Identificación de vulnerabilidades en tumores sólidos: aportes hacia una medicina personalizada?

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1 Identificación de vulnerabilidades en tumores sólidos: aportes hacia una medicina personalizada? Alberto Ocana Albacete University Hospital Salamanca May 19th, 2016

2 WHAT IS PERSONALIZED MEDICINE? Molecular alteration targeted agents companion diagnostic

3 Drugs with companion diagnostic Ocana A et al, Oncotarget 2016

4 Meta-analyses companion vs non-companion diagnostics PFS OS

5 Meta-analyses of toxicities

6 Methods to identify oncogenic and non-oncogenic vulnerabilities How to evaluate novel agents against them Our personal experience

7 Synthetic Lethality Interactions Ocana A and Pandiella A, Personalized therapies in the cancr omics era. Mol Cancer 2010

8 Summary Mutation and copy number analyses Phospho-kinase profiling Transcriptomic analyses Synthetic Lethality Interactions- Evaluation of new drugs Academic iniciatives: Drug developer software as a tool

9 Mutation and copy number analyses No very useful if not linked with a functional evaluation in a specific genetic context A somatic cancer driver event may depend on the constellation of polymorphisms already present in an individual s germline. (Germline variants single nucleotide polymorphisms, SNPs).

10 But it can be useful for: Clonal evolution of tumors Heterogeneity of tumors Monitor response to treatments and identify mechanism of resistance Single cell sequencing Circulating tumor DNA As a part of a global study; pathway level alterations Example: Evaluation of mutations in ER using circulating DNA in patients treated with palbociclib + hormonotherapy

11 Phospho-kinase profiling

12 Human samples protein extraction phosphokinase evaluation-----drug selection

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15 Software tools: Gene-drugs

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17 Phase Ib/II Trial of BEZ235 With Paclitaxel in Patients With HER2 Negative, Locally Advanced or Metastatic Breast Cancer. NCT

18 Transcriptomic analyses

19 to identify biological functions with druggable genes like kinases-- linked with outcome to identify gene signatures asociated with worse outcome in relevant clinical situations

20 Normal Breast Basal Like Breast Cancer Stem Cell 10 Deregulated genes Protein kinases with increased expression Druggable targets Angiogenesi s Response to drug 9 8 Probe Set Gene Name Fold Change _at NEK2. NIMA (never in mitosis gene a)-related kinase 2 18,24 Cell migration Regulation of immune system process Regulation of cell death Transcription factor _at PBK. PDZ binding kinase 12, _at TTK protein kinase 11, _s_at AURKA. Aurora kinase A 10, _at AURKB. Aurora kinase B 4, _at BUB1. Budding uninhibited by benzimidazoles 1 homolog 11, _at BUB1B. Budding uninhibited by benzimidazoles 1 homolog beta 6, _at CDK1. CDC2. Cell division cycle 2, G1 to S and G2 to M 17,95 TTK protein kinase. AURKA. Aurora kinase A PLK1. Polo-like kinase 1. Cell cycle 3 Cell cycle genes _at MAPK6. Mitogen-activated protein kinase 6 6,27 Response to stress _at PLK1. Polo-like kinase 1 6,13 Cell differentiation % of genes included Drug Target IC50 nm MDA-MB-231 HS578T BT549 HCC3153 Volasertib PLK1. Polo-like kinase 1 7,5 7, Alisertib AURKA. Aurora kinase A Docetaxel Inhibitor of depolymerisation of microtubules AZ3146 TTK protein kinase HCC3153 BT549 HS578T MDA HS MDA-MB- BT HCC MDA HS BT HCC

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22 Luminal tumors OS

23 OVARIAN SURFACE EPITHELIA (OSE) OVARIAN CANCER EPITHELIAL CELLS (CEPISs) 2925 deregulated genes 4 fold change 98 kinases 32 kinases with decreased expression 66 kinases with increased expression angiogenesis Angiogenesis Growth growth factor factor proto-oncogene Proto-oncogene extracellular matrix Extracellular matrix Cell cell adhesion Cell cell cycle cycle cytoskeleton Cytoskeleton Gene functions % of genes included Ocana A, et al. Oncotarget in press 14 kinases with increased expression involved in cell cycle TTK protein kinase. CDC28 protein kinase regulatory subunit 2. CHK1 checkpoint homolog (S. pombe). NIMA (never in mitosis gene a)-related kinase 2. AURKA. Aurora kinase A. AURKB. Aurora kinase B. BUB1 Budding uninhibited by benzimidazoles 1 homolog (yeast). BUB1ß Budding uninhibited by benzimidazoles 1 homolog beta (yeast). CDKN2A. Cyclin-dependent kinase inhibitor 2A. NIMA (never in mitosis gene a)-related kinase 4. CDC2. Cell division cycle 2, G1 to S and G2 to M. GAK. Cyclin G associated kinase. GSG2. Germ cell associated 2 (haspin). MAPK12. Mitogen-activated protein kinase 12.

24 Combination of five genes (A and B, respectively in stage I/II and stage I (in early stage) ovarian cancer for PFS

25 .to evaluate the mechanism of action of new compounds to find synergistic interactions

26 EC70124 (IC50 dose) RNA (12, 24, 48 hours) Gene expression analyses Functional genomics

27 Gene Set Enrichment Analyses-Cytoscape

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29 Synthetic Lethality Interactions- Evaluation of new drugs

30 Functional genomics

31 Normal Breast Basal Like Breast Cancer Stem Cell 10 Deregulated genes Protein kinases with increased expression Druggable targets Angiogenesi s Response to drug Cell migration Regulation of immune system Regulation cell death Transcription factor Cell cycle Response to stress Cell differentiation BET Inhibitors JQ1 Cell cycle genes Probe Set Gene Name Fold Change _at NEK2. NIMA (never in mitosis gene a)-related kinase 2 18, _at PBK. PDZ binding kinase 12, _at TTK protein kinase 11, _s_at AURKA. Aurora kinase A 10, _at AURKB. Aurora kinase B 4, _at BUB1. Budding uninhibited by benzimidazoles 1 homolog 11, _at BUB1B. Budding uninhibited by benzimidazoles 1 homolog beta 6, _at CDK1. CDC2. Cell division cycle 2, G1 to S and G2 to M 17, _at MAPK6. Mitogen-activated protein kinase 6 6, _at PLK1. Polo-like kinase 1 6,13 TTK protein kinase. AURKA. Aurora kinase A PLK1. Polo-like kinase % of genes included

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33 Lentiviral shrna library + stress condition

34 Academic iniciatives: Drugdeveloper software as a tool

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37 MD Anderson Experience 50 genes---35 actionable

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40 Summary Integrating omics Confirm with functional genomics Confirm with biochemical evaluation: genomic context dependent Personalized medicine: Softwares: far away to be accurate Personalized clinical trials or studies, are under evaluation

41 Thank you for your atention?????? Questions???