P. micra was significantly enriched in fecal samples and tissue biopsies of CRC patients
Using large-scale shotgun metagenome sequences of fecal samples and 16S sequencing of tissue biopsies, we have recently demonstrated that P. micra was highly enriched in both stool and tissues of CRC patients as compared with healthy subjects in a meta-analysis (Figure S1A) [38, 39].
To validate the enrichment of P. micra in fecal samples of patients with CRC, we analysed the gut metagenome sequences of individual cohorts (France (control, n = 66; CRC, n = 89) and Austria (control, n = 63 and CRC, n = 46) (Fig. 1A). The abundance of P. micra in fecal samples of patients with CRC was significantly higher than in normal control subjects in both European cohorts (P < 0.01). Furthermore, a geographically-matched independent Chinese cohort (control, n = 110; CRC, n = 111) consistently confirmed that P. micra was significantly enriched in fecal samples of patients with CRC (P < 0.001) (Fig. 1B).
To further verify the results from metagenome sequencing data, the abundance of P. micra was detected by real-time quantitative PCR using additional 181 control and 128 CRC fecal samples as well as 61 mucosal samples of normal colon and 52 pairs of colorectal carcinoma-adjacent normal and cancerous mucosae from Beijing and Hong Kong. qPCR confirmed the enrichment of P. micra in both fecal and mucosal samples of patients with CRC compared with control samples (P < 0.0001) (Fig. 1C and 1D). Taken together, these results showed increased prevalence of P. micra in feces as well as tumor biopsy samples in colorectal neoplasms and suggest a potential functional role for this bacterium in tumorigenesis.
P. micra-conditioned medium promotes proliferation of colonic cells
A strain of P. micra was successfully isolated from the fecal sample of a CRC patient (Figure S1B). Analysis of chromatograms showed nearly identical sequence match of its 16S rRNA gene sequence with those of P. micra strains deposited in the NCBI RefSeq database (Figure S1C). Growth dynamics and colony morphology of this P. micra strain were showed in Figure S2. To investigate the functional role of P. micra, we performed MTT assays on various colonic cell lines with the conditioned medium of P. micra. Interestingly, P. micra-conditioned medium significantly promoted the proliferation of both normal colonic epithelial cell line, NCM460 and cancer cell lines, HT29 and Caco2 compared with E. coli-conditioned medium and broth control groups (Fig. 2A). To verify the MTT viability assay, we performed colony formation assays on the colonic cell lines co-cultured with bacterial conditioned medium. We found that the P. micra-conditioned medium consistently increased the clonogenicities of normal colonic epithelial cell line NCM460 as well as cancer cell lines HT29 and Caco2 when compared with control groups (Fig. 2B).
P. micrapromotes intestinal tumorigenesis in conventional Apcmin/+ mice by triggering inflammation
Next, we determined whether P. micra could drive tumorigenesis in a murine Apcmin/+ model of CRC. Before oral gavage with P. micra, the resident microbiota was depleted using a cocktail of broad-spectrum antibiotics (ampicillin 0.2 g/L, vancomycin 0.1 g/L, neomycin 0.2 g/L, and metronidazole 0.2 g/L) in drinking water for 2 weeks. Mice were then orally gavaged with P. micra, E. coli or broth control 3 times per week for 8 weeks (Fig. 3A). Depletion of fecal bacterial DNA shown by a 10-fold reduction of total bacteria in the feces was confirmed by real-time quantitative PCR analyses (Fig. 3B). The abundance of P. micra was increased after P. micra introduction (Fig. 3B). Mice were sacrificed after 10 weeks. We observed significantly more tumors in mice inoculated with P. micra than the E. coli and PBS control groups (p < 0.01), suggesting that P. micra may play a pro-tumorigenic role in vivo (Fig. 3C and 3D); the tumor load was consistently higher in P. micra-gavaged group than control groups (p < 0.01) (Fig. 3D).
To gain insights into the potential mechanisms underlying the tumorigenic role of P. micra, we examined inflammation scores of proximal and distal colons and found that the inflammation scores were significantly higher in the mice gavaged with P. micra compared to E. coli and broth control groups (Fig. 3E). In the lamina propria of colonic tissues, flow cytometry analyses showed increased levels of Th2 and Th17 cell infiltration, and reduced number of Th1 cells (Fig. 3F). Together, these results suggest that the promotion of colonic tumor formation by P. micra in Apcmin/+ mice was associated with Th17 inflammatory response.
