Genomic Analysis of Prostate Cancer Cells

1
Genomic Analysis of Prostate Cancer Cells Using
Agilent Array Technology
Vanitha Bhoopalan
Semail Ulgen
Yildirim Department of Cellular and Molecular
Biology Department of
Mathematics
Introduction KAI1/CD82 belongs to the
transmembrane 4 super family (TM4SF). These
tetraspanins have implicated in the regulation of
cell motility, morphology, fusion, signaling,
fertilization, and differentiation.
Microarray Technology makes it possible to
simultaneously observe thousands of genes in
action and to dissect the functions, the
regulatory mechanisms, and the interaction
pathways of the entire genome. We compare the
gene expression of the tetraspanin KAI1/CD82 in
prostate tumor metastasis human cells.
Computational methods or softwares such as
Bioconductors, Matlab, GeneSpring etc. able us to
integrate and understand the avalanche of genome
data generated by Agilent Microarray Technology.
We analyze data obtained for two groups of cells
by using ANOVA and T-test.

• Conclusions
• Studied different methods of analyzing large
  amount of data sets
• Studied the Agilent data and Agilent technology
• Studied Microarray technology
• Read and studied the GeneSpring technology
• Read and studied the Bioconductor (LIMMA
  project) technology
• Got familiar with a relatively new problem in
  human prostate cancer
• Got familiar with a cancer metastasis suppressor
  tetraspanin KAI1/CD82
• Contacted Van Andel Institute for gene
  expression of eight plate-cell cultures. We are
  waiting for the results. We expect to get a
  result of Highly conserved consensus
• sequence gene mutation. If this happens, this
  might shed a light on future cancer research and
  a possible permanent cure for cancer.

Background A recent study (Sridhar and
Miranti,2006) showed that tetraspanin KAI1/CD82
is a cancer metastasis suppressor. The mechanism
of KAI1/CD82-mediated metastasis suppression
remains unclear. Restoration of CD82 expression
to physiological levels in the metastatic
prostate cell line PC3 inhibits integrin-mediated
cell migration and invasion, but does not
affect integrin expression.

• Objectives
• To learn DNA Microarray Technology
• To learn and experience the computational
  techniques to analyse microarray data set
• To analyse the array data statistical analysis
  of by using both Matlab and Agilent Technology
  and compare the results
• To find the Regulatory Gene Sequence in the
  expression of KAI1/CD82 in prostate cancer cells
• Research Question
• What is the Gene Sequence that regulates the gene
  expression of KAI1/CD82 in prostate cancer cells?
  

• Data Collection
• Normal and Prostate Tumor Human Cells cultured
  by Dr. Suganthi Sridhar at CHS Building at GVSU
• Agilent Data Set provided in Spread sheet by Van
  Andel Institute by Microarray Technology
• G x n, where G is the number of genes that have
  expression levels measured in each of the n
  samples

• Funding Sources
• Graduate Studies Grant Administration (Vanitha
  Bhoopolan is awarded 500 for this project by
  GSGA.)
• Grand valley State University , Grand Rapids,
  MI.
• Van Andel Institute, Grand Rapids, MI (We used
  lab facilities and collaborated with the
  Institute researchers.)

• Methods
• DNA Agilent Microarray Technology
• Down stream analysis
• Matlab
• ANOVA and T-test

• Data Analysis
• Supervised Classification technique
• ANOVA and T-test
• Euclidean Metric or information-theoretic
  techniques

Priscilla Kimboko, Ph.D. Dean of Graduate
Studies and Grants Administration
Kyle Furge, Ph.D., Van Andel Institute Computati
onal Biology
Cyndi Miranti, Ph.D. Van Andel Institute Integrin
Signaling and Tumorigenesis
Acknowledgements We would like to thank Prof.
Manish Chakrabarti, Prof. David Elrod, Prof.
Suganthi Sridhar, Paul Norton from VAI, Kyle
Furge from VAI, Prof. Priscilla Kimboko from
Graduate Studies and Grant Administration for
supporting our project at all steps.
Suganthi Sridhar, Ph.D. Assistant
Professor Department of Cellular and Molecular
Biology
Manish Chakrabarti, Ph.D. Assistant
Professor Department of Mathematics Department
of Cellular and Molecular Biology
David Elrod, Ph.D. Coordinator of Professional
Science Masters Program

• Limitations
• Laboratory test results are not accessible yet
• GeneSpring is not accessible at GVSU anymore
• Instead of using eight plates of cultured cells,
  we had to use four plates. We had to get rid of
  four replicas, because of financial problems.