The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

Dohlman, Anders B.; Mendoza, Diana; Ding, Shengli; Gao, Michael; Dressman, Holly K.; Iliev, Iliyan D.; Lipkin, Steven M.; Shen, Xiling

doi:10.1016/j.chom.2020.12.001

Cited by 145 publications

(133 citation statements)

References 82 publications

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“…RNA-seq data from the TCGA database could be applied to estimate microbial composition in tumor tissues (38). We comprehensively analyzed the correlations between microbiota abundance and the T-cell inflamed score.…”

Section: Ifitm3 Correlates With Emerging Immunobiomarkers In Blcamentioning

confidence: 99%

Interferon-Induced Transmembrane Protein 3 Shapes an Inflamed Tumor Microenvironment and Identifies Immuno-Hot Tumors

Cai

Sun

et al. 2021

Front. Immunol.

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Interferon-induced transmembrane protein 3 (IFITM3) is an interferon-induced membrane protein, which has been identified as a functional gene in multiple human cancers. The role of IFITM3 in cancer has been preliminarily summarized, but its relationship to antitumor immunity is still unclear. A pancancer analysis was conducted to investigate the expression pattern and immunological role of IFITM3 based on transcriptomic data downloaded from The Cancer Genome Atlas (TCGA) database. Next, correlations between IFITM3 and immunological features in the bladder cancer (BLCA) tumor microenvironment (TME) were assessed. In addition, the role of IFITM3 in estimating the clinical characteristics and the response to various therapies in BLCA was also evaluated. These results were next confirmed in the IMvigor210 cohort and a recruited cohort. In addition, correlations between IFITM3 and emerging immunobiomarkers, such as microbiota and N6-methyladenosine (m6A) genes, were assessed. IFITM3 was enhanced in most tumor tissues in comparison with adjacent tissues. IFITM3 was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), cancer immunity cycles, and inhibitory immune checkpoints. In addition, IFITM3 was associated with an inflamed phenotype and several established molecular subtypes. IFITM3 expression also predicted a notably higher response to chemotherapy, anti-EGFR therapy, and immunotherapy but a low response to anti-ERBB2, anti-ERBB4, and antiangiogenic therapy. In addition, IFITM3 was correlated with immune-related microbiota and m6A genes. In addition to BLCA, IFITM3 is expected to be a marker of high immunogenicity in most human cancers. In conclusion, IFITM3 expression can be used to identify immuno-hot tumors in most cancers, and IFITM3 may be a promising pancancer biomarker to estimate the immunological features of tumors.

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Section: Ifitm3 Correlates With Emerging Immunobiomarkers In Blcamentioning

confidence: 99%

Interferon-Induced Transmembrane Protein 3 Shapes an Inflamed Tumor Microenvironment and Identifies Immuno-Hot Tumors

Cai

Sun

et al. 2021

Front. Immunol.

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“…Because oral and gut microbiomes were predictive of each other and over-representations of several oral bacteria as F. nucleatum were detected in the stool from patients with CRC, microbial-biomarkers of CRC could be also investigated in oral samples [ 33 , 40 ]. Recently, Dohlman et al discovered promising endogenous microbial DNA signatures in blood samples from CRC patients featuring mucosal barrier injury in CRC [ 41 ].…”

Section: Gut Microbiota Biomarker For Cancer Screeningmentioning

confidence: 99%

“…Recently, a study by Iyadorai et al, reporting lower levels of colonization, confirmed this higher prevalence of CoPEC in CRC patient mucosa [ 118 ]. In addition, it was demonstrated that genes in the pks island were significantly more prevalent in tissue than blood, suggesting that E. coli strains expressing this gene are associated with CRC tissues [ 41 ]. Our team also reported that colonization of the intestinal mucosa by CoPEC was more prevalent in patients with stage III or IV CRC than in those with stage I CRC, suggesting a possible link with cancer aggressiveness [ 16 ].…”

Section: Colibactin-producing E Coli In the Intestinal Microbiotamentioning

confidence: 99%

Gut Microbiota as Potential Biomarker and/or Therapeutic Target to Improve the Management of Cancer: Focus on Colibactin-Producing Escherichia coli in Colorectal Cancer

Véziant

Villéger

Barnich

et al. 2021

Cancers

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The gut microbiota is crucial for physiological development and immunological homeostasis. Alterations of this microbial community called dysbiosis, have been associated with cancers such colorectal cancers (CRC). The pro-carcinogenic potential of this dysbiotic microbiota has been demonstrated in the colon. Recently the role of the microbiota in the efficacy of anti-tumor therapeutic strategies has been described in digestive cancers and in other cancers (e.g., melanoma and sarcoma). Different bacterial species seem to be implicated in these mechanisms: F. nucleatum, B. fragilis, and colibactin-associated E. coli (CoPEC). CoPEC bacteria are prevalent in the colonic mucosa of patients with CRC and they promote colorectal carcinogenesis in susceptible mouse models of CRC. In this review, we report preclinical and clinical data that suggest that CoPEC could be a new factor predictive of poor outcomes that could be used to improve cancer management. Moreover, we describe the possibility of using these bacteria as new therapeutic targets.

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“…Nejman et al (2020) constructed lots of controls to reduce contamination. Recently, the Cancer Microbiome Atlas provided a protocol to control for sample contamination (Dohlman et al, 2021). It is critical to set up rigorous contamination controls, and choose the proper sample collection sites, as well as types of microbial analysis, to investigate the tumor microbiome.…”

Section: Discussionmentioning

confidence: 99%

The Interaction Between the Microbiome and Tumors

Zong

Zhou

Liao

et al. 2021

Front. Cell. Infect. Microbiol.

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Cancer is a significant global health problem and is characterized by a consistent increase in incidence and mortality rate. Deciphering the etiology and risk factors are essential parts of cancer research. Recently, the altered microbiome has been identified within the tumor microenvironment, tumor tissue, and even nonadjacent environments, which indicates a strong correlation between the microbiome and tumor development. However, the causation and mechanisms of this correlation remain unclear. Herein, we summarized and discussed the interaction between the microbiome and tumor progression. Firstly, the microbiome, which can be located in the tumor microenvironment, inside tumor tissues and in the nonadjacent environment, is different between cancer patients and healthy individuals. Secondly, the tumor can remodel microbial profiles by creating a more beneficial condition for the shifted microbiome. Third, the microbiome can promote tumorigenesis through a direct pathogenic process, including the establishment of an inflammatory environment and its effect on host immunity. The interactions between the microbiome and tumors can promote an understanding of the carcinogenesis and provide novel therapeutic strategies for cancers.

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The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

Cited by 145 publications

References 82 publications

Interferon-Induced Transmembrane Protein 3 Shapes an Inflamed Tumor Microenvironment and Identifies Immuno-Hot Tumors

Interferon-Induced Transmembrane Protein 3 Shapes an Inflamed Tumor Microenvironment and Identifies Immuno-Hot Tumors

Gut Microbiota as Potential Biomarker and/or Therapeutic Target to Improve the Management of Cancer: Focus on Colibactin-Producing Escherichia coli in Colorectal Cancer

The Interaction Between the Microbiome and Tumors

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