AGBT 2010 - Yardena Samuels - NHGRI
Mutational Analysis of the Melanoma Genome
Histological progression of Melanocyte Transformation
- too much detail to copy down
Goals:
- mutational analysis of signal transduction gene families in genome
- evaluate most highly mutated gene family members
- translational
Somatic mutation analysis.
- matched tumor normal
- make cell lines
Tumor Bank establishment
- 100 tumor normal samles
- also have original OCT blocks
- have clinical information
- do SNP detection for matching normal/tumor
- 75% of cells are cancer
- look for highly mutated oncogenes
Start looking for somatic mutations
- looking at TK family (kinome)
- known to be frequently mutated by cancer
Sanger did this in the past, but only did 6 melanomas
- two phases: discovery, validation
- started with 29 samples - all kinase domains
- looked for somatic mutations
- move on to sequence all domains...
- 99 NS mutations
- 19 genes
[She's talking fast, and running through the slides fast! I can't keep up no matter how fast I type.]
Somatic mutations in ERBB4 - 19% in total
- one alteration was known in lung cancer
[Pathway diagram - running through the members VERY quickly] (Hynes and Lane, Nature Reviews)
Which mutation to investigate? Able to use crystal structure to identify location of mutations. Select for the ones that were previously found in EGFR1 and (something else?)
Picked 7 mutations, cloned and over-expressed - basic biochemistry followed.
[Insert westerns here - pricket et al Nature Genetics 41, 2009]
ERBB4 mutations have increased basal activity - also seen in melanoma cells
Mutant ERBB4 promotes NIH3T3 Transformation
Expression of Mutant ERBB4 Provides an Essential cell Survival Signal in Melanoma
- oncogene addiction
Is this a good target in the clinic.
- used lapatinib.
- showed that it also works here in melanoma. Mutant ERBB4 sensitizes cells to lapatinib
- mechanism is apoptosis
- it does not kill 100% of cells - may be necessary to combine it with other drugs.
conclusions
- ERBB4 is mutated in 19% of melanomas
- reiterate poitns
- new oncogene in melanoma
- can use lapatinib
[only got 4 of the 8 or 9]
Future studies
- maybe use in clinics - trying a clinical trial.
- will isolated tumor dna w ICM
... test several hypotheses.
- sensitivity to lapatinib
What else should be sequenced? not taking into account whole genome sequencing.
- look at crosstalk to get good targets
- List of targets. (mainly transduction genes)
Want to look at other cancers, where whole exome was done.
- revealed : few gene alterations in majority of cancers. Limited number of siganlling pathways. Pathway oriented models will work better than Gene oriented models
[ chart that looks like london subway system... have no idea what it was.]
Personalized Medicine
- their next goal.
[great talk - way too fast, and is cool, but no NGS tie in. Seems odd that she's picking targets this way - WGSS would make sense, and narrow things down faster.]
Histological progression of Melanocyte Transformation
- too much detail to copy down
Goals:
- mutational analysis of signal transduction gene families in genome
- evaluate most highly mutated gene family members
- translational
Somatic mutation analysis.
- matched tumor normal
- make cell lines
Tumor Bank establishment
- 100 tumor normal samles
- also have original OCT blocks
- have clinical information
- do SNP detection for matching normal/tumor
- 75% of cells are cancer
- look for highly mutated oncogenes
Start looking for somatic mutations
- looking at TK family (kinome)
- known to be frequently mutated by cancer
Sanger did this in the past, but only did 6 melanomas
- two phases: discovery, validation
- started with 29 samples - all kinase domains
- looked for somatic mutations
- move on to sequence all domains...
- 99 NS mutations
- 19 genes
[She's talking fast, and running through the slides fast! I can't keep up no matter how fast I type.]
Somatic mutations in ERBB4 - 19% in total
- one alteration was known in lung cancer
[Pathway diagram - running through the members VERY quickly] (Hynes and Lane, Nature Reviews)
Which mutation to investigate? Able to use crystal structure to identify location of mutations. Select for the ones that were previously found in EGFR1 and (something else?)
Picked 7 mutations, cloned and over-expressed - basic biochemistry followed.
[Insert westerns here - pricket et al Nature Genetics 41, 2009]
ERBB4 mutations have increased basal activity - also seen in melanoma cells
Mutant ERBB4 promotes NIH3T3 Transformation
Expression of Mutant ERBB4 Provides an Essential cell Survival Signal in Melanoma
- oncogene addiction
Is this a good target in the clinic.
- used lapatinib.
- showed that it also works here in melanoma. Mutant ERBB4 sensitizes cells to lapatinib
- mechanism is apoptosis
- it does not kill 100% of cells - may be necessary to combine it with other drugs.
conclusions
- ERBB4 is mutated in 19% of melanomas
- reiterate poitns
- new oncogene in melanoma
- can use lapatinib
[only got 4 of the 8 or 9]
Future studies
- maybe use in clinics - trying a clinical trial.
- will isolated tumor dna w ICM
... test several hypotheses.
- sensitivity to lapatinib
What else should be sequenced? not taking into account whole genome sequencing.
- look at crosstalk to get good targets
- List of targets. (mainly transduction genes)
Want to look at other cancers, where whole exome was done.
- revealed : few gene alterations in majority of cancers. Limited number of siganlling pathways. Pathway oriented models will work better than Gene oriented models
[ chart that looks like london subway system... have no idea what it was.]
Personalized Medicine
- their next goal.
[great talk - way too fast, and is cool, but no NGS tie in. Seems odd that she's picking targets this way - WGSS would make sense, and narrow things down faster.]
Labels: AGBT 2010
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