Program Official

Principal Investigator

Awardee Organization

University Of California, San Diego
United States

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

Engineering Native E. coli to Detect, Report, and Treat Colorectal Cancer

Despite its overall decreasing occurrence, colorectal cancer (CRC) remains the fourth most common cause of cancer deaths in the US. Unfortunately, epidemiological studies demonstrate an alarming increase in incidence in populations below the age of 50, who are not routinely screened. Furthermore, CRC detection is difficult in high-risk groups, including those with a genetic predisposition (e.g. familial adenomatous polyposis), disease traits (e.g. inflammatory bowel disease), or from certain demographics (e.g. Black-Americans). Thus, there is a significant need for the development of innovative solutions for the early detection of CRC and the prevention of the transition from adenoma to CRC. To address this need, our interdisciplinary research team will develop genetically engineered bacteria using synthetic biology approaches to identify early CRC development, monitor and report changes in the adenoma and CRC microenvironment, and prevent cancer progression. To achieve the above objectives, engineered bacteria have to engraft and colonize the hostile luminal environment, sense and distinguish an abnormal environmental signal, compute this signal, and express a reporter or a therapeutic agent. However, appropriate vectors with these features remain lacking, constraining synthetic biology applications for cancer research. Importantly, CRC is highly associated with E. coli, for which we have many synthetic biology tools. Furthermore, our preliminary proof-of-concept studies have revealed that native E. coli can be engineered to perpetually colonize fully conventional (i.e. non-microbiome depleted) hosts and to execute functions of interest, e.g., deconjugation of luminal bile acids. Deconjugated bile acid and resultant farnesoid X receptor (FXR) agonism can suppress CRC development, indicating a potential therapeutic use of engineered native bacteria. Building on our strong supportive preliminary results, we will identify native E. coli from healthy, adenoma, and CRC tissues of a genetic model of CRC and engineer them to detect and treat CRC in response to the cancer microenvironment. Furthermore, we will characterize the effects of different tumor environment factors on the colonization and performances of engineered native E. coli in the colon organoid model in an organ-on-chip with the support of mathematical modeling, thereby identifying specific CRC signals for programming the responses of engineered native E. coli as CRC reporters and therapeutics. Finally, we will engineer native bacteria to detect and attenuate the progression of CRC by quantitatively reporting the level of CRCrelated cysteine proteases and selectively inhibiting their activity. The research described in this proposal will generate new, much-needed synthetic biology vectors that can be developed as biosensors and therapeutics of adenoma and CRC, as well as many other diseases. Furthermore, this project will enrich our fundamental knowledge about the CRC-microbiome relationship and elucidate the roles of cysteine proteases in CRC progression and treatment.


  • Siguenza N, Russell BJ, Richter RA, Zarrinpar A. Complete Genome Sequence of an Escherichia coli Strain Isolated from Laboratory Mouse Stool for Use as a Chassis for Transgene Delivery to the Murine Microbiome. Microbiology resource announcements. 2023 Apr 18;12(4):e0101422. Epub 2023 Mar 1. PMID: 36856451
  • Dantas Machado AC, Brown SD, Lingaraju A, Sivaganesh V, Martino C, Chaix A, Zhao P, Pinto AFM, Chang MW, Richter RA, Saghatelian A, Saltiel AR, Knight R, Panda S, Zarrinpar A. Diet and feeding pattern modulate diurnal dynamics of the ileal microbiome and transcriptome. Cell reports. 2022 Jul 5;40(1):111008. PMID: 35793637
  • Dantas Machado AC, Ramos SF, Gauglitz JM, Fassler AM, Petras D, Aksenov AA, Kim UB, Lazarowicz M, Barnard Giustini A, Aryafar H, Vodkin I, Warren C, Dorrestein PC, Zarrinpar A, Zarrinpar A. Portosystemic shunt placement reveals blood signatures for the development of hepatic encephalopathy through mass spectrometry. Nature communications. 2023 Aug 31;14(1):5303. PMID: 37652904
  • Russell BJ, Brown SD, Siguenza N, Mai I, Saran AR, Lingaraju A, Maissy ES, Dantas Machado AC, Pinto AFM, Sanchez C, Rossitto LA, Miyamoto Y, Richter RA, Ho SB, Eckmann L, Hasty J, Gonzalez DJ, Saghatelian A, Knight R, Zarrinpar A. Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes. Cell. 2022 Aug 18;185(17):3263-3277.e15. Epub 2022 Aug 4. PMID: 35931082
  • Zhang J, Hasty J, Zarrinpar A. Live bacterial therapeutics for detection and treatment of colorectal cancer. Nature reviews. Gastroenterology & hepatology. 2024 May;21(5):295-296. PMID: 38355755
  • Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R. The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Gastroenterology. 2023 Jun;164(7):1069-1085. Epub 2023 Feb 24. PMID: 36841488
  • Goens D, Virzi NE, Jung SE, Rutledge TR, Zarrinpar A. Obesity, Chronic Stress, and Stress Reduction. Gastroenterology clinics of North America. 2023 Jun;52(2):347-362. Epub 2023 Apr 7. PMID: 37197878
  • Petersen MC, Gallop MR, Flores Ramos S, Zarrinpar A, Broussard JL, Chondronikola M, Chaix A, Klein S. Complex physiology and clinical implications of time-restricted eating. Physiological reviews. 2022 Oct 1;102(4):1991-2034. Epub 2022 Jul 14. PMID: 35834774
  • Brevi A, Zarrinpar A. Live Biotherapeutic Products as Cancer Treatments. Cancer research. 2023 Jun 15;83(12):1929-1932. PMID: 37317784
  • Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R. Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution. mSystems. 2023 Aug 31;8(4):e0000623. Epub 2023 Jun 23. PMID: 37350611