Exploring Comprehensive Gene Expression Analysis of Prostate Cancer Reveals Distinct

Transcriptional Programs Associated With Metastatic Disease Through GenMAPP &

MappFinder

LaTulippe Eva, Satagopan Jaya, Smith Alex, Scher Howard, Scardino Peter, Reuter Victor, and William G. Cancer

Research 2002 Aug 1; 62, 4499-4506.

Kevin Paiz-Ramirez

Janelle N. Ruiz

Biology 398.01

Department of Biology

Loyola Marymount University

April 21, 2010

Outline

I. Previous study examined differences in gene expression b/w primary and metastatic tumors

II. Using GenMAPP and MAPPFinder to reexamine microarray data

I. Method and

III. Results—gene ontological differences b/w:I. Metastatic versus Primary tumors

II. Hormone-treated versus Primary tumors

III. Hormone-treated versus Metastatic tumors

IV. Androgen-induced versus Metastatic tumors

IV. InterpretationI. Significance of differences in biological processes between

four groups

V. References

Previous study explored function of unknown genes which may identify potential

therapeutic targets• La Tullippe, et al. performed high-throughput gene expression using Affymetrix chips to study prostate cancer metastasis

• Used tissue biopsies collected from 1993-1999 from: – 3 non-cancerous patients– 23 primary prostate cancer patients– 9 metastatic prostate cancer patients

• Genes were considered to be differentially expressed if they differed 3 fold between groups

• Highly differentially expressed genes between metastatic and primary tumors involved in:– Cell cycle regulation; mitosis; signaling; DNA replication

We sought to reexamine the microarray data of La Tullippe, et al. using an

alternative method

• Purpose: confirm findings of previous study and search for novel cellular processes involved in metastasis

• Method: – GenMAPP and MAPPFinder– Group highly differentially expressed genes based on

similarities in biological processes– MAPPs represent biological pathways and other

functional groupings of genes– Genes assigned to gene ontology (GO) terms based

on model organism database

Running GenMAPP & MAPPfinder to determine differences in gene ontology

between groups

• The Log2 of the ratio of the means was calculated for:– Metastatic vs. primary tumors– Hormone-treated vs. primary tumors– Hormone-treated vs. metastatic tumors– Androgen-independent vs. primary tumors

• Number of errors: 1793/11977

• Our statistical criteria:– Z score > 2– P value <0.05– Number changed: >3 or <100

Increased Decreased

Increased & Decreased Processes between Metastatic and Primary Tumors

Increased & Decreased Processes between Metastatic and Primary Tumors

• Increases centered on:– Mitosis– Spindle organization– Chromosome segregation– DNA replication

• Decreases centered on:– Muscle contraction– Chromatin remodeling complex– Oxidoreductase activity

Increase Decrease

Increased & Decreased Processes between Hormone-Treated and Primary

Tumors

Increased & Decreased Processes between Hormone-Treated and Primary

Tumors

• Increases centered on:– Activation of MAPK activity– Leukocyte chemotaxis– Metanephros development– Immune response

• Decreases centered on:– Nucleosome activity– Chromatin activity– Chromosomal activity– DNA packaging

Increased Processes b/w Hormone-Treated and Metastatic Tumors

•Muscle contraction (6)•Change in muscle geometry in response to hormone treatment

•Immune response (4)•Hormone-treated tumors more likely to be recognized by immune system

•Activity of enzymes that break down proteins (2)•Break down of tumor in response to hormone treatment

•Cell signaling (2)•Calcium-mediated signaling; mechanoreceptor differentiation

•Retinoid binding (2) and Glutathione transferase activity (1)

•Increased development of genitalia (1) •Genital maturation, progress through cell cycle to cell death or senescence

Decreased Processes b/w Hormone-Treated and Metastatic Tumors

•Immune Regulation (3) •Cytokine binding, T-cell proliferation•Conflicting – less likely to be attacked by immune system?

•Response to radiation (1) •Hormone treatment and radiation in conflict?

•Cell signaling (4)

•Light Sensitivity (5)•Phototransduction; transferring light (photons) into signals •Photodynamic therapy for prostate cancer (http://www.prostatepdt.com)

•Regulation of catabolism + polymetabolic processed (2)

•Fidelity during transcription/translation (4) •DNA replication/repair; RNA pol. activity; RNA pol. binding

• •Cell signaling (2)

•Retinoid binding (2) and Glutathione transferase activity (1)

• Actin filaments (1) –•Changing structure of tumor in response to hormone treatment

•Increased development of genitalia (1) –•Genital maturation, progress through cell cycle to cell death or senescence

Increased Processes b/w Androgen-Independent and Primary Tumors

• Mitosis/cell cycle (5)• M phase, regulation, cell cycle checkpoint, chromatin segregation

• Spindle structures (4)• Important in cell division

• Deoxyribonuclease (1) and exonuclease activity (1)• Nucleic acid degradation

• Damaged DNA binding (1)• Indicates increased DNA damage

• Cell Signaling (3)• Negative regulation of transferase; protein kinase activity

• Spliceosome assembly (1)

• Microtubule motor activity (1)

Decreased Processes b/w Androgen-Independent and Primary Tumors

• Ion channels (4)• Extracellular ligand-gated; excitatory extracellular ligand-gated; anion

binding chloride ion binding; etc

• Cell Signaling (4)• NADP; synapse

• Receptor Activity (6)• GABA; GABA-A; glutamate; neuropeptide (binding; transport)

• Muscle Contraction (1) • Change in shape; AI larger

• Negative regulation of cell size/growth (2)

• Acute Phase Response (1)

• Monooxygenase activity (1)

Metastatic tumors demonstrate greater cell cycle activity than primary tumors

• Metastatic tumors show greater relative levels of genes involved in mitotic processes

– Replicate faster than primary tumors– Confirms La Tullippe, et al. proliferation data

• Metastatic tumors show decrease in muscle contraction

– These tumor cells may tend to grow larger than primary tumors

• Metastasis tumors show decrease in chromatin remodeling

– Loss of chromatin remodeling may be important to metastasis

Hormone therapy may be more effective in treating primary than metastatic tumors

• Primary tumors treated with hormone therapy show:– Increase in immune activation– Decrease in chromosomal activity indicating a possible

decrease in cell replication

• Metastatic tumors treated with hormone therapy show:– Increase and decrease in immune response– Increase in development of genitalia– Increase in cell signaling– Decrease response to radiation and light therapy– Decrease in fidelity during transcription/translation

Androgen-Independent (AI) tumors are similar in their biological processes to

metastatic tumors

• AI tumors show greater relative levels of genes involved in mitotic processes

– Replicate faster than primary tumors

• AI tumors show decrease in muscle contraction– AI may grow larger than primary tumors

• AI tumors have greater nucleic acid degradation processed than primary tumors

• AI tumors show decrease in cell signaling/ion channel activity

– AI tumors may not respond as well to hormone treatment as primary tumors

References

• LaTulippe E, Satagopan J, Smith A, Scher H, Scardino P, Reuter V, and Gerald WL. Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastatic disease. Cancer Res 2002 Aug 1; 62(15) 4499-506.