Analysis of alternative spicing in the transcriptome of osteosarcoma

Abstract

Aim: We have assessed the extent of alternative splicing in osteosarcoma samples and further examined the relationship between alternative transcripts and gene expression. Methods: We performed whole transcriptome analysis of osteosarcoma bone samples and sequenced total RNA from 36 fresh‐frozen samples (18 tumour bone samples and 18 non‐tumour paired samples) in matched pairs for each osteosarcoma patient. Data were analysed with Python package HTSeq and R package DEXSeq developed to analyse differential exon usage in transcriptome data. FDR correction was used to adjust nominal P‐values to obtain genome‐wide statistical significance. Results: We identified statistically significant (FDR below .05) differences in alternative splicing of 4175 transcripts. Several different alternative transcripts from the same genes were expressed, in the leptin receptor overlapping transcript, LEPROT; we detected 26 transcripts to be differentially expressed between tumour and normal tissue. Some transcripts were over‐expressed in the tumour and some transcripts were over‐expressed in normal tissue. The function of LEPROT gene is not fully understood, but it is involved in the regulation of leptin by interacting with the leptin receptor. Also, LEPROT regulates growth hormone‐dependent signalling and activity of the growth hormone receptor. Most of the differentially expressed genes were expressed as different alternative forms indicating prevalent and massive alternative splicing in osteosarcoma. Conclusions: Alternative splicing is prevalent in osteosarcoma and its regulation may play a significant role in sarcoma development. This is a good example of how differential splicing could be involved in the tumorigenesis and further studies need to consider this as an important molecular mechanism