Circulating tumour cells and changes in expression in colorectal cancer

1. Circulating tumour
cells and changes
in expression in
colorectal cancer
Luke Zappia
Supervisors: Dr Arthur Hsu, A/Prof Fred Hollande
Department of Pathology, The University of Melbourne

2. Cancer
is bad

3. Colorectal Cancer: Tumor Sizes
For the National Cancer Institute ©2005 Terese Winslow, U.S. Govt. has certain rights

5. Our
study

6. Lab work by Fanny Grillet, Julie Pannequin
CNRS Institute of Functional Genomics, Montpellier
GFP*

7. GFP* GFP* GFP*
*

8. Datasets
Experiment 1
- 2 Primary
- 2 CTC
- 2 Mouse Primary
- 3 Mouse Blood
- 3 Mouse Liver
Experiment 2
- 3 CTC41
- 3 CTC44
- 3 CTC45
- 3 CPP44
- 2 DLD1
Cell lines - from a study by Mouradov et al.

9. Analysis
ALIGNMENT
COUNTING
TESTING
GENE SETS
TopHat2
featureCounts
GAGE

10. edgeR DESeq
DESeq2
limma-
voom

11. github.com/lazappi/RNAtools

12. Human
samples

13. Different methods

14. Overlap between methods

15. Gene sets
10 significant pathways
3 down-regulated
(ECM interactions)
7 up-regulated
(3 drug resistance)

16. Stem cell lists

17. CTC lists

18. EMT list
Epithelial
29 differentially expressed
22 up-regulated
Mesenchymal
8 differentially expressed
8 down-regulated

19. Mouse
samples

21. Results
Blood vs primary
139 genes
Liver vs primary
48 genes
Liver vs blood
5 genes

22. Cell lines

24. RPKM data

25. Clustering

26. Comparison
Differential expression
5093 genes (459 all four)
70% down-regulated
Gene sets
13 pathways
3 down-regulated ECM pathways

27. What did
we learn?

28. Increased drug resistance
Reduced ECM interactions
Epithelial state
Consistency with CTC studies
Multiple methods improve testing
May be subgroups
Outcomes

29. Further work
Replicate with other cell lines, cancer types
Incorporate lab results
Combining results
Integrating datasets

30. Acknowledgements
Supervisors
Arthur Hsu
Fred Hollande
Cell lines
Fanny Grillet
Julie Pannequin
Sequencing
Kym Pham
Christina Molck
Department
Olga, Greg, Graham
Support
VLSCI
Graham Taylor
Images
Hepatocellular Carcinoma, FNA Pathological and
histological images courtesy of Ed Uthman at flickr,
via Wikimedia Commons
Micrograph showing tumour budding in colorectal
carcinoma, H&E stain By Nephron (Own work), via
Wikimedia Commons