Exosomes and Pancreatic Cancer

Transcription

1 Exosomes and Pancreatic Cancer Anirban Maitra, M.B.B.S. Professor of Pathology and Translational Molecular Pathology Sheikh Ahmed Pancreatic Cancer Research Center University of Texas MD Anderson Cancer Center

2 Liquid Biopsy Platform for Therapeutic Monitoring in Pancreatic Cancer

3 Components of Cancer Liquid Biopsy

4 Pancreatic cancer exosomes contain high molecular weight dsdna amenable to genomic analysis Healthy individual PDAC Patient San Lucas et al. Ann Oncol 2016

5 Detection of mutant BRCA2 in exodna by NGS ExoDNA PBMC: Ref: V3091I:

6 Liquid Biopsies can enable serial monitoring of genomic alterations during the course of therapy Rapid Autopsy (02/2015) Metastatic Neuroendocrine neoplasms, with ductal features San Lucas et al. Ann Oncol 2016

7 NGS on ExoRNA can find expressed mutations, fusion transcripts & neoantigens GENE_1 GENE_1_CHR GENE_1_POS GENE_2 GENE_2_CHR GENE_2_POS SLC26A9 chr TBC1D22A chr ZSWIM7 chr RFTN1 chr MTRNR2L1 chr ENSG chrm 2817 AIFM3 chr NAALADL2 chr ACAP2 chr ELK1 chrx RANBP17 chr GOLGA4 chr PCBD2 chr ENSG chrm FGFR1 chr PRKCQ chr Expressed fusions (tumor neoantigens) Monitoring tumor antigens

8 Longitudinal Monitoring of Treatment Response 68yo female, metastatic PDAC Mutant KRAS in ExoDNA tightly correlates with clinical evolution.

9 N o n -P r o g r e s s io n P r o g r e s s io n Surge in ExoDNA Correlates with Progression in Unresectable Pancreatic Cancer >1% ExoDNA Mutant Allele Fraction P r o g r e s s io n N o p ro g r e s s io n M u t a n t K R AS s u r g e in e x o D N A ( AF > 1 % ) p < M K 4 6 G V 3 6 M K 5 3 G V 1 3 B W 0 3 M K 1 3 M K 0 3 G V 3 2 G V 1 2 M K 6 1 G V 1 6 M K 6 5 G V 0 3 G V 2 3 G V 1 7 G V 0 7 G V 2 4 M K 0 4 G V 1 0 M K 1 9 B W 0 6 N o m u t a n t K R AS s u r g e in e x o D N A ( AF 1 % ) M u ta n t K R A S s u rg e (A F > 1 % ) in e x o D N A P ro g re s s io n S u rv iv a l a fte r p ro g re s s io n D e a th C e n s o re d N o o f p a tie n ts w ith u n r e s e c ta b le p a n c re a tic c a n c e r G V 2 7 G V 3 7 M K 5 1 G V 4 2 M K 5 5 M K 7 5 M K 8 6 B W 1 0 M K 9 7 M K 6 7 G E M + A B R F O L F IR IN O X P alliative chem orad iation B e s t s u p p o rtiv e c a re T im e (d a y s )

10 Surge in ExoDNA Correlates with Progression in Locally Advanced Pancreatic Cancer Stable disease based on imaging and CA weeks Mutant KRAS surge in exodna Overt liver metastasis No liver metastasis Over liver metastasis

11 Early Detection of Pancreatic Cancer Based on titration experiments, we are able to repeatedly detect mutations at a 0.01% mutant allele frequency. Allenson et al. Ann Oncol 2017

12 Early Detection of Pancreatic Cancer (and a specter of overdiagnosis)

13 Conditioned media Identifying Cancer Specific Exosomes Through an Antibody Cocktail Exosome isolation Surface protein biotinylation Lysis and capture of biotinylated proteins GPC1 Captured fraction: Surface Flowthrough: Cargo Reversed-phase protein fractionation Trypsin digestion LC-MS/MS of individual fractions Maitra & Hanash Lab

14 C A (U /m L ) Cancer Specific Exosomes Enhance Mutant KRAS Detection and Facilitate Molecular Barcoding (Specificity) /1 8 / /2 4 / /2 8 / /2 8 / /2 1 / /2 2 / /2 / /2 5 / /2 8 / a n d M u ta n t a lle le fre q u e n c y (M A F, % ) S u m o f lo n g e s t d ia m e te r (S L D, m m ) C A S L D c fd N A M A F e x o D N A M A F D is ta l p a n c r e a te c to m y ( R 1 ) F O L F IR IN O X P A R P in h ib ito r ( R u c a p a r ib ) L a p a r o s c o p ic p a r tia l h e p a te c to m y (s e g m e n t 2 ) G E M + A B R + C IS C a r c in o m a to s is P e r ito n e i & L iv e r m e ta s ta s is R e g io n a l L N re c u rr e n c e & C a rc in o m a to s is p e r ito n e i N e w L iv e r m e ta s ta s is In c r e a s e d liv e r m e ta s ta s is

15 Two Parting Caveats on Longitudinal Monitoring with Liquid Biopsies C CRC sample exokras mutant call rate exoapc mutant call rate exobraf mutant call rate Exo MYC mutant call rate D CRC sample exodna Muta on Detec on Rate Prospec ve 4/12 (33.3%) 3/12 (25%) 0/12 (0) 5/12 (41.6%) Retrospec ve 2/5 (40%) 0/5 (0) 0/5 (0) 1/5 (20%) Total 6/17 (35.2%) 3/17 (17.6%) 0/17 (0) 6/17 (35.2%) Prospec ve 8/12 (66.6%) Retrospec ve 2/5 (40%) Total 10/17 (58.8%) E Longitudinal monitoring is possible in other solid cancers (e.g., CRC). Possible applications: Mechanisms of resistance CMS classification (ExoRNA profile) Plasma is not the only source for exodna Pleural Fluid Urine

16 Acknowledgements Hector Alvarez Kelvin Allenson Anthony San Lucas Vincent Bernard Pagan Jonathan Castillo Mark Hurd Gauri Vardhachary Robert Wolff Matthew Katz Jason Fleming Michael Kim Ching-wei Tzeng Sam Hanash Michela Capello Cancer Prevention and Research Institute of Texas National Cancer Institute