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Molecular Diagnostics

A blood-based circulating microbial metagenomic panel for early diagnosis and prognosis of oesophageal adenocarcinoma

British Journal of Cancer volume 127, pages 2016–2024 (2022)Cite this article

Subjects

Abstract

Background

Emerging evidence indicates the potential clinical significance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in oesophageal adenocarcinoma (EAC) patients, particularly as novel non-invasive, early detection, surveillance and prognostic classifiers.

Methods

Metagenome sequencing was performed on 81 serum specimens collected across EAC spectrum, with sequencing reads classified using Bracken and MetaPhlAn3. Followed by the Linear Discriminant Analysis effect size (LEfSe) method to identify microbial profiles between groups. Logistic regression and Kaplan–Meier analyses were used to build classifiers.

Results

A significant loss of alpha and beta diversity was identified in serum specimens from EAC patients. We observed a shift in microbial taxa between each group—at the phylum, genus, and species level—with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 (95% CI: 0.78–0.95; P < 0.001) and this panel in conjunction with the TNM stage was a robust predictor of overall survival (≥24 months; AUC = 0.84 (95% CI: 0.66–0.92; P = 0.006)).

Conclusion

This study firstly describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC.

Translational relevance

Accumulating data indicates the clinical relevance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in patients with oesophageal adenocarcinoma (EAC). Herein, we performed metagenome sequencing in serum specimens from EAC patients 81 collected across EAC spectrum and observed a significant loss of alpha and beta diversity, with a shift in microbial taxa between each group—at the phylum, genus, and species level—with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 and this panel, in conjunction with the TNM stage, was a robust predictor of overall survival. This study for the first time describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC.

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Fig. 1: Alpha and beta diversity analysis between patients with GERD, BE, dysplasia and EAC.
Fig. 2: Relative abundance of microbial taxa at the phylum, genus and species level.
Fig. 3: Linear Discriminant Analysis (LDA) effect size (LEfSe) and logistic regression analysis showing the potential of metagenome panel as a diagnostic biomarker.
Fig. 4: Metagenome panel as a predictive biomarker of overall survival (OS) in patients with EAC.

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Data availability

The datasets used for this study are available from the corresponding author on reasonable request.

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Acknowledgements

We would like to thank Dr. John Gillece and Dr. Sarah Highlander for their expertise and hard work in data analysis and for providing their critical insights into the analysis of microbial metagenome sequencing data.

Funding

This work was supported by CA72851, CA181572, CA184792, CA202797 and CA227602 grants from the National Cancer Institute, National Institutes of Health.

Author information

Authors and Affiliations

  1. Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, PA, USA

    Ali H. Zaidi, Ashten N. Omstead, Anastasia Gorbonova, Rubab Mansoor, Blair A. Jobe & Patrick L. Wagner

  2. Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA

    Muhammad Yogi Pratama & Ajay Goel

  3. The Allegheny Health Network, Center of Excellence in Biofilm Research, Pittsburgh, PA, USA

    Rachael Melton-Kreft

  4. The Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA

    Ronan J. Kelly

  5. City of Hope Comprehensive Cancer Center, Duarte, CA, USA

    Ajay Goel

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  1. Ali H. Zaidi
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Contributions

AHZ (conceptualisation: lead; funding acquisition: equal; methodology: equal; writing—review and editing: equal). MYP (data curation: lead; formal analysis: equal; methodology: equal; writing—original draft: lead; writing—review and editing: equal). ANO (data curation: equal; formal analysis: supporting; validation: supporting; writing—original draft: lead; writing—review and editing: supporting). AG (resources: supporting; writing—review and editing: supporting). RM (resources: supporting; writing—review and editing: supporting). RM-K (resources: supporting; writing—review and editing: supporting). BAJ (resources: supporting; validation: supporting; writing—review and editing: supporting). PLW (resources: supporting; validation: supporting; writing—review and editing: supporting). RJK (resources: supporting; validation: supporting; writing—review and editing: supporting). AG (conceptualisation: lead; funding acquisition: lead; methodology: equal; writing—review and editing: equal). All authors read and approved the final manuscript.

Corresponding author

Correspondence to Ajay Goel.

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The study was conducted in accordance with the Declaration of Helsinki. Written informed consent was obtained from all patients, and the study was approved by the institutional review boards of the participating institutions.

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Zaidi, A.H., Pratama, M.Y., Omstead, A.N. et al. A blood-based circulating microbial metagenomic panel for early diagnosis and prognosis of oesophageal adenocarcinoma. Br J Cancer 127, 2016–2024 (2022). https://doi.org/10.1038/s41416-022-01974-5

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