P. micra promotes colonic cell proliferation in germ-free mice
Germ-free mice model was used to further ascertain the function of P. micra in promoting CRC, Germ-free mice of 8-weeks-old were randomly assigned to 3 groups and gavaged with 1 × 108 CFU of P. micra, E. coli, or broth once. At three time points (8 weeks, 20 weeks, and 32 weeks), 5 mice from each group mice were sacrificed (Fig. 4A). To investigate whether P. micra could promote epithelial cell proliferation, we performed Ki-67 IHC staining on the colon tissues. The protein levels of Ki-67 were not significantly different among all groups at week 8. Interestingly, the protein levels of Ki-67 were higher in the P. micra group than the control group at week 20 and 32 (Fig. 4B). The ability of P. micra in promoting cell proliferation in the colonic epithelial tissues was confirm by increased PCNA protein expression, in P. micra-gavaged germ-free mice as compared with broth and E. coli control groups (Fig. 4C). These findings confirmed the results from in vitro MTT and colony formation assays and indicated that P. micra could promote colonic cell proliferation.
Altered expression of cell proliferation-related genes in P. micra-induced tumorigenesis in germ-free mice
The potential mechanisms underlying the tumorigenic role of P. micra in germ-free mice were determined by Cancer Gene expression analysis, which indicated that cell proliferation-related pathways were altered (Fig. 5A). We found downregulation of genes in apoptotic pathways; FasL, Casp7, cellular senescence; Map2k3 and DNA damage and repair; Gadd45g. Genes that are known to function in angiogenesis (Pgf, Tek, Angpt1, Fit1) and regulate cell proliferation (Tbx2, Mki67, Mcm2, Cdc20) were found to be upregulated. In addition, stemness associated genes (Sirt1, Bmi1) and those involved with invasion and metastasis (Cdh2, Foxc2, Snai1) were observed to have more than 2 fold increased expression in P. micra induced tumorigenesis (Fig. 5B).
Altered expression of immune responses and inflammation related genes in P. micra-induced tumorigenesis in germ-free mice
The Mouse Inflammatory Response and Autoimmunity PCR Array was used to analyse potential contribution of inflammation to the role of P. micra in colon tumorigenesis in germ-free mice. Significant up-regulation (48 transcripts) and down-regulation (6 transcripts) of gene expression were observed at 32 weeks after gavage with P. micra. Differentially expressed genes included interleukin 17a (Il17a), Il22, and Il23a, which encode 3 cytokines secreted by Th17 lymphocytes. We found the upregulation of genes that function in chemotaxis of immune cells including neutrophil chemotaxis (Cxcl1, Cxcl2, Cxcl5, Cxcl9, Cxcr2, Cxcr4 and Ccl20), T-lymphocyte chemotaxis (CCr4, Ccl17, Ccl19, Ccl22, Ccl24, Cxcl9, Cxcl10 and Cxcl11), and monocyte chemotaxis (Ccl1, Ccl2, Ccl3, Ccl4, Ccl5, Ccl7 and Ccl8) (Fig. 5C and 5D). In addition, genes in pro-inflammatory response pathway (IL1α, IL1β, Il1rn, Tlr2, Tlr4, Il1rap, Ifnγ and Ltb), and humoral response pathway (Ccr7, Tnf-α, Il1b, Il6, Nfkb1 and Itgb2) demonstrated increased expression in P. micra gavaged mice compared to control. However, Ccl11, Ccl25, Kng1, Il9 and Crp were downregulated in P. micra-gavaged mice. Quantitative RT-PCRs using specific primer-probes were performed on genes identified in the microarray study and confirmed the changes in expression of Tnf-α, Il17a, Il6 and Cxcr1 (Fig. 5E). These genes corresponded to altered immune state involving chemotaxis, antigen presentation, pro-inflammatory response and the Th17 pathway. Taken together, these results suggest that tumor-promoting effect of P. micra is associated with altered immune responses and enhanced inflammation in the gut.