The Sequencing and Non-coding RNA Program, a service of the Center for Targeted Therapy, offers MD Anderson investigators cutting-edge, emerging technology and expertise in functional genomics for the discovery of new non-coding RNAs (ncRNA) and expression profiling for known ncRNAs to further their cancer research.
- SOLiD™ System/Ion Proton
A “next generation” genome sequencing technology platform that provides broad applications for various forms of genome sequencing; gene expression, epigenetic and transcriptome profiling; and small RNA discovery. Applications include: whole genome sequencing; targeted genome re-sequencing; whole transcriptome, small RNA and mRNA expression sequencing and profiling; de novo sequencing; ChIP-sequencing; and epigenetic methylation sequencing and profiling. No other institution, at this time, is utilizing this technology as a service for its scientists.
- ncRNA/miRNA Expression Array Profiling
Conducted on in-house microarray platforms and has the capacity to profile up to approximately 48 samples per week. The program’s director, Chang-gong Liu, Ph.D., developed the first-ever ncRNA/miRNA microarray platform.
- Full-service support for all Affymetrix GeneChip® microarray technology including genome-wide mRNA expression profiling, SNP genotyping and ChIP-on-Chip, to name but a few. Turnaround time is approximately three-to-five days.
- Support gene expression quantitation and the detection of SNPs utilizing the Applied Biosystems Fast Real-Time PCR System with a turnaround time of approximately two-to-three hours.
- Within one hour, the program can provide quantification and analysis of DNA, RNA, proteins and cells with the Agilent 2100 Bioanalyzer and the Thermo Scientific NanoDrop™ 1000 Spectrophotometer.
About Non-Coding RNAs
The study of non-coding RNAs (ncRNAs), and specifically microRNAs (miRNAs), represents one of the most active research areas in molecular biology and continues to shed light on the human genome. Non-coding RNAs are molecules that are not translated into proteins and they play an important role in cancer initiation, progression and metastases. Already miRNAs have shown promise as diagnostic and prognostic markers in cancer and as targets for the development of new therapeutic approaches. The CTT brings MD Anderson to the forefront of this emerging field of cancer research by introducing its newest offering – the ncRNA Program.
Non-coding RNAs (ncRNAs) are a new class of RNA transcribed from 80% of the human genome and can be classified based on sizes as small as ~18 to 40 nucleotides (nts) that includes miRNA, siRNA, piwiRNA, rasiRNA and large ncRNA sized more than 50 nts. They are transcribed from intergenic, intronic, antisense and interleaved regions and overlap with protein-coding genes.
MicroRNAs (miRNAs) sized from 19 to 25 nts that cleaved from 70 to 100 nts hairpin pre-miRNA precursors, represent n newly discovered class of short, small, non-coding RNAs that serve as negative regulators for protein-coding gene expression.
Since the first miRNA, Lin 4, was discovered in 1993 in C. elegans, more than 9,000 miRNA genes have been identified in vertebrate, flies, worms, plants and even in viruses (Griffiths-Jones et al., 2006) using cloning and sequencing techniques. The updated human miRNoma contains more than 900 mature microRNAs encoded from 721 precursor sequences (Sanger miRbase Version 14). While the precise number of miRNA genes in the human genome is still unknown (Berezikov et al. 2005), the total number of miRNA precursors is expected to surpass the 1,000 mark (Bentwich et al., 2005) and potentially reach as high as 25,000 (Miranda et al., 2006).
Predictions suggest that miRNAs regulate approximately 30% of protein-coding genes in the human genome that relate to development, differentiation, proliferation, apoptosis, house-keeping, metabolism and signaling pathways (Lewis et al., 2005). The ncRNA Program at MD Anderson offers two technologies for research of ncRNAs: microarrays and SOLiD™ next generation sequencing.
- Microarrays were developed as a powerful high throughput technology to monitor thousands of mRNA or ncRNA by transcriptional profiling in a single experiment. In order to gain more insight into the biological functions specifically related to miRNAs globally and understand the involvement of miRNAs in human cancer, we developed a high throughput custom miRNA array platform that profiled and analyzed more than 10,000 primary tumors or cell lines (Liu et al., 2008). We found that miRNA expression signatures are a powerful tool to classify tumors or sub-classify every type of human cancer (Volinia et al., 2006; Iorio et al., 2007). The miRNA profiling data from cancers that has been collected suggests that mis-regulations of miRNA expression are key components in biological processes – including the pathways leading to cancers.
- Small RNA-seq and whole transcriptome-seq by SOLiD™ next generation sequencing enables us to sequence not only all known expressed, small and large non-coding RNA and protein-coding mRNA globally in one single experiment for signatures, but it is also a powerful approach for non-coding biomarker discovery in cancers.