Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes

• Published in: BMC medical genomics 2011-02, Vol.4 (1), p.19-19, Article 19
• Main Authors: Beck, Dominik, Ayers, Steve, Wen, Jianguo, Brandl, Miriam B, Pham, Tuan D, Webb, Paul, Chang, Chung-Che, Zhou, Xiaobo
• Format: Article
• Language: English
• Subjects: Bioinformatics; Bone marrow; Computational Biology; Disease; DNA sequencing; Exons; Gene Expression Profiling; Gene Expression Regulation; Genetic aspects; Genetic transcription; Genomes; Humans; Myelodysplastic syndromes; Myelodysplastic Syndromes - genetics; Myelodysplastic Syndromes - metabolism; Myelodysplastic Syndromes - pathology; Nucleic Acid Conformation; Nucleotide sequencing; Physiological aspects; RNA; RNA polymerase; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; RNA, Small Untranslated - chemistry; RNA, Small Untranslated - metabolism; RNA, Small Untranslated - physiology; Sequence Analysis, RNA; Studies; Transcription, Genetic
• ISSN: 1755-8794; 1755-8794
• DOI: 10.1186/1755-8794-4-19

Myelodysplastic Syndromes (MDSS) are pre-leukemic disorders with increasing incident rates worldwide, but very limited treatment options. Little is known about small regulatory RNAs and how they contribute to pathogenesis, progression and transcriptome changes in MDS. Patients' primary marrow cells were screened for short RNAs (RNA-seq) using next generation sequencing. Exon arrays from the same cells were used to profile gene expression and additional measures on 98 patients obtained. Integrative bioinformatics algorithms were proposed, and pathway and ontology analysis performed. In low-grade MDS, observations implied extensive post-transcriptional regulation via microRNAs (miRNA) and the recently discovered Piwi interacting RNAs (piRNA). Large expression differences were found for MDS-associated and novel miRNAs, including 48 sequences matching to miRNA star (miRNA*) motifs. The detected species were predicted to regulate disease stage specific molecular functions and pathways, including apoptosis and response to DNA damage. In high-grade MDS, results suggested extensive post-translation editing via transfer RNAs (tRNAs), providing a potential link for reduced apoptosis, a hallmark for this disease stage. Bioinformatics analysis confirmed important regulatory roles for MDS linked miRNAs and TFs, and strengthened the biological significance of miRNA*. The "RNA polymerase II promoters" were identified as the tightest controlled biological function. We suggest their control by a miRNA dominated feedback loop, which might be linked to the dramatically different miRNA amounts seen between low and high-grade MDS. The presented results provide novel findings that build a basis of further investigations of diagnostic biomarkers, targeted therapies and studies on MDS pathogenesis.