Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice

Joshua S. Son, Shanawaj Khair, Donald W. Pettet, Nengtai Ouyang, Xinyu Tian, Yuanhao Zhang, Wei Zhu, Gerardo Mackenzie, Charles E. Robertson, Diana Ir, Daniel N. Frank, Basil Rigas, Ellen Li

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80% of sporadic human colorectal adenomas and carcinomas. To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APCMin/+ and 30 congenic wild type (WT) mice. The results demonstrate that similar to 12-14 week old APCMin/+ mice with intestinal neoplasia, 6 week old APCMin/+mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon. Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APCMin/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ≥ 2, FDR <0.05). Hierarchical clustering of the DEGs was carried out by using 1-r dissimilarity measurement, where r stands for the Pearson correlation, and Ward minimum variance linkage, in order to reduce the number of input variables. When the cluster centroids (medians) were included along with APC genotype as input variables in a negative binomial (NB) regression model, four of seven mouse gene clusters, in addition to APC genotype, were significantly associated with the increased relative abundance of Bacteroidetes spp. Three of the four clusters include several downregulated genes encoding immunoglobulin variable regions and non-protein coding RNAs. These results support the concept that mutation of the APC gene alters colonic-microbial interactions prior to polyposis. It remains to be determined whether interventions directed at ameliorating dysbiosis in APCMin/+ mice, such as through probiotics, prebiotics or antibiotics, could reduce tumor formation.

Original languageEnglish (US)
Article numbere0127985
JournalPLoS One
Volume10
Issue number6
DOIs
StatePublished - Jun 29 2015
Externally publishedYes

Fingerprint

APC Genes
mucosa
Mucous Membrane
digestive system
Genes
Microbial Interactions
Bacteroidetes
mice
adenoma
Adenoma
Mutation
mutation
genes
neoplasms
carcinoma
Genotype
Dysbiosis
Immunoglobulin Variable Region
Congenic Mice
RNA Sequence Analysis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Son, J. S., Khair, S., Pettet, D. W., Ouyang, N., Tian, X., Zhang, Y., ... Li, E. (2015). Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice. PLoS One, 10(6), [e0127985]. https://doi.org/10.1371/journal.pone.0127985

Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice. / Son, Joshua S.; Khair, Shanawaj; Pettet, Donald W.; Ouyang, Nengtai; Tian, Xinyu; Zhang, Yuanhao; Zhu, Wei; Mackenzie, Gerardo; Robertson, Charles E.; Ir, Diana; Frank, Daniel N.; Rigas, Basil; Li, Ellen.

In: PLoS One, Vol. 10, No. 6, e0127985, 29.06.2015.

Research output: Contribution to journalArticle

Son, JS, Khair, S, Pettet, DW, Ouyang, N, Tian, X, Zhang, Y, Zhu, W, Mackenzie, G, Robertson, CE, Ir, D, Frank, DN, Rigas, B & Li, E 2015, 'Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice', PLoS One, vol. 10, no. 6, e0127985. https://doi.org/10.1371/journal.pone.0127985
Son, Joshua S. ; Khair, Shanawaj ; Pettet, Donald W. ; Ouyang, Nengtai ; Tian, Xinyu ; Zhang, Yuanhao ; Zhu, Wei ; Mackenzie, Gerardo ; Robertson, Charles E. ; Ir, Diana ; Frank, Daniel N. ; Rigas, Basil ; Li, Ellen. / Altered interactions between the gut microbiome and colonic mucosa precede polyposis in APCMin/+ mice. In: PLoS One. 2015 ; Vol. 10, No. 6.
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abstract = "Mutation of the adenomatous polyposis coli (APC gene), an early event in the adenoma-carcinoma sequence, is present in 70-80{\%} of sporadic human colorectal adenomas and carcinomas. To test the hypothesis that mutation of the APC gene alters microbial interactions with host intestinal mucosa prior to the development of polyposis, culture-independent methods (targeted qPCR assays and Illumina sequencing of the 16S rRNA gene V1V2 hypervariable region) were used to compare the intestinal microbial composition of 30 six-week old C57BL/6 APCMin/+ and 30 congenic wild type (WT) mice. The results demonstrate that similar to 12-14 week old APCMin/+ mice with intestinal neoplasia, 6 week old APCMin/+mice with no detectable neoplasia, exhibit an increased relative abundance of Bacteroidetes spp in the colon. Parallel mouse RNA sequence analysis, conducted on a subset of proximal colonic RNA samples (6 APCMin/+, 6 WT) revealed 130 differentially expressed genes (DEGs, fold change ≥ 2, FDR <0.05). Hierarchical clustering of the DEGs was carried out by using 1-r dissimilarity measurement, where r stands for the Pearson correlation, and Ward minimum variance linkage, in order to reduce the number of input variables. When the cluster centroids (medians) were included along with APC genotype as input variables in a negative binomial (NB) regression model, four of seven mouse gene clusters, in addition to APC genotype, were significantly associated with the increased relative abundance of Bacteroidetes spp. Three of the four clusters include several downregulated genes encoding immunoglobulin variable regions and non-protein coding RNAs. These results support the concept that mutation of the APC gene alters colonic-microbial interactions prior to polyposis. It remains to be determined whether interventions directed at ameliorating dysbiosis in APCMin/+ mice, such as through probiotics, prebiotics or antibiotics, could reduce tumor formation.",
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