Finding Biomarkers Specific for Early Stages of Lung Cancer Using SAGE Data

1
Finding Biomarkers Specific for Early Stages of
Lung Cancer Using SAGE Data
Chan, Timothy1, MacAulay, Calum2, Lam, Wan2 ,
Lam, Stephen2 , Lonergan, Kim2 , Ng,
Raymond2. University of British Columbia,
Vancouver, Canada BC Cancer Agency, Vancouver,
Canada
Overview
Criteria for CIS Biomarker
Desmosomes

• Fold change of CIS/Normal average expression
  must be 10
• Fold change of CIS/Normal average expression
  must be 5
• Fold change of CIS/Metaplasia average expression
  must be 2
• Permutation score 2.35 for both sets (p-value
  of 0.01)

• The 5-year survival rate of an advanced lung
  cancer patient is only about 10.
• If the cancer is caught early at the CIS
  (carcinoma in situ) stage, the 5-year survival
  rate is 90.
• Currently, there are no studies have isolated
  biomarkers for this elusive CIS stage.

Results

• We propose using lung SAGE data to isolate genes
  specific for CIS stages of lung cancer that are
  not present in bronchial metaplasia tissue.

• After applying the above criteria we obtained 18
  tags.
• 14 had unigene ids and 11 mapped to genes with
  names.

Top 18 Filtered Tags
Objective

• To find a set of candidate genes that are
  highly expressed in the CIS stages and lowly
  expressed in normal tissues, metaplasia tissues,
  and invasive tissues.
• To determine whether these genes are good
  candidate biomarkers from a biological stand
  point.
• To discover whether the expression level of
  these genes associated genes lead to the
  understanding of the inner workings of the early
  stages of the disease.

• Desmocollin 2 and desmoglein 3 are major
  components of cell adhesion molecules which play
  an important role in epithelial adhesion.
• Other desmosome families of the armadillo
  proteins (PKPs) and plakins were also found to be
  higher expressed (refer to boxplots).
• Squamous cell carcinoma cells overxpressing
  desmosomal cadherins have been shown to inhibit
  invasion.

Methodology
Other Genes
Sample Genes

• Othere genes involved include ones involved in
  EGFR trafficking, phosphatase genes, and a
  tyrosine kinase receptors.
• All the genes were looked up on NCBIs EST
  database to find where they are expressed. All
  these genes were found to be expressed in various
  tissues.

• A calcium-dependent glycoprotein that is a member
  of the desmocollin subfmaily of the cadherin
  superfamily
• Found primarily in epithelial cells where they
  constitute the adhesive proteins of the desmosome
  cell-cell junction anad are required for cell
  adhesion

• To conduct our experiment we used 1 metaplasia
  library, 15 smoked-damaged (normal) libraries, 6
  invasive libraries, and 5 CIS libraries.

27 SAGE
Conclusion
Steps

• From our results we were unable to find a clear
  biomarker found that was exclusive to its tissue
  type (that is only found or produced by lung).
• Our study on the mRNA levels of the
  intercellular adhesion molecules suggest that
  when a squamous lung cell enters the early stages
  of lung cancer, adhesion genes are up regulated.
• As it enters the invasive stages, we hypothesize
  that these cancer cells have obtained the ability
  to obtain its own nutrients and thus do not need
  to anchor onto bronchial epithelial tissues.
• Interestingly, oral squamous cell carcinoma
  cells overexpressing desmosomal cadherins have
  been shown to inhibit invasion.

• A calcium-binding transmembrane glycoprotien
  component of desmosomes in vertebrate and
  epithelial cells.
• A member of the cadherin cell adhesion molecule.

Associated Genes
NOTE pink box is the best mapped tag
Future Directions
PKP3 (PLAKOPHILIN 3)

• Biological validation involving protein
  expression is required for our above hypothesis
  as SAGE only looks at the cell at the mRNA level.
  
• Analysis of other pathways involving the other
  set of genes need to done.
• It would be also interesting to look at the
  genes that are turned off or down-regulated in
  CIS stages but abundantly expressed in normal and
  invasive stages.

JUP (Plakoglobin)