Tissue-associated microbial detection in cancer using human sequencing data

Rodriguez, Rebecca M.; Khadka, Vedbar S.; Menor, Mark; Hernandez, Brenda Y.; Deng, Youping

doi:10.1186/s12859-020-03831-9

Cited by 9 publications

(10 citation statements)

References 89 publications

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“…In GI cancers, the microbiota has been recognized to be related to chemotherapy, radiotherapy, and immunotherapy efficacy (7,8,12,13), indicating that the intestinal microbiota is a novel target to improve anti-tumor treatment (13). The presence of microbes within tumors and adjacent normal tissues may indicate disease progression and their potential roles in cancer pathogenesis (14)(15)(16). Understanding the alterations in the microbial community and abundance in GI organs thus aids in the study of GI cancer diagnosis and therapy.…”

Section: Introductionmentioning

confidence: 99%

Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer

Wang

et al. 2021

Front. Oncol.

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The gut microbiota has been previously linked with tumorigenesis and gastrointestinal cancer progression; however, intra-tumor microbiota analysis has just emerged and deserves increasing attention. Based on the public databases of The Cancer Microbiome Atlas (TCMA) and The Cancer Genome Atlas (TCGA), this study identified the tissue/organ microbial signatures generated from 443 biosamples of four major gastrointestinal cancer types, including esophageal carcinoma (ESCA), which further includes esophageal adenocarcinoma (EAD) and esophageal squamous cell carcinoma (ESCC), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ). According to partial least squares discrimination analysis (PLS-DA), the profile differences in microbial communities between the tumor and normal samples were not particularly noticeable across the four cancer cohorts, whereas paired comparison analyses revealed several specific differences in bacteria between tumor and normal samples in the EAD, STAD, and COAD samples. The taxa classified from the phylum to genus level revealed a trend of distinguishable microbial profiles between upper and lower gastrointestinal tumors. The Bacteroidetes/Firmicutes ratio in lower gastrointestinal tract tumors was nearly three times that in upper gastrointestinal tract tumors. We also determined the relative tissue/organ-prevalent microbes for each of the four cohorts at the order and genus levels. Microbe Alistipes, Blautia, Pasteurellales, and Porphyromonas compositions were correlated with the clinical characteristics of patients with gastrointestinal cancer, particularly colorectal cancer. Taken together, our findings indicate that microbial profiles shift across different gastrointestinal cancer types and that microbial colonization is highly site-specific. Composition of specific microbes can be indicative of cancer stage or disease progression. Overall, this study indicates that the microbial community and abundance in human tissues can be determined using publicly available data, and provides a new perspective for intra-tissue/organ microbiota research.

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Section: Introductionmentioning

confidence: 99%

Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer

Wang

et al. 2021

Front. Oncol.

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“…The existing relationship between AG Abs and the gastrointestinal microbiota community is worthy of attention. There is a rather indirect relationship between patient survival and the studied AG Abs, mediated by the presence of microorganisms that promote or inhibit cancer progression [73].…”

Section: Paradigm Of Microbial Origin Of Ag Abs Stimulusmentioning

confidence: 99%

“…The culture-independent method of next-generation sequencing (NGS) has tremendously simplified 16S rRNA gene sequencing to providing comprehensive data [139]. Using NGS to determine tumour-associated microbiota, together with the study of AG Abs profiling and immune response, can elucidate the role of microbiota and AG Abs in cancer pathogenesis and provide clinically relevant bioinformatics [73].…”

Section: Prospects and Challenges Of Integrative Glycome And Microbiome Researchmentioning

confidence: 99%

Prospects and Challenges of the Study of Anti-Glycan Antibodies and Microbiota for the Monitoring of Gastrointestinal Cancer

Smorodin

2021

IJMS

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Over the past decades, a large amount of data has been accumulated in various subfields of glycobiology. However, much clinically relevant data and many tools are still not widely used in medicine. Synthetic glycoconjugates with the known structure of glycans are an accurate tool for the study of glycan-binding proteins. We used polyacrylamide glycoconjugates (PGs) including PGs with tumour-associated glycans (TAGs) in immunoassays to assess the prognostic potential of the serum level of anti-glycan antibodies (AG Abs) in gastrointestinal cancer patients and found an association of AG Abs with survival. The specificity of affinity-isolated AG Abs was investigated using synthetic and natural glycoconjugates. AG Abs showed mainly a low specificity to tumour-associated and tumour-derived mucins; therefore, the protective role of the examined circulating AG Abs against cancer remains a challenge. In this review, our findings are analysed and discussed in the context of the contribution of bacteria to the AG Abs stimulus and cancer progression. Examples of the influence of pathogenic bacteria colonising tumours on cancer progression and patient survival through mechanisms of interaction with tumours and dysregulated immune response are considered. The possibilities and problems of the integrative study of AG Abs and the microbiome using high-performance technologies are discussed.

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“…Microbiological infections account for up to 20% of the total global cancer burden, one of the leading causes of morbidity and mortality worldwide [ 1 , 2 ]. Despite overall declining mortality rates in the United States, cancer remains the leading cause of death in the population including Asian Americans, Native Hawaiians, and persons of Hispanic origin [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

Bacterial Diversity Correlates with Overall Survival in Cancers of the Head and Neck, Liver, and Stomach

et al. 2021

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One in five cancers is attributed to infectious agents, and the extent of the impact on the initiation, progression, and disease outcomes may be underestimated. Infection-associated cancers are commonly attributed to viral, and to a lesser extent, parasitic and bacterial etiologies. There is growing evidence that microbial community variation rather than a single agent can influence cancer development, progression, response to therapy, and outcome. We evaluated microbial sequences from a subset of infection-associated cancers—namely, head and neck squamous cell carcinoma (HNSC), liver hepatocellular carcinoma (LIHC), and stomach adenocarcinoma (STAD) from The Cancer Genome Atlas (TCGA). A total of 470 paired tumor and adjacent normal samples were analyzed. In STAD, concurrent presence of EBV and Selemonas sputigena with a high diversity index were associated with poorer survival (HR: 2.23, 95% CI 1.26–3.94, p = 0.006 and HR: 2.31, 95%CI 1.1–4.9, p = 0.03, respectively). In LIHC, lower microbial diversity was associated with poorer overall survival (HR: 2.57, 95%CI: 1.2, 5.5, p = 0.14). Bacterial within-sample diversity correlates with overall survival in infection-associated cancers in a subset of TCGA cohorts.

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Tissue-associated microbial detection in cancer using human sequencing data

Cited by 9 publications

References 89 publications

Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer

Global Analysis of Microbiota Signatures in Four Major Types of Gastrointestinal Cancer

Prospects and Challenges of the Study of Anti-Glycan Antibodies and Microbiota for the Monitoring of Gastrointestinal Cancer

Bacterial Diversity Correlates with Overall Survival in Cancers of the Head and Neck, Liver, and Stomach

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