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Bacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence

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Abstract

Bacteremia poses great risk for morbidity and mortality for immunocompromised cancer patients. Although the presence of bacteria within solid tumors is gaining greater attention, few studies have analyzed species of bacteria in the blood and their effect on cancer clinical outcomes. Using the Kraken 2 taxonomic profiling tool, we classified bacteria present in blood and primary tumors of cervical cancer and melanoma cases. The Cancer Genome Atlas (TCGA) melanoma blood exome files with Pseudomonas species were found to represent a worse disease-free survival (DFS) probability, while a worse overall survival (OS) result was evidenced for both the TCGA and Moffitt Cancer Center melanoma datasets. Cervical cancer cases with reads representing the Bradyrhizobium genus and Bradyrhizobium sp. BTAi1 found in blood and tumor exome files were found to have lower DFS. Additionally, reduced DFS and OS were observed for cervical cancer cases positive for Bacteroides species including Bacteroides fragilis. This study provides novel evidence and a novel approach for indicating that bacteria in blood is associated with cancer recurrence. These findings may guide the development of more efficient prognostic and screening tools related to bacterial blood infections of melanoma and cervical cancer patients.

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Data availability

Data generated in this study are available in the supporting online material. Any additional information related to these data can be had by emailing the corresponding author.

Abbreviations

BAM:

Binary alignment map

CESC:

Cervical squamous cell cancer

dbGaP:

Database of genotypes and phenotypes

DFS:

Disease-free survival

GDC:

Genomic data commons

KM:

Kaplan–Meier

NCBI:

National Center for Biotechnology Information

OS:

Overall survival

SKCM:

Skin cutaneous melanoma

TCGA:

The cancer genome atlas

WXS:

Whole exome sequence

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Acknowledgements

Authors thank USF research computing and Ms. Corinne Walters for managing the extensive admin support for obtaining approvals for database access.

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Authors and Affiliations

  1. Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Bd. MDC7, Tampa, FL, 33612, USA

    Jessica U. Quach, Michael J. Diaz, Taha I. Huda, Konrad J. Cios & George Blanck

  2. Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA

    Jacob C. Kinskey

  3. Department of Internal Medicine, Yale University, New Haven, CT, 06520, USA

    Saif Zaman

  4. Research Computing, University of South Florida, Tampa, FL, 33620, USA

    John E. Desantis

  5. Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA

    George Blanck

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Contributions

JUQ: conceptualization; formal analysis; methodology; software; visualization; writing—review and editing. MJD: methodology; software. TIH: resources; methodology; software. JCK: resources; methodology; software. SZ: methodology; software. JED: methodology; software. KJC: methodology; software. GB: project administration; resources; supervision; writing—review and editing.

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Correspondence to George Blanck.

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Quach, J.U., Diaz, M.J., Huda, T.I. et al. Bacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence. Mol Biotechnol 65, 1476–1484 (2023). https://doi.org/10.1007/s12033-023-00663-9

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