Integrative Analysis of Next Generation Sequencing for Small Non-Coding RNAs and Transcriptional Regulation in Myelodysplastic Syndromes.
Jose M Gonzalez-Berjon, Dominik Beck, Steve Ayers, Jianguo Wen, Miriam Brandl, Tuan Pham, Paul Webb, Xiaobo Zhou, Chung Che Chang. The Methodist Hospital and The Methodist Hospital Research Institute, Houston, TX; The University of New South Wales, Canberra, ACT, Australia; The Methodist Hospital Research Institute, Houston, TX; Weill Cornell Medical College, New York, NY
Background: Myelodysplastic Syndromes (MDS) are pre-leukemic disorders with very limited treatment options. Little is known about small regulatory RNAs and how they contribute to pathogenesis progression and transcriptome changes in MDS. This study represents the initial step of a comprehensive study about the role of small RNAs in MDS using next generation sequencing (NGS) technologies.
Design: We performed high-throughput next generation sequencing of small RNAs (RNA-seq) on primary bone marrow cells from control, low-grade: refractory anemia (RA) and high-grade: refractory anemia with excess blast (RAEB2) MDS on an Illumina Genome Analyzer IIx. All reads were trimmed (length 22 bp) and aligned against the current version of the human genome (GRCh37). Analysis pipeline that handled raw reads, sequence alignment, data storage as well as integrative read annotation was developed in house and implemented.
Results: In the early phase (low-grade) MDS, extensive post-transcriptional regulation via microRNAs (miRNA) and the recently discovered Piwi interacting RNAs (piRNA) were observed. 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 the 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 (in contrast to low-grade MDS).
Conclusions: Our results suggest that NGS is an important tool to explore the small RNAome for undertanding MDS pathogenesis. Many of our findings are not achievable by the microarray-based technology. For example, the identification of increased expression of piRNAs in RA can potentially protect DNA from the accumulation of mutations and may contribute to less likelihood of transforming to AML as contrast to high-grade MDS. Further studies are warranted to experimentally substantiate our observations and to develop biomarkers for the diagnosis and treatment of MDS.
Monday, February 28, 2011 9:30 AM
Poster Session I Stowell-Orbison/Surgical Pathology/Autopsy Awards Poster Session # 164, Monday Morning