IDDF2024-ABS-0170 Metagenomic analyses highlight strain-level, age-independent and immunotherapy-associated microbial signatures in colorectal cancer

Background

To characterize the microbiome in early-onset colorectal cancer (aged <50, EOCRC) and late-onset CRC (aged ≥50, LOCRC) patients.

Methods

460 CRC patients (167 EOCRC) were recruited in Guangzhou, and deep shotgun metagenomic sequencing was applied to stool and saliva samples. De novo genome assembly, binning, inStrain, StrainPhlAn and MetaPhlAn analyses were performed. Stool metagenomes from a Fudan study (Yang et al., 2021) consisting of 50 EOCRC, 50 LOCRC and 100 age-matched controls were also included.

Results

Despite age being a determining factor for the gut microbiome, our analyses found limited associations between the gut microbiome and age in CRC. Well-known CRC-associated taxa (IDDF2024-ABS-0170 Figure 1. CRC-associated taxa and genes enriched in both EOCRC and LOCRC (a)) and genes (IDDF2024-ABS-0170 Figure 1. CRC-associated taxa and genes enriched in both EOCRC and LOCRC (b)) were consistently enriched in both EOCRC and LOCRC. In the strain-level analysis on Fusobacterium nucleatum (Fn), we identified two Fn subspecies animalis Clades (Fna C1 and C2), with Fna C2 as the dominant strain (IDDF2024-ABS-0170 Figure 2. Distribution of Fna C1 and Fna C2 in CRC patients (a)). This observation is in line with a Nature study (Zepeda-Rivera et al., 2024). We confirmed that fadA abundance did not differ in patients carrying either Fna C1 or C2 (IDDF2024-ABS-0170 Figure 2. Distribution of Fna C1 and Fna C2 in CRC patients (b)). More importantly, we found that both the abundances of Fna C1 and C2 were associated with mismatch repair and HER2 expression status (IDDF2024-ABS-0170 Figure 2. Distribution of Fna C1 and Fna C2 in CRC patients (c,d)), suggesting their potential roles in CRC clinical outcomes. We identified two distinct Bacteroides fragilis (Bf) strain clusters with high genome-wide similarity to the reference genomes of strain NCTC 9343 and Q1F2 respectively (IDDF2024-ABS-0170 Figure 3. Two distinct Bf strain clusters in CRC patients (a)). Intriguingly, the abundance and prevalence of Bf toxin gene bft were significantly higher in patients with strain NCTC9343 than Q1F2 (IDDF2024-ABS-0170 Figure 3. Two distinct Bf strain clusters in CRC patients (b)). Only one strain cluster was identified for Escherichia coli (Ec) (IDDF2024-ABS-0170 Figure 4. Correlations between Ec and pks genomic island (a)). A positive correlation between pks genomic island and Ec was observed in the Guangzhou cohort, but no correlation in the Fudan cohort, indicating population heterogeneity. Lastly, we found that the baseline compositions of gut and oral microbiome had remarkable differences between patients with different responses in anti-PD1 treatment (IDDF2024-ABS-0170 Figure 5. Gut and oral microbes associated with anti-PD1 treatment response).

Conclusions

Our results highlight striking similarities in microbial signatures between EOCRC and LOCRC, emphasizing the important roles of microbiome in CRC biology and treatment.