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Background  A growing number of severe  Mycoplasma pneumoniae  pneumonia (MPP) cases have been reported recently. However, the pathogenesis of severe MPP is not clear. In the current study, transcriptome sequencing was used to identify gene expression and alternative splicing profiles to provide insights into the pathogenesis of severe MPP.    Methods  RNAs of bronchoalveolar lavage fluid (BALF) samples from three severe MPP children and three mild MPP children were analyzed respectively by deep sequencing followed by computational annotation and quantification.    Results  The gene expression analysis revealed 14 up-regulated and 34 down-regulated genes in severe MPP children comparing to mild MPP children. The top 10 most up-regulated genes were  IGHV1-69 ,  CH17-472G23.1 ,  ATP1B2 ,  FCER2 ,  MUC21 ,  IL13 ,  FCRLB ,  CLEC5A ,  FAM124A , and  INHBA . The top 10 most down-regulated genes were  OSTN-AS1 ,  IL22RA2 ,  COL3A1 ,  C1orf141 ,  IGKV2-29 ,  RP11-731F5.2 ,  IGHV4-4 ,  KIRREL ,  DNASE1L3 , and  COL6A2 . Clustering analysis revealed similar expression pattern of  CLEC5A ,  IL13 ,  FCER2 , and  FLT1 . Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed changes related to primary immunodeficiency in severe MPP children comparing to mild MPP children; the pathway involves  CD19 ,  TNFRSF13C ,  CD79A , and  AICDA  genes. Among the differentially expressed genes, significant alternative splicing events were found in  FCER2  and  FCRLA .    Conclusions  The current study on RNA sequencing provides novel insights into the pathogenesis of severe MPP in terms of gene expression and alternative splicing. The up-regulation of  IL13 ,  FCER2 ,  FLT1 , and  CLEC5A  and the down-regulation of  CD79A ,  AICDA ,  CD19 , and  TNFRSF13C  may contribute to the pathogenesis of severe MPP. The differential expressions of  FCER2  and  FCRLA  could be due to their alternative splicing.    Electronic supplementary material  The online version of this article (doi:10.1186/s40246-017-0101-y) contains supplementary material, which is available to authorized users.

human genomics

Transcriptome analysis of bronchoalveolar lavage fluid from children with severe Mycoplasma pneumoniae pneumonia reveals novel gene expression and immunodeficiency