Program Official

Principal Investigator

Awardee Organization

University Of Tx Md Anderson Can Ctr
United States

Fiscal Year
Activity Code
Early Stage Investigator Grants (ESI)
Not Applicable
Project End Date

Longitudinal therapeutic monitoring of colorectal cancer patients using exosome-based liquid biopsies

Exosomes are bi-layered lipid microvesicles containing DNA, RNA and proteins, which have emerged as an important avenue for cell-cell communication in cancer. Our team has performed pioneering studies on the utility of circulating exosomes for genomic and transcriptomic profiling of visceral cancers that are challenging to sample longitudinally. Specifically, we have demonstrated the remarkable integrity of the nucleic acid cargo (exoDNA and exoRNA) contained within exosomes, which makes them readily amenable to next generation sequencing (NGS). The objective of this proposal is to establish the utility of liquid biopsies that enrich for high quality exosomes as a platform for therapeutic stratification and disease monitoring in advanced colorectal cancer (CRC). In Aim 1 will meticulously evaluate the most appropriate methodology for reproducible and sensitive isolation of circulating exosomes from metastatic CRC patients using gradient ultracentrifugation versus two of the most commonly used commercial kits. We will develop perform rigorous biological and technical reproducibility assays on the isolated exosomes and nucleic acid cargo that will develop standards necessary for translation of exosomal-based “liquid biopsy” to a clinical molecular diagnostics laboratory (MDL). We will also perform mass spectrometry-based proteomic profiling of exosomes isolated from a panel of CRC organoid models versus control organoids and cell lines, in order to identify the surface proteins (“surfaceome”) present on CRC-derived exosomes. The surfaceome data will serve as an invaluable tool for enrichment of cancerspecific exosomes in low-volume tumor settings, such as minimal residual disease monitoring. In Aim 2, we will compare targeted mutation panel and copy number profiles of tissue samples in patients undergoing surgical debulking for metastatic (m)CRC, with that of corresponding plasma exoDNA-derived profiles. The remarkable preservation of exoRNA within exosomes will allow us to perform RNA-Seq and compare the consensus molecular subtype (CMS) classification obtained by shed exosomes versus metastatic tissues. Finally, in Aim 3, we will longitudinally monitor cohorts of surgically resected CRC patients, or mCRC patients on two prospective clinical trials, using exosomes as a molecular tool for identifying disease recurrence and emergence of treatment resistance, respectively. The first trial will evaluate for emergence of low frequency KRAS mutations and other secondary drivers of resistance to EGFR-based therapies. The second trial is an immunotherapy trial of multivalent peptide vaccine, where exoRNA data will also be used to predict, and then monitor, expressed neoantigens in mCRC samples, using bioinformatics tools we have developed for mapping transcript data to HLA-presented peptides on the cancer cell surface. The long-term goal of these studies is to generate the compendium of standards and assays needed for successful translation of exosomes as a liquid biopsy platform to the clinical realm.


  • Ideno N, Yamaguchi H, Ghosh B, Gupta S, Okumura T, Steffen DJ, Fisher CG, Wood LD, Singhi AD, Nakamura M, Gutkind JS, Maitra A. GNASR201C Induces Pancreatic Cystic Neoplasms in Mice That Express Activated KRAS by Inhibiting YAP1 Signaling. Gastroenterology. 2018 Nov;155(5):1593-1607.e12. Epub 2018 Aug 22. PMID: 30142336
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  • Sveen A, Kopetz S, Lothe RA. Biomarker-guided therapy for colorectal cancer: strength in complexity. Nature reviews. Clinical oncology. 2020 Jan;17(1):11-32. Epub 2019 Jul 9. PMID: 31289352
  • Johnson B, Kopetz S. Applying Precision to the Management of BRAF-Mutant Metastatic Colorectal Cancer. Targeted oncology. 2020 Oct;15(5):567-577. PMID: 32889679
  • Bernard V, Kim DU, San Lucas FA, Castillo J, Allenson K, Mulu FC, Stephens BM, Huang J, Semaan A, Guerrero PA, Kamyabi N, Zhao J, Hurd MW, Koay EJ, Taniguchi CM, Herman JM, Javle M, Wolff R, Katz M, Varadhachary G, Maitra A, Alvarez HA. Circulating Nucleic Acids Are Associated With Outcomes of Patients With Pancreatic Cancer. Gastroenterology. 2019 Jan;156(1):108-118.e4. Epub 2018 Sep 19. PMID: 30240661
  • Kolbinger FR, Bernard V, Lee JJ, Stephens BM, Branchi V, Raghav KPS, Maitra A, Guerrero PA, Semaan A. Significance of Distinct Liquid Biopsy Compartments in Evaluating Somatic Mutations for Targeted Therapy Selection in Cancer of Unknown Primary. Journal of gastrointestinal cancer. 2023 Dec;54(4):1276-1285. Epub 2023 Mar 2. PMID: 36862364
  • Goggins MG, Lippman SM, Constantinou PE, Jacks T, Petersen GM, Syngal S, Maitra A. Intercepting Pancreatic Cancer: Our Dream Team's Resolve to Stop Pancreatic Cancer. Pancreas. 2018 Nov-Dec;47(10):1175-1176. PMID: 30325853
  • Loree JM, Dowers A, Tu D, Jonker DJ, Edelstein DL, Quinn H, Holtrup F, Price T, Zalcberg JR, Moore MJ, Karapetis CS, O'Callaghan CJ, Waring P, Kennecke HF, Hamilton SR, Kopetz S. Expanded Low Allele Frequency RAS and BRAF V600E Testing in Metastatic Colorectal Cancer as Predictive Biomarkers for Cetuximab in the Randomized CO.17 Trial. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Jan 1;27(1):52-59. Epub 2020 Oct 21. PMID: 33087330
  • Lee MS, Kopetz S. Are Homologous Recombination Deficiency Mutations Relevant in Colorectal Cancer? Journal of the National Cancer Institute. 2022 Feb 7;114(2):176-178. PMID: 34469539
  • Wolff RA, Wang-Gillam A, Alvarez H, Tiriac H, Engle D, Hou S, Groff AF, San Lucas A, Bernard V, Allenson K, Castillo J, Kim D, Mulu F, Huang J, Stephens B, Wistuba II, Katz M, Varadhachary G, Park Y, Hicks J, Chinnaiyan A, Scampavia L, Spicer T, Gerhardinger C, Maitra A, Tuveson D, Rinn J, Lizee G, Yee C, Levine AJ. Dynamic changes during the treatment of pancreatic cancer. Oncotarget. 2018 Feb 13;9(19):14764-14790. doi: 10.18632/oncotarget.24483. eCollection 2018 Mar 13. PMID: 29599906
  • Bent A, Kopetz S. Going with the Flow: The Promise of Plasma-Only Circulating Tumor DNA Assays. Clinical cancer research : an official journal of the American Association for Cancer Research. 2021 Oct 15;27(20):5449-5451. Epub 2021 Aug 13. PMID: 34389607
  • Fonseca AL, Kirkwood K, Kim MP, Maitra A, Koay EJ. Intraductal Papillary Mucinous Neoplasms of the Pancreas: Current Understanding and Future Directions for Stratification of Malignancy Risk. Pancreas. 2018 Mar;47(3):272-279. PMID: 29424809
  • Corvigno S, Johnson AM, Wong KK, Cho MS, Afshar-Kharghan V, Menter DG, Sood AK. Novel Markers for Liquid Biopsies in Cancer Management: Circulating Platelets and Extracellular Vesicles. Molecular cancer therapeutics. 2022 Jul 5;21(7):1067-1075. PMID: 35545008
  • Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Kun W, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype. Cancer research. 2024 May 15;84(10):1719-1732. PMID: 38451249
  • Menter DG, Afshar-Kharghan V, Shen JP, Martch SL, Maitra A, Kopetz S, Honn KV, Sood AK. Of vascular defense, hemostasis, cancer, and platelet biology: an evolutionary perspective. Cancer metastasis reviews. 2022 Mar;41(1):147-172. Epub 2022 Jan 12. PMID: 35022962
  • Bernard V, Semaan A, Huang J, San Lucas FA, Mulu FC, Stephens BM, Guerrero PA, Huang Y, Zhao J, Kamyabi N, Sen S, Scheet PA, Taniguchi CM, Kim MP, Tzeng CW, Katz MH, Singhi AD, Maitra A, Alvarez HA. Single-Cell Transcriptomics of Pancreatic Cancer Precursors Demonstrates Epithelial and Microenvironmental Heterogeneity as an Early Event in Neoplastic Progression. Clinical cancer research : an official journal of the American Association for Cancer Research. 2019 Apr 1;25(7):2194-2205. Epub 2018 Nov 1. PMID: 30385653
  • Eluri M, Kopetz S, Parseghian CM. Truncal Dynamics May Trump: Serial ctDNA to Predict Early Therapeutic Response. Clinical cancer research : an official journal of the American Association for Cancer Research. 2023 Jan 17;29(2):302-304. PMID: 36378102