Expanding the Colorectal Cancer Biomarkers Based on the Human Gut Phageome

• Published in: Microbiology spectrum 2021-12, Vol.9 (3), p.e0009021-e0009021
• Main Authors: Shen, Siyuan, Huo, Dongxue, Ma, Chenchen, Jiang, Shuaiming, Zhang, Jiachao
• Format: Article
• Language: English
• Subjects: Austria; bacteriophage; Bacteriophages; Bacteriophages - classification; Bacteriophages - genetics; Bacteriophages - isolation & purification; biomarkers; Biomarkers, Tumor; China; Cohort Studies; Colitis, Ulcerative - virology; colorectal cancer; Colorectal Neoplasms - virology; Crohn Disease - virology; Feces - virology; Gastrointestinal Tract - virology; Humans; Japan; Metagenome; Research Article; Virome
• ISSN: 2165-0497; 2165-0497
• DOI: 10.1128/SPECTRUM.00090-21

With the increasing prevalence of colorectal cancer (CRC), extending the present biomarkers for the diagnosis of colorectal cancer is crucial. Previous studies have highlighted the importance of bacteriophages in gastrointestinal diseases, suggesting the potential value of gut phageome in early CRC diagnostic. Here, based on 317 metagenomic samples of three discovery cohorts collected from China (Hong Kong), Austria, and Japan, five intestinal bacteriophages, including Fusobacterium nucleatum, and Parvimonas micra phages were identified as potential CRC biomarkers. The five CRC enriched bacteriophagic markers classified patients from controls with an area under the receiver-operating characteristics curve (AUC) of 0.8616 across different populations. Subsequently, we used a total of 80 samples from China (Hainan) and Italy for validation. The AUC of the validation cohort is 0.8197. Moreover, to further explore the specificity of the five intestinal bacteriophage biomarkers in a broader background, we performed a confirmatory meta-analysis using two inflammatory bowel disease cohorts, ulcerative colitis (UC) and Crohn's disease (CD). Excitingly, we observed that the five CRC-enriched phage markers also exhibited high discrimination in UC (AUC = 78.02%). Unfortunately, the five CRC-rich phage markers did not show high resolution in CD (AUC = 48.00%). The present research expands the potential of microbial biomarkers in CRC diagnosis by building a more accurate classification model based on the human gut phageome, providing a new perspective for CRC gut phagotherapy. Worldwide, by 2020, colorectal cancer has become the third most common cancer after lung and breast cancer. Phages are strictly host-specific, and this specificity makes them more accurate as biomarkers, but phage biomarkers for colorectal cancer have not been thoroughly explored. Therefore, it is crucial to extend the existing phage biomarkers for the diagnosis of colorectal cancer. Here, we innovatively constructed a relatively accurate prediction model, including: three discovery cohorts, two additional validation cohorts and two cross-disease cohorts. A total of five possible biomarkers of intestinal bacteriophages were obtained. They are Phage, Fusobacterium nucleatum Phage, Fusobacterium nucleatum Phage, Fusobacterium nucleatum Phage, and Parvimonas micra Phage. This study aims at identifying fine-scale species-strain level phage biomarkers for colorectal cancer diseases, so as to expand th