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RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach

Author

Listed:
  • Gregory D. Poore

    (University of California San Diego)

  • Evguenia Kopylova

    (University of California San Diego
    Clarity Genomics)

  • Qiyun Zhu

    (University of California San Diego)

  • Carolina Carpenter

    (University of California San Diego)

  • Serena Fraraccio

    (University of California San Diego)

  • Stephen Wandro

    (University of California San Diego)

  • Tomasz Kosciolek

    (University of California San Diego
    Jagiellonian University in Krakow)

  • Stefan Janssen

    (University of California San Diego
    Justus Liebig University Gießen)

  • Jessica Metcalf

    (Colorado State University)

  • Se Jin Song

    (University of California San Diego)

  • Jad Kanbar

    (University of California San Diego)

  • Sandrine Miller-Montgomery

    (University of California San Diego
    University of California San Diego)

  • Robert Heaton

    (University of California San Diego)

  • Rana Mckay

    (University of California San Diego Health)

  • Sandip Pravin Patel

    (University of California San Diego
    University of California San Diego Health)

  • Austin D. Swafford

    (University of California San Diego)

  • Rob Knight

    (University of California San Diego
    University of California San Diego
    University of California San Diego
    University of California San Diego)

Abstract

Systematic characterization of the cancer microbiome provides the opportunity to develop techniques that exploit non-human, microorganism-derived molecules in the diagnosis of a major human disease. Following recent demonstrations that some types of cancer show substantial microbial contributions1–10, we re-examined whole-genome and whole-transcriptome sequencing studies in The Cancer Genome Atlas11 (TCGA) of 33 types of cancer from treatment-naive patients (a total of 18,116 samples) for microbial reads, and found unique microbial signatures in tissue and blood within and between most major types of cancer. These TCGA blood signatures remained predictive when applied to patients with stage Ia–IIc cancer and cancers lacking any genomic alterations currently measured on two commercial-grade cell-free tumour DNA platforms, despite the use of very stringent decontamination analyses that discarded up to 92.3% of total sequence data. In addition, we could discriminate among samples from healthy, cancer-free individuals (n = 69) and those from patients with multiple types of cancer (prostate, lung, and melanoma; 100 samples in total) solely using plasma-derived, cell-free microbial nucleic acids. This potential microbiome-based oncology diagnostic tool warrants further exploration.

Suggested Citation

  • Gregory D. Poore & Evguenia Kopylova & Qiyun Zhu & Carolina Carpenter & Serena Fraraccio & Stephen Wandro & Tomasz Kosciolek & Stefan Janssen & Jessica Metcalf & Se Jin Song & Jad Kanbar & Sandrine Mi, 2020. "RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach," Nature, Nature, vol. 579(7800), pages 567-574, March.
  • Handle: RePEc:nat:nature:v:579:y:2020:i:7800:d:10.1038_s41586-020-2095-1
    DOI: 10.1038/s41586-020-2095-1
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    Cited by:

    1. Yunmin Yang & Binbin Chu & Jiayi Cheng & Jiali Tang & Bin Song & Houyu Wang & Yao He, 2022. "Bacteria eat nanoprobes for aggregation-enhanced imaging and killing diverse microorganisms," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Lingjing Jiang & Niina Haiminen & Anna‐Paola Carrieri & Shi Huang & Yoshiki Vázquez‐Baeza & Laxmi Parida & Ho‐Cheol Kim & Austin D. Swafford & Rob Knight & Loki Natarajan, 2022. "Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data," Biometrics, The International Biometric Society, vol. 78(3), pages 1155-1167, September.
    3. Leandro C. Hermida & E. Michael Gertz & Eytan Ruppin, 2022. "Predicting cancer prognosis and drug response from the tumor microbiome," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    4. Jakob Woerner & Yidi Huang & Stephan Hutter & Carmelo Gurnari & Jesús María Hernández Sánchez & Janet Wang & Yimin Huang & Daniel Schnabel & Michael Aaby & Wanying Xu & Vedant Thorat & Dongxu Jiang & , 2022. "Circulating microbial content in myeloid malignancy patients is associated with disease subtypes and patient outcomes," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    5. Zheng Sun