General Technique

Massive Parallel Signature Sequencing (MPSS), pioneered by Sydney Brenner at the former Lynxgen Therapeutics, Inc. (now Solexa, Inc.), operationally does the following. The individual 3´ restriction fragments from a cDNA library of 1,000,000 clones may be each coupled to one of a million beads, the sequence on each bead amplified, the beads arrayed in a flow cell, and then each of the bead DNA fragments are sequenced simultaneously for 20 residues to provide a million signature sequences. Thus, in a single run, 500,000 to one million transcripts can be identified, and the corresponding transcriptome (collection of mRNAs in a cell type or tissue) quantitatively characterized analyzing about five times as many mRNAs as are contained in the typical cell (cells typically have about 200,000 mRNAs). The results are reported as individual transcripts/million transcripts. For more detailed description of the technology, please go to Solexa´s website. Http://www.lynxgen.com/wt/tert.php3?page_name=mpss

Purpose/use/application of the technique:

Using MPSS technology, one can visualize mRNAs present at a low copy level per cell (1-30 copies per cell). More importantly, quantitative changes in low abundance mRNAs can readily be measured. The high sensitivity of the MPSS technology is the key to quantifying the behavior of some low-abundance transcription factors and signal transduction factors that are key players in gene regulatory networks and protein networks, respectively. MPSS is currently the best technology available to delineate the "part lists" of a system, a critical starting point for a systems approach to disease. Solexa Inc.and other companies are developing next generation technologies for generating MPSS-type data.

Example(s) of projects at ISB that use this technique:

1. Systems biology of prostate cancer (Biaoyang Lin)
2. Systems biology of chemotherapy response in ovarian cancer (Biaoyang Lin)
3. MPSS analysis of islet cells (Inyoul Lee, Nathan Goodman)
4. LPS-activated macrophage gene expression (Jared Roach)

Representative publication(s):

Biaoyang Lin, James T. White, Wei Lu, Tao Xie, Angelita G. Utleg, Xiaowei Yan, Eugene C. Yi, Paul Shannon, Irina Khrebtukova, Paul H. Lange, David R. Goodlett, Daixing Zhou, Thomas J. Vasicek, and Leroy Hood. Evidence for the Presence of Disease-Perturbed Networks in Prostate Cancer Cells by Genomic and Proteomic Analyses: A Systems Approach to Disease. Cancer Research. 2005 April;15; 65:(8).

G. A. Stolovitzky, A. Kundaje, G. A. Held, K. H. Duggar, C. D. Haudenschild, D. Zhou , T. J. Vasicek, K. D. Smith, A. Aderem, and J. C. Roach. Statistical analysis of MPSS measurements: Application to the study of LPS-activated macrophage gene expression . PNAS. February, 2005