Combined tumor-associated microbiome and immune gene expression profiling predict response to neoadjuvant chemo-radiotherapy in locally advanced rectal cancer

• Published in: Oncoimmunology Vol. 14; no. 1; p. 2465015
• Main Authors: Roesel, Raffaello, Strati, Francesco, Basso, Camilla, Epistolio, Samantha, Spina, Paolo, Djordjevic, Julija, Sorrenti, Elisa, Villa, Martina, Cianfarani, Agnese, Mongelli, Francesco, Galafassi, Jacopo, Popeskou, Sotirios G., Facciotti, Federica, Caprera, Cecilia, Melle, Federica, Majno-Hurst, Pietro Edoardo, Franzetti-Pellanda, Alessandra, De Dosso, Sara, Bonfiglio, Ferdinando, Frattini, Milo, Christoforidis, Dimitrios, Iezzi, Giandomenica
• Format: Journal Article
• Language: English
• Published: United States Taylor & Francis 01.12.2025; Taylor & Francis Group
• Subjects: Adult; Aged; Female; Gastrointestinal Microbiome; Gene Expression Profiling; Humans; Immune cell gene profiling; intratumoral microbiota; LARC; Male; Middle Aged; nCRT; Neoadjuvant Therapy; Original Research; predictive signature; Rectal Neoplasms - genetics; Rectal Neoplasms - immunology; Rectal Neoplasms - microbiology; Rectal Neoplasms - pathology; Rectal Neoplasms - therapy; Transcriptome; Treatment Outcome; intratumoral microbiota; nCRT; Immune cell gene profiling; LARC; predictive signature
• DOI: 10.1080/2162402X.2025.2465015
• ISSN: 2162-402X; 2162-4011

Locally advanced rectal cancer (LARC) is treated with neoadjuvant chemo-radiotherapy (nCRT) followed by surgery. A minority of patients show complete response (CR) to nCRT and may avoid surgery and its functional consequences. Instead, most patients show non-complete response (non-CR) and may benefit from additional treatments to increase CR rates. Reliable predictive markers are lacking. Aim of this study was to identify novel signatures predicting nCRT responsiveness. We performed a combined analysis of tumor-associated microbiome and immune gene expression profiling of diagnostic biopsies from 70 patients undergoing nCRT followed by rectal resection, including 16 with CR and 54 with non-CR. Findings were validated by an independent cohort of 49 patients, including 7 with CR and 42 with non-CR. Intratumoral microbiota significantly differed between CR and non-CR groups at genus and species level. Colonization by bacterial species of genera was consistently associated with CR, whereas abundance of , , and species predicted non-CR. Immune gene profiling revealed a panel of 59 differentially expressed genes and significant upregulation of IFN-gamma and -alpha response in patients with CR. Integrated microbiome and immune gene profiling analysis unraveled clustering of microbial taxa with each other and with immune cell-related genes and allowed the identification of a combined signature correctly identifying non-CRS in both cohorts. Thus, combined intratumoral microbiome-immune profiling improves the prediction of response to nCRT. Correct identification of unresponsive patients and of bacteria promoting responsiveness might lead to innovative therapeutic approaches based on gut microbiota pre-conditioning to increase nCRT effectiveness in LARC.