Gene Expression and Cancer

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Gene Expression and Cancer

• Presentation Inna Weiner

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Cancer

• Cellular level overproliferation of the cell
• Tissue level cells deviate from their natural
  place in the tissue and spread
• 3 main principles
• Tumors are mono-clonal
• DNA mutations (6-7 usually)
• Selection (from bad to worse)

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Cellular mechanisms in cancer

• Signaling pathways damage
• Tumor cells uncontrolled proliferation
• Growth factors constitutive activity
• Constitutive up/down regulation
• DNA repair problem
• Apoptosis mechanism not active
• Cells acquire metastatic potential

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Primary Tumor
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Cancer metastatic pathway
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Articles

• A molecular signature of metastasis in primary
  solid tumors.
• S. Ramaswamy et al. Nature Genetics, 2002
• Robustness, scalability, and integration of a
  wound-response gene expression signature in
  predicting breast cancer survival.
• H. Y. Chang et al. PNAS, 2005
• An oncogenic KRAS2 expression signature
  identified by cross-species gene-expression
  analysis.
• A. Sweet-Cordero et al. Nature Genetics, 2004

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• A molecular signature of metastasis in primary
  solid tumors
• Sridhar Ramaswamy, Ken N. Ross, Eric S. Lander
  Todd R. Golub
• Nature Genetics, December 2002

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Motivation for Predicting Metastasis

• Metastasis (Greek change of the state) spread
  of cancer from its primary site to other places
  in the body (e.g., brain, liver)

• Metastasis is the principal event leading to
  death in individuals with cancer

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Model of Metastasis

• Most primary tumor cells have low metastatic
  potential
• Rare cells (estimated at less than 1 in
  10,000,000) within large primary tumors acquire
  metastatic capacity through somatic mutation

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Metastatic Phenotype

• Has the ability to
• migrate from the primary tumor
• survive in blood or lymphatic circulation
• invade distant tissues
• establish distant metastatic nodules
• Supported by animal models

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Setup

• 12 metastatic adenocarcinoma nodules of diverse
  origin (lung, breast, prostate, colorectal,
  uterus, ovary)
• 64 primary adenocarcinomas representing the same
  spectrum of tumor types

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Hypothesis a gene-expression program of
metastasis may already be present in the bulk of
some primary tumors at the time of diagnosis
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Hypothesis testing

• 62 stage I/II primary lung adenocarcinomas
• Hierarchical clustering in the space 128
  metastases-derived genes

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Clinical Outcome Prediction
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Generality of metastatic signature
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17-gene metastatic signature
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17-gene metastatic signature
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17-gene metastatic signature
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17-gene metastatic signature
Downregulation Tumor suppressor
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Novel Model of Metastasis

• Prevailing Model incidence of metastasis is
  related to the number of cells susceptible to
  metastasis-promoting mutations, and hence to
  tumor size

• New Model the propensity to
  metastasize reflects the predominant genetic
  state of a primary tumor

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Critical View

• The authors did not prove that there is a single
  cell with all metastatic functions
• Maybe a small fraction of primary tumors (the
  biggest?) did acquire metastatic-potential cells

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• Robustness, scalability, and integration of a
  wound-response gene expression signature in
  predicting breast cancer survival
• H. Y. Chang, D. S. A. Nuyten, J. B. Sneddon, T.
  Hastie, R. Tibshirani, T. Sørlie, H. Dai, Y. D.
  He, L. J. vant Veer, H. Bartelink, M. van de
  Rijn, P. O. Brown, and M. J. van de Vijver
• PNAS, March 8, 2005

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Chang et al (2004), PLoS

• Hypothesis
• Molecular program of normal wound healing might
  play an important role in cancer metastasis
• Procedure
• Measured gene expression of serum response of
  cultured fibroblasts from 10 anatomic sites in
  vitro
• Result
• Identified a set of core serum response genes
  and their canonical expression profile in
  fibroblasts activated with serum

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512 core serum response genes were identified and
were considered representative of a wound
signature
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Chang et al (2004)Identified Annotations of
Genes

• Matrix remodeling
• Cytoskeletal rearrangement
• Cellcell signaling
• Angiogenesis
• Cell motility

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• Robustness, scalability, and integration of a
  wound-response gene expression signature in
  predicting breast cancer survival
• H. Y. Chang, D. S. A. Nuyten, J. B. Sneddon, T.
  Hastie, R. Tibshirani, T. Sørlie, H. Dai, Y. D.
  He, L. J. vant Veer, H. Bartelink, M. van de
  Rijn, P. O. Brown, and M. J. van de Vijver
• PNAS, March 8, 2005

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Performance of wound-response signature
295 breast cancer samples using 442 available
core serum response genes
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Chang et al (2004) Clinical Outcome Prediction
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Scalable Prognostic Score

• Problem Hierarchical clustering provides
  biologically arbitrary threshold
• Solution Create the centroid of the differential
  expression in response to serum in cultured
  fibroblasts from 10 anatomic sites (Chang, 2004)
• Score corr (centroid, new example)

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Improving Clinical Decision Making

• 30 of women with early breast cancer develop
  metastasis
• For young women chemotherapy increases 10 year
  survival at 10
• Chemotherapy does not benefit for 89-93 of all
  breast cancer patients

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Summary

• Mechanism-driven approach to prognostic biomarker
  discovery on a genome scale
• Uncovered the catalog of genes involved in a
  potentially new cellular process that defines the
  clinical biology of breast cancer
• pathogenic mechanisms
• potential targets for treatment
• New findings applicable for clinical decision
  making

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Cancer course, I. Ben-Neria
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The MAP-K cascade Protein-Protein interactions
bridging the plasma membrane and the nucleus
Cancer course, I. Ben-Neria
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RAS Activation
RAS is oncogenic due to constitutive activation
in the GTP-bound form
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• An oncogenic KRAS2 expression signature
  identified by cross-species gene-expression
  analysis.
• A. Sweet-Cordero, S. Mukherjee, A Subramanian, H.
  You, J.J. Roix, C. Ladd-Acosta, T. R. Golub and
  T.Jacks
• Nature Genetics, December 2004

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Why use animal models?

• Initiated by single well-characterized event
• Discover novel pathways obscure in human data
• Endogenous activation of oncogenes in vivo is
  distinct from overexpression in vitro

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Experimental Setup

• Goal build animal model for human lung
  adenocarcinoma
• Create KrasLA mouse model Mice with sporadically
  activated Kras2 through spontaneous homologous
  recombination
• Mice develop lung adenoma
• Through time acquire characteristics similar to
  human tumor nuclear atypia and high
  mitotic index

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Gene Set Enrichment Analysis (GSEA)
Is Rank-Ordered Gene List (from human analysis)
enriched in independent a priori defined Gene set
(from mouse model)?
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Gene Set Enrichment Analysis (GSEA)
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Comparison of Gene Expression in mouse and human
lung cancer

• Using GSEA was found
• Differentially expressed genes in KrasLA mouse
  model were significantly enriched in Human Lung
  Adenocarcinoma but not in other lung subtypes
• NNK mouse model (induced by chemical mutogen)
  adenoma and carcinoma did not provide enriched
  Differentially Expressed Gene Set
• Mouse tumor from KrasLA and NNK model were not
  distinguishable histologically

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Oncogenic KRAS2 signature

• 89 differentialy expressed genes (upregulated) in
  KrasLA mouse model that contributed maximally to
  the GSEA score in human data set

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KRAS2 signature verification (1)

• KRAS2 signature is enriched in pancreatic
  adenocarcinoma
• KRAS2 mutation occurs in gt90 of pancreatic
  adenocarcinomas
• ? Link between KRAS2 signature and mutation of
  KRAS2

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KRAS2 signature verification (2)

• Real-time PCR analysis of expression of selected
  KRAS2 signature genes (in human cell lines)

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KRAS2 signature verification (3)

• Knock-down of KRAS2 in human lung cancer cell line

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Summary

• Integrative analysis of mouse model and human
  cancer can
• Validate the animal model
• Extract an evidence of oncogene-specific program
• Compare several models against human cancer types
• In this research were identified many potential
  effectors of KRAS2
• New directions for anti-Ras pathway therapeutic
  strategies

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