genomic analysis methods for identification of cancer ... fall ci4cc 2017.pdf · isabel bjork holly...
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Lauren Sanders, PhD student Treehouse Childhood Cancer Initiative
UC Santa Cruz
CI4CC Fall 2017 Symposium & Workshop October 24, 2017
Genomic Analysis Methods for Identification of Cancer Driver
Pathways in Childhood Brain Tumors
• Treehouse genomic analysis of pediatric tumors
• Motivation
• Gene expression outlier analysis
• Outlier analysis of diffuse intrinsic pontine glioma
• Outlier gene identification in DIPG cohort
• Validation in DIPG cell lines
Outline
• Treehouse genomic analysis of pediatric tumors
• Motivation
• Gene expression outlier analysis
• Outlier analysis of diffuse intrinsic pontine glioma
• Outlier gene identification in DIPG cohort
• Validation in DIPG cell lines
Outline
GadGetz,BroadIns/tute
PediatriccancersAdultcancersassociatedwithcarcinogen
Pediatric cancers are different: fewer and distinct mutations than found in adult cancers
- Adult cancer genomes often have many (order of 100 or more) mutations - Pediatric cancer genomes often have few (order of 10 or fewer) mutations
Can genomics point to more treatments for children with cancer?
• Treehouse genomic analysis of pediatric tumors
• Motivation
• Gene expression outlier analysis
• Outlier analysis of diffuse intrinsic pontine glioma
• Outlier gene identification in DIPG cohort
• Validation in DIPG cell lines
Outline
Focus on RNA expression
• Hypothesis: RNA gene expression can be used as
a proxy for protein & pathway activity
Focus on RNA expression
• Hypothesis: RNA gene expression can be used as
a proxy for protein & pathway activity
• Many cancer pathways already have adult drugs developed to target them
Focus on RNA expression
• Hypothesis: RNA gene expression can be used as
a proxy for protein & pathway activity
• Many cancer pathways already have adult drugs developed to target them
• Can we find abnormal activity of cancer pathways in pediatric tumors?
livercarcinoma
prostateadenocarcinoma
kidneycarcinomabreastcarcinoma
thyroidcarcinoma
ovariancystadenocarcinoma
glioma
glioblastoma
11,000+ tumors 78 tumor types
Treehouse cancer compendium
TumorMap:LaurenSanders,TeresaSwatloski,YuliaNewton
Expression level of gene in other cancers
Gene expressed at an abnormally high level “up outlier”
Gene expressed at an abnormally
low level “down outlier”
Treehouse gene expression outlier analysis
Outlieranalysis:1)Lessonslearnedfromtheapplica2onofwhole-genomeanalysistothetreatmentofpa2entswithadvancedcancersColdSpringHarbMolCaseStud.2015Oct;1(1):a000570.2)Evolu2onofanadenocarcinomainresponsetoselec2onbytargetedkinaseinhibitorsGenomeBiol.2010;11(8):R82.
Two Types of Outlier Analysis Pan-cancer analysis The sample is compared to the pan-cancer compendium of 11,000+ other tumor samples Pan-disease analysis The sample is compared to only the samples from the tumor types most similar to the sample itself
Treehouse gene expression outlier analysis
• Treehouse genomic analysis of pediatric tumors
• Motivation
• Gene expression outlier analysis
• Outlier analysis of diffuse intrinsic pontine glioma
• Outlier gene identification in DIPG cohort
• Validation in DIPG cell lines
Outline
Diffuse Intrinsic Pontine Glioma (DIPG)
• Affects 200-300 children in the US per year • Surgical resection is impossible, chemotherapy has been
ineffective, and radiation therapy is only palliative
• Few recurrent mutations; and those that are recurrent are not clinically actionable
• Can gene outlier analysis identify clinically actionable over-expressed genes in DIPG?
Outlier analysis identifies known overexpressed genes in a subset of DIPG
PNOCdata:AdamResnick,MikePrados,SabineMueller
PNOCdata:AdamResnick,MikePrados,SabineMueller
Outlier analysis identifies known overexpressed genes in a subset of DIPG
Outlier analysis of DIPG identifies known overexpressed genes: PIK3C2A & PTCH1
PIK3C2Aexpression PTCH1expression
PTCH1overexpressioninDIPG:Compara2veMul2dimensionalMolecularAnalysesofPediatricDiffuseIntrinsicPon2neGliomaRevealsDis2nctMolecularSubtypes,ActaNeuropathol.2014Jun;127(6):881–895.PIK3C2AoverexpressioninDIPG:Mesenchymaltransi2onandPDGFRAamplifica2on/muta2onarekeydis2nctoncogeniceventsinpediatricdiffuseintrinsicpon2negliomas,PLoSOne.2012;7(2):e30313
PNOCdata:AdamResnick,MikePrados,SabineMueller
HMGCR–hydroxy-methylglutarylCoAreductaseHARS–his/dyl-tRNAsynthetase
Outlier analysis of DIPG identifies two novel overexpressed genes
• Treehouse genomic analysis of pediatric tumors
• Motivation
• Gene expression outlier analysis
• Outlier analysis of diffuse intrinsic pontine glioma
• Outlier gene identification in DIPG cohort
• Validation in DIPG cell lines
Outline
Outlier analysis of DIPG cell lines
PNOCdata:AdamResnick,MikePrados,SabineMueller
HMGCR–hydroxy-methylglutarylCoAreductaseHARS–his/dyl-tRNAsynthetase
Carnosine HARSac/vity
Simvasta/n HMGCRac/vity
CanthedrugcrosstheBBB?
Yes
Yes
Carnosine HARSac/vity
Simvasta/n HMGCRac/vity
CanthedrugcrosstheBBB?
Yes
Yes
CourtesyofDr.SameerAgnihotri,UniversityofPi`sburgh
Viability assays: DIPG cell lines
CourtesyofDr.SameerAgnihotri,UniversityofPi`sburgh
Viability assays: normal brain cells
NormalHumanAstrocytes NormalNeuralStemCells
Gene expression outlier analysis
• Identification of potential therapeutic targets in DIPG patient tumors
• Target validation in DIPG cell lines revealed decreased viability
Next steps
• Pathway analysis: Cholesterol biosynthesis pathway
• Evaluate outlier analysis in larger cohort of DIPG cell lines
Conclusions & Next Steps
UCSC Treehouse Team
Olena Morozova Isabel Bjork Holly Beale Jacob Pfeil
Ellen Kephart Ann Durbin
Sofie Salama David Haussler
University of Pittsburgh Sameer Agnihotri
Acknowledgements
PNOC Consortium Sabine Mueller Michael Prados Adam Resnick
Funding