Transporter Expression in the Gut and Tumors

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Transporter Expression in the Gut and Tumors
Pascale Anderle, ISREC
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Overview

• Genomic profiling of transporters in Caco-2 cells
  and human intestine using a custom array
• Genomic profiling of transporters along the mouse
  intestine using Affymetrix GeneChips
• Identification of transporters responsible for
  chemo-sensitivity and chemo-resistance using a
  custom array

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Evaluation of Transporter and Channel Genes in
the Intestine
Reference

• Goals
• Caco-2 cells Differentiated cells vs.
  undifferentiated cells
• Small intestinal and colonic tissues vs. Caco-2
  cells

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Differentiation of Caco-2 cells
Time
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Summary

• Differentiation of Caco-2 cells
• During differentiation Expression pattern
  changes
• Up and down regulation usually lt 2 fold
• Significant changes between 5 days to 1 week and
  1 week to 2 weeks
• No significant changes between 2 weeks and 3
  weeks
• Genes in general related to ion household
• No major differences between flasks and filters
  (except GLUT3)
• Typical small intestinal transporters not
  especially up regulated in differentiated cells
• Comparison Tissue vs. Caco-2 Cells
• Changes more pronounced between tissue and cell
  line than between undifferentiated and
  differentiated cells
• Tissue vs. Caco-2 cells More ratios gt 2 fold
• No trend observed undiff. cells to diff. cells
  colon-like to small intestinal-like cells

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Genomic Profiling of Membrane Transporters in the
Intestine
Objective Identification of putative
segment-specific and non-specific specific drug
carriers
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Accurate Annotation of Probe Sets
A crucial step in classifying genes into
different molecular functions is the use of a
consistent and universal classification system
and a precise annotation of Affymetrix probe sets.

• Mapping of single probes and attributing of
  annotation tags to each probe set (quality tags)
• Assigning of flags to differentially regulated
  probe sets (F, G, 1)

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Isrec Ontologizer Io
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Regulation of Transporters along the Intestine
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Fold Changes along the Intestine
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Expression along the Crypt-Villus Axis
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Summary

• Majority of transporters not significantly
  expressed along the intestine
• Carriers and in particular the classes
  symporters and antiporters change
  significantly
• Transporter subclasses change along the whole
  intestine, most between ileum and colon
• Similar number of transporters over-expressed in
  small and large intestine, but generally
  transporters are expressed at higher levels in
  the small intestine
• Most differently regulated transporters are
  similarly expressed along the small intestine,
  yet various transporters are clearly
  segment-specific
• Most transporters similarly expressed in humans
  and mice
• Regulation of expression in whole tissue is a
  good indicator of the combined changed in
  epithelial crypt and villus cells
• Identification of various new candidate carriers
  for drug delivery (mRNA ? protein)

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Expression of Transporters in Cancers
Reference
Goal Study the role of transporters in
cancer-sensitivity and cancer-resistance
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NCI Database
Scherf et al. 2000, Nature Genetics
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SLCs Chemo-sensitivity and -resistance
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Sorted correlation coefficients
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Effects of regulation of transporters on
dose-response curves
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Summary

• Important role of transporters in
  chemo-sensitivity and-resistance
• ABCB1 and ABCB5 identified as resistance genes
  for various compounds
• SLC29A1, nucleoside transporter, identified as
  sensitivity gene
• Collection of information bits to perform
  follow-up studies

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Acknowledgments I
UCSF/OSU Wolfgang Sadée Vera Rakhmanova Ying
Huang Shoshana Brown Audrey Papp Zunyan Dai Joe
DeRisi Adam Carroll Jingchun Zhu
Xenoport Katie Woodford Noa Zerangue
National Cancer Institute John
Weinstein Kimberly Bussey Catalin Barbacioru Uma
Shankavaram William C. Reinhold
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Acknowledgments II
ISREC Jean-Pierre Kraehenbuhl Martin Rumbo
Bioinformatics Core Facility Thierry
Sengstag Mauro Delorenzi
Nestlé Muriel Fiaux Robert Mansourian David
Mutch Matthew-Alan Roberts Gary Williamson
Swiss Institute of Bioinformatics Philipp
Bucher Christian Iseli Viviane Praz