1. 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

2. Outline I.Previous study examined differences in gene expression between primary and metastatic tumors II.Using GenMAPP and MAPPFinder to reexamine microarray data 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.Interpretation I.Significance of differences in biological processes between four groups V.References

3. 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

4. Reexamining Microarray Data Using GenMAPP and MAPPFinder 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

5. Preparing Data for GenMAPP The Log 2 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 –Percent Changed Raged 15-18

6. Increased Processes Between Metastatic and Primary Tumors

7. Metastatic and Primary Tumors Presented Increases in Mitosis Mitosis Relates to cell division Spindle Organization Assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle. Chromosome Segregation The process by which chromosomes are organized into specific structures and then physically separated to two or more sets. DNA Replication Initiative Involves the separation of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.

8. Decreased Processes Between Metastatic and Primary Tumors

9. Metastatic and Primary Tumors Presented Decreases in Muscle Function Muscle Contraction Force generated within muscle tissue involving chemo-mechanical energy conversion carried out by the actin/myosin complex activity Chromatin Remodeling Complex Any complex that mediates dynamic changes in eukaryotic chromatin Oxidoreductase Activity The oxidation state of an atom within a molecule is altered.

10. Increased Processes Between Hormone Treated and Primary Tumors

11. Hormone Treated and Primary Tumors Presented Increases in Chemotaxis Activation of MAPK Activity Activates inactive enzyme MAP kinase Leukocyte Chemotaxis Movement of Leukocytes in response to external stimulus Metanephros Development Development of the kidneys Immune Response

12. Decreased Processes Between Hormone Treated and Primary Tumors

13. Hormone Treated and Primary Tumors Presented a Decrease in Nucleosome Activity Nucleosome Activity Increase in Nucleosome activity, the primary packing unit of DNA Chromatin Activity Including Chromatin assembly and Chromosomal part DNA Packaging Any process by which DNA and associated proteins are formed into a compact orderly structure.

14. Increased Processes Between Hormone- Treated and Metastatic Tumors Muscle contraction Change in muscle geometry in response to hormone treatment Immune response Hormone-treated tumors more likely to be recognized by immune system Activity of enzymes that break down proteins Break down of tumor in response to hormone treatment Cell signaling Calcium-mediated signaling; mechanoreceptor differentiation Retinoid binding and Glutathione Transferase activity Increased development of genitalia Genital maturation, progress through cell cycle to cell death or senescence

15. Decreased Processes Between Hormone- Treated and Metastatic Tumors Immune Regulation Cytokine binding, T-cell proliferation Conflicting – less likely to be attacked by immune system? Response to radiation Hormone treatment and radiation in conflict? Cell signaling Light Sensitivity Phototransduction; transferring light (photons) into signals Photodynamic therapy for prostate cancer (http://www.prostatepdt.com) Regulation of catabolism and polymetabolic processed Fidelity during transcription/translation DNA replication/repair; RNA polymerase activity; RNA polymerase 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

16. Increased Processes Between Androgen- Independent and Primary Tumors Mitosis/cell cycle M phase, regulation, cell cycle checkpoint, chromatin segregation Spindle structures Important in cell division Deoxyribonuclease and exonuclease activity Nucleic acid degradation Damaged DNA binding Indicates increased DNA damage Cell Signaling Negative regulation of transferase; protein kinase activity Spliceosome assembly Microtubule motor activity

17. Decreased Processes Between Androgen-Independent and Primary Tumors Ion channels Extracellular ligand-gated; excitatory extracellular ligand-gated; anion binding chloride ion binding; etc Cell Signaling NADP; synapse Receptor Activity GABA; GABA-A; glutamate; neuropeptide (binding; transport) Muscle Contraction Change in shape; AI larger Negative regulation of cell size/growth Acute Phase Response Monooxygenase activity

18. 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

19. Hormone Therapy May be More effective in Treating Primary Tumors 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

20. Androgen-Independent 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

21. 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.