J Castillo1, V Bernard1,2, F A San Lucas3, K Allenson4, M Capello5, D U Kim1, P Gascoyne6, F C Mulu1, B M Stephens1, J Huang1, H Wang7, A A Momin7, R O Jacamo8, M Katz4, R Wolff9, M Javle9, G Varadhachary9, I I Wistuba10, S Hanash5, A Maitra1,11, H Alvarez1,11. 1. Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA. 2. The University of Texas MD Anderson Cancer UTHealth Graduate School of Biomedical Sciences, Houston, USA. 3. Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, USA. 4. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA. 5. Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, USA. 6. ContinuumDx, Houston, USA. 7. McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, USA. 8. Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, USA. 9. Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA. 10. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA. 11. Department of Sheikh Ahmed Pancreatic Cancer Research Center, The University of Texas MD Anderson Cancer Center, Houston, USA.
Abstract
Background: Detection of circulating tumor DNA can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We carried out a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal 'surfaceome' in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling. Patients and methods: Surface exosomal proteins were profiled in 13 human PDAC and 2 non-neoplastic cell lines by liquid chromatography-mass spectrometry. A total of 173 prospectively collected blood samples from 103 PDAC patients underwent exosome isolation. Droplet digital PCR was used on 74 patients (136 total exosome samples) to determine baseline KRAS mutation call rates while patients were on therapy. PDAC-specific exosome capture was then carried out on additional 29 patients (37 samples) using an antibody cocktail directed against selected proteins, followed by droplet digital PCR analysis. Exosomal DNA in a PDAC patient resistant to therapy were profiled using a molecular barcoded, targeted sequencing panel to determine the utility of enriched nucleic acid material for comprehensive molecular analysis. Results: Proteomic analysis of the exosome 'surfaceome' revealed multiple PDAC-specific biomarker candidates: CLDN4, EPCAM, CD151, LGALS3BP, HIST2H2BE, and HIST2H2BF. KRAS mutations in total exosomes were detected in 44.1% of patients undergoing active therapy compared with 73.0% following exosome capture using the selected biomarkers. Enrichment of exosomal cargo was amenable to molecular profiling, elucidating a putative mechanism of resistance to PARP inhibitor therapy in a patient harboring a BRCA2 mutation. Conclusion: Exosomes provide unique opportunities in the context of liquid biopsies for enrichment of tumor-specific material in circulation. We present a comprehensive surfaceome characterization of PDAC exosomes which allows for capture and molecular profiling of tumor-derived DNA.
Background: Detection of circulating tumor DNA can be limited due to their relative scarcity in circulation, particularly while patients are actively undergoing therapy. Exosomes provide a vehicle through which cancer-specific material can be enriched from the compendium of circulating non-neoplastic tissue-derived nucleic acids. We carried out a comprehensive profiling of the pancreatic ductal adenocarcinoma (PDAC) exosomal 'surfaceome' in order to identify surface proteins that will render liquid biopsies amenable to cancer-derived exosome enrichment for downstream molecular profiling. Patients and methods: Surface exosomal proteins were profiled in 13 human PDAC and 2 non-neoplastic cell lines by liquid chromatography-mass spectrometry. A total of 173 prospectively collected blood samples from 103 PDAC patients underwent exosome isolation. Droplet digital PCR was used on 74 patients (136 total exosome samples) to determine baseline KRAS mutation call rates while patients were on therapy. PDAC-specific exosome capture was then carried out on additional 29 patients (37 samples) using an antibody cocktail directed against selected proteins, followed by droplet digital PCR analysis. Exosomal DNA in a PDAC patient resistant to therapy were profiled using a molecular barcoded, targeted sequencing panel to determine the utility of enriched nucleic acid material for comprehensive molecular analysis. Results: Proteomic analysis of the exosome 'surfaceome' revealed multiple PDAC-specific biomarker candidates: CLDN4, EPCAM, CD151, LGALS3BP, HIST2H2BE, and HIST2H2BF. KRAS mutations in total exosomes were detected in 44.1% of patients undergoing active therapy compared with 73.0% following exosome capture using the selected biomarkers. Enrichment of exosomal cargo was amenable to molecular profiling, elucidating a putative mechanism of resistance to PARP inhibitor therapy in a patient harboring a BRCA2 mutation. Conclusion: Exosomes provide unique opportunities in the context of liquid biopsies for enrichment of tumor-specific material in circulation. We present a comprehensive surfaceome characterization of PDAC exosomes which allows for capture and molecular profiling of tumor-derived DNA.
Authors: Katherine S Yang; Hyungsoon Im; Seonki Hong; Ilaria Pergolini; Andres Fernandez Del Castillo; Rui Wang; Susan Clardy; Chen-Han Huang; Craig Pille; Soldano Ferrone; Robert Yang; Cesar M Castro; Hakho Lee; Carlos Fernandez Del Castillo; Ralph Weissleder Journal: Sci Transl Med Date: 2017-05-24 Impact factor: 17.956
Authors: Andrew V Biankin; Nicola Waddell; Karin S Kassahn; Marie-Claude Gingras; Lakshmi B Muthuswamy; Amber L Johns; David K Miller; Peter J Wilson; Ann-Marie Patch; Jianmin Wu; David K Chang; Mark J Cowley; Brooke B Gardiner; Sarah Song; Ivon Harliwong; Senel Idrisoglu; Craig Nourse; Ehsan Nourbakhsh; Suzanne Manning; Shivangi Wani; Milena Gongora; Marina Pajic; Christopher J Scarlett; Anthony J Gill; Andreia V Pinho; Ilse Rooman; Matthew Anderson; Oliver Holmes; Conrad Leonard; Darrin Taylor; Scott Wood; Qinying Xu; Katia Nones; J Lynn Fink; Angelika Christ; Tim Bruxner; Nicole Cloonan; Gabriel Kolle; Felicity Newell; Mark Pinese; R Scott Mead; Jeremy L Humphris; Warren Kaplan; Marc D Jones; Emily K Colvin; Adnan M Nagrial; Emily S Humphrey; Angela Chou; Venessa T Chin; Lorraine A Chantrill; Amanda Mawson; Jaswinder S Samra; James G Kench; Jessica A Lovell; Roger J Daly; Neil D Merrett; Christopher Toon; Krishna Epari; Nam Q Nguyen; Andrew Barbour; Nikolajs Zeps; Nipun Kakkar; Fengmei Zhao; Yuan Qing Wu; Min Wang; Donna M Muzny; William E Fisher; F Charles Brunicardi; Sally E Hodges; Jeffrey G Reid; Jennifer Drummond; Kyle Chang; Yi Han; Lora R Lewis; Huyen Dinh; Christian J Buhay; Timothy Beck; Lee Timms; Michelle Sam; Kimberly Begley; Andrew Brown; Deepa Pai; Ami Panchal; Nicholas Buchner; Richard De Borja; Robert E Denroche; Christina K Yung; Stefano Serra; Nicole Onetto; Debabrata Mukhopadhyay; Ming-Sound Tsao; Patricia A Shaw; Gloria M Petersen; Steven Gallinger; Ralph H Hruban; Anirban Maitra; Christine A Iacobuzio-Donahue; Richard D Schulick; Christopher L Wolfgang; Richard A Morgan; Rita T Lawlor; Paola Capelli; Vincenzo Corbo; Maria Scardoni; Giampaolo Tortora; Margaret A Tempero; Karen M Mann; Nancy A Jenkins; Pedro A Perez-Mancera; David J Adams; David A Largaespada; Lodewyk F A Wessels; Alistair G Rust; Lincoln D Stein; David A Tuveson; Neal G Copeland; Elizabeth A Musgrove; Aldo Scarpa; James R Eshleman; Thomas J Hudson; Robert L Sutherland; David A Wheeler; John V Pearson; John D McPherson; Richard A Gibbs; Sean M Grimmond Journal: Nature Date: 2012-10-24 Impact factor: 49.962
Authors: F A San Lucas; K Allenson; V Bernard; J Castillo; D U Kim; K Ellis; E A Ehli; G E Davies; J L Petersen; D Li; R Wolff; M Katz; G Varadhachary; I Wistuba; A Maitra; H Alvarez Journal: Ann Oncol Date: 2015-12-17 Impact factor: 32.976
Authors: Kai Liang; Fei Liu; Jia Fan; Dali Sun; Chang Liu; Christopher J Lyon; David W Bernard; Yan Li; Kenji Yokoi; Matthew H Katz; Eugene J Koay; Zhen Zhao; Ye Hu Journal: Nat Biomed Eng Date: 2017-02-06 Impact factor: 25.671
Authors: Tessa Ys Le Large; Giulia Mantini; Laura L Meijer; Thang V Pham; Niccola Funel; Nicole Ct van Grieken; Bart Kok; Jaco Knol; Hanneke Wm van Laarhoven; Sander R Piersma; Connie R Jimenez; G Kazemier; Elisa Giovannetti; Maarten F Bijlsma Journal: JCI Insight Date: 2020-08-06
Authors: Joseph Carmicheal; Chihiro Hayashi; Xi Huang; Lei Liu; Yao Lu; Alexey Krasnoslobodtsev; Alexander Lushnikov; Prakash G Kshirsagar; Asish Patel; Maneesh Jain; Yuri L Lyubchenko; Yongfeng Lu; Surinder K Batra; Sukhwinder Kaur Journal: Nanomedicine Date: 2018-12-11 Impact factor: 5.307
Authors: Steven G Griffiths; Alan Ezrin; Emily Jackson; Lisa Dewey; Alan A Doucette Journal: Cell Stress Chaperones Date: 2019-10-24 Impact factor: 3.667
Authors: Vincent Bernard; Dong U Kim; F Anthony San Lucas; Jonathan Castillo; Kelvin Allenson; Feven C Mulu; Bret M Stephens; Jonathan Huang; Alexander Semaan; Paola A Guerrero; Nabiollah Kamyabi; Jun Zhao; Mark W Hurd; Eugene J Koay; Cullen M Taniguchi; Joseph M Herman; Milind Javle; Robert Wolff; Matthew Katz; Gauri Varadhachary; Anirban Maitra; Hector A Alvarez Journal: Gastroenterology Date: 2018-09-19 Impact factor: 22.682