“Identification and Analysis of Programmed Cell Death
Genes in Drosophila melanogaster and Human Cancer using Bioinformatic Analysis
of Gene Expression Data”
Wednesday, December 7, 2005, 12:30 pm, Room 203, Graduate
Student Centre
SUPERVISORY COMMITTEE
Dr. Steven Jones, Research Supervisor (Medical Genetics)
Dr. Marco Marra (Medical Genetics)
Dr. Dixie Mager (Medical Genetics)
Dr. Aly Karsan (Pathology and Laboratory Medicine)
Dr. Sharon Gorski (Molecular Biology and Biochemistry,
SFU)
EXAMINING COMMITTEE
Chair: Dr. Michael Underhill (Cellular and Physiological
Sciences)
Supervisory Committee: Dr. Steven Jones, Research
Supervisor (Medical Genetics), Dr. Marco Marra (Medical Genetics), Dr. Aly
Karsan (Pathology and Laboratory Medicine)
University Examiners: Dr. Tom Grigliatti (Zoology/Medical
Genetics), Dr. Ivan Sadowski (Biochemistry)
External Examiner: Dr. Mark Adams, Department of Genetics,
Case Western Reserve University, Cleveland, OH, USA.
ABSTRACT
Programmed cell death (PCD), or cell suicide, encompasses
multiple pathways including apoptosis and autophagy and is essential for
development, cellular homeostasis, and prevention of cancer cell growth. I
describe here the development and use of bioinformatic methods to identify
and analyze genes involved in PCD, both in the model organism Drosophila
melanogaster and in human cancer, by analysis of large-scale gene expression data.
An approach was developed to correctly identify genes from serial analysis of
gene expression (SAGE) data, distinguish the set of genes not accessible to the
SAGE method, and determine the optimal set of enzymes for Drosophila, C.
elegans, and human SAGE library construction. In Drosophila metamorphosis the
salivary gland undergoes autophagic PCD, whereby cellular components are engulfed
and degraded by cytoplasmic vacuoles, with additional hallmarks of
apoptosis. This is an excellent model in which to study the genes involved in PCD.
Transcriptional profiling of this tissue by expressed sequence tags (ESTs) and serial
analysis of gene expression (SAGE) identified many genes differentially regulated
prior to cell death, including genes known to be death regulators, genes in related
pathways, genes of no known function, and potentially novel unannotated genes. The
PCD-associated genes found in this analysis were then used to identify similar genes
in the human genome that are differentially expressed in cancer, which have the
potential to be involved in PCD and in oncogenesis. The pattern of genes expressed
suggests a role for autophagy associated processes in cancer progression. To
examine this further, expression of the autophagy gene LC3 was examined in
multiple cancer types, subtypes, and stages. LC3 expression is decreased significantly
in several cancer types and also during cancer progression, suggesting a
tissue- and stage-specific role for autophagy in regulating oncogenesis. In
summary, methods for gene expression analysis were developed and applied to
examine the genes involved in programmed cell death, particularly autophagy,
and the roles of these processes in cancer.
PUBLICATIONS
Pleasance
ED and Jones SJM. 2005. Evaluation of SAGE tags for
transcriptome study. In: Wang SM, ed., SAGE: Current Technologies and Applications.
Horizon Scientific Press, Norwich, UK. p. 1-27.
Griffith OL, Pleasance
ED, Fulton DL, Oveisi-Fordoei M, Ester M, Siddiqui A, and Jones SJM. 2005. Large scale comparison of publicly
available SAGE, cDNA
microarray, and oligonucleotide microarray expression data
for global co-expression analysis. Genomics 84: 476-488.
Pleasance
ED, Marra MA, and Jones SJM. 2003. Assessment of SAGE in
transcript identification. Genome Res 13(6), 1203-1215.
Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Zuyderduyn SD, Jones SJ, and Marra MA. 2003.
A SAGE approach to discovery of genes involved in autophagic cell death. Curr
Biol 13(4):358-63. Robertson G, Bilenky M, Lin K, He A, Yuen W, Dagpinar M,
Varhol R, Teague K, Griffith OL, Zhang X, Pan Y, Hassel M, Sleumer MC, Pan W,
Pleasance ED, Chuang M, Hao H, Li YY, Robertson N, Fjell C, Li B,
Montgomery SB, Astakhova T, Zhou J, Sander J, Siddiqui AS and Jones SJM. 2005. cisRED:
A database system for genome scale computational discovery of regulatory
elements. Nucleic Acids Res., in press.
SELECTED PRESENTATIONS
Pleasance ED, Sleumer MC, Bilenky M, Chuang M, Dagpinar M,
Griffith OL, He A, Lin K, Montgomery S, Oveisi M, Pan W, Robertson G,
Robertson N, Teague K, Varhol R, Yuen W, Zhang X, Gorski SM, Siddiqui A, and
Jones SJM. A method for genome-wide cis-regulatory element discovery in Drosophila
melanogaster. Poster presentation at Genome Informatics, Cold Spring Harbor,
NY, Oct. 28-Nov. 1, 2005.
Pleasance ED, Gorski SM, Marra MA, and Jones SJM. SAGE
database analysis of programmed cell death in Drosophila melanogaster and
cancer. Poster presentation at Genomics Forum Research Exchange 2005, Vancouver, BC,
Apr. 1, 2005.
Pleasance ED, Gorski SM, Marra MA, and Jones SJM. Expression,
interaction, and comparative genomics approaches to study programmed cell
death. Poster
presentation at The Biology of Genomes, Cold Spring
Harbor, NY, May 12-16, 2004.
Pleasance ED, Gorksi SM, Griffith OL, Marra MA, and Jones
SJM. Programmed
cell death in cancer: Expression patterns of genes
involved in apoptosis and
autophagic cell death. Poster presentation at Annual
Cancer Conference,
Vancouver, BC, Nov. 28-29, 2003.
Pleasance ED, Varhol R, Zuyderduyn S, Marra MA, and Jones
SJM. Assessment of SAGE in transcript identification based on a new method of
tag-to-gene mapping. Oral presentation at SAGE 2003, Amsterdam, The
Netherlands, Jan. 17-19, 2003. Pleasance ED, Chittaranjan S, Freeman JD, Varhol RJ,
Zuyderduyn SD, Marra MA, Gorski SM, and Jones SJM. Bioinformatic analysis of SAGE
data and applications to programmed cell death. Poster presentation at Annual
Cancer Conference, Vancouver, BC, Nov. 29-30, 2002.
AWARDS
Academic Scholarships:
2004-2006 Canadian Institutes for Health Research CGS-DRA
2002-2005 Michael Smith Foundation for Health Research
Trainee Award
2002-2004 Natural Sciences and Engineering Research
Council PGS-B
