblast cells and identified differential expression of genes in these two karyotypes. Functional analysis revealed that these differentially expressing genes are associated with bone differentiation, glucose metabolism and gonadal development pathways. We also report differential expression of lincRNAs in X monosomic cells. Our observations provide a basis for evaluation of cellular and molecular mechanism(s) in the establishment of Turner syndrome phenotypes
Differentially expressed long non-coding RNAs in 45,X and 46,XX fibroblast cells at P value<0.001 and FDR (q) value<0.05.
<p>Differentially expressed long non-coding RNAs in 45,X and 46,XX fibroblast cells at P value<0.001 and FDR (q) value<0.05.</p
Heat Map depicting the expression levels 116 significantly differentially expressed genes in 45,X and 46,XX fibroblast cells.
<p>Heat Map depicting the expression levels 116 significantly differentially expressed genes in 45,X and 46,XX fibroblast cells.</p
Validation of RNA-seq results by qRT-PCR.
<p>In total, five genes including XIST (lincRNA) were selected for real time data validation. Relative expression and FPKM values (log10) are shown for 45,X and 46,XX conditions. qRT-PCR results are found to correlate with RNA seq data, hence further confirming the expression dataset.</p
Summary of RNA-seq data generated and mapping statistics.
<p>Total number of reads generated and mapped after quality filtering for both 45,X and 46,XX human fibroblast cells.</p