Supervisory
Committee: Dr. Marco Marra, Research Supervisor (Medical Genetics), Dr.
Steven Jones, Research Supervisor (Medical Genetics), Dr. Pamela Hoodless
(Medical Genetics)
University
Examiners: Dr. Angela Brooks-Wilson (Medical Genetics)
ABSTRACT
Since the first reported isolation of immortalized human embryonic
stem cell (hESC) lines in 1998, methods for directing their differentiation to
various specialized derivatives has been extensively demonstrated and provides
hope for future therapeutic applications. Furthermore, hESCs offer unique opportunities
for investigations of the molecular mechanisms governing early embryonic
development and oncogenesis. Global gene expression profiles of the 8
undifferentiated hESC lines were created using Serial Analysis of Gene
Expression (SAGE). It is widely established that SAGE is qualitative and quantitative,
producing a digital transcriptome survey of known and novel transcripts. We
have generated 12 long SAGE libraries from 8 undifferentiated hESC lines (NIH
stem cell registry code BG01, ES03, ES04, WA01, WA07, WA09, WA13, and WA14) and analyzed
2,613,475 total tags corresponding to 379,465 unique tag types (transcripts).
Through the employ of various comprehensive tag-to-gene mapping resources I
have provided a detailed survey of the genes expressed and differentially expressed
in multiple hESC lines. A suite of stemnessassociated factors was observed in
the hESC SAGE data. We also observed molecular components of several pathways involved
in embryonic development, the cell cycle, and programmed cell death. The study
of these data has identified transcripts up-regulated in hESCs compared with 72
normal human SAGE libraries. The development of a robust computational approach
to identify "novel" transcripts in hESCs has elucidated at least 301
candidates that may be integral to human pluripotent stem cells. These studies
represent an important step in the development of high throughput approaches to
an analysis of early human developmental processes and will be a strategic
element in more comprehensive interspecies comparisons of ES cells to identify preserved
control mechanisms.
SELECTED PUBLICATIONS
Martin Hirst, Allen Delaney, Sean Rogers, Angelique Schnerch, Deryck Persaud, Michael O’Connor, Thomas Zeng, Michelle Moksa, Stephanie
Menzies, Ágnes Baross Jaswinder Khattra, Stephanie Menzies, Asim
Siddiqui, Robert Holt, Steven Jones, James A. Thomson, Connie J. Eaves, Marco A. Marra.
LongSAGE Transcriptome analysis of Nine Human Embryonic Stem Cell
Lines reveals novel transcripts and an over representation of RNA binding
proteins. (Submitted).
Yun Zhao, Afshin Raouf, David Kent, Jaswinder Khattra,
Allen Delaney, Angelique Schnerch,
Jennifer Asano, Helen MacDonald, Christina Chan, Steven Jones, Marco A. Marra & Connie J. Eaves. PCR-SAGE: Development,
Validation and Application to CD34+ Cells from Normal Adult Human Bone Marrow.
(Submitted)
Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH,
Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG,
Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E,
Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J,
Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF,
Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin
TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki
Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL,
Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh
E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey
J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M,
Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson
RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood
J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL,
Krzywinski MI, Liao N, Morrin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM,
Schnerch A, Schein JE, Jones SJ,
Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J; MGC Project Team. 2004. The status, quality, and
expansion of the NIH full-length cDNA project: the Mammalian Gene Collection
(MGC). Genome Res. 14(10B):2121-7.
Prasad SS, Schnerch
A, Lam DY, To E, Jim J, Kaufman PL, Matsubara JA. 2002. Immunohistochemical investigations of neurofilament M' and
alphabeta-crystallin in the magnocellular layers of the primate lateral geniculate
nucleus. Mol Brain Res. 109(1-2):216-20.
SELECTED PRESENTATIONS
BC Cancer Agency Thursday Student Seminars. Vancouver,
British Columbia. June 2005. Schnerch, A. Global Transcriptome Analysis of
Undifferentiated Stem Cell Lines Using SAGE. Invited presentation.
Canada’s Michael Smith Genome Sciences Centre Bioinformatics
Seminar.
Vancouver, British Columbia. May 2003. Schnerch, A.
Bioinformatic
Approaches for Molecular Profiling in Stem Cells. Invited
Presentation.
SAGE Congress. Amsterdam, The Netherlands. January 2003.
Schnerch, A.,
Asano, J., Chan, S., Khattra, J., Oveisi, M., Pleasance,
E., Ruzanov, P., Varhol, R., Vatcher, G., Zuyderduyn, S., Eaves, C.J., Humphries.
K., Thomson, J.A., Jones, S., and Marra, M. Global Gene Expression Profiling
in Murine and Human Embryonic Stem Cells using SAGE and Affymetrix
GeneChips. Invited Presentation and Abstract.
GRADUATE STUDIES
Field of
Study: Stem cell analysis using SAGE.
Courses:
MEDI 590 Molecular Regulation of Cell Growth Dr. S. Pelech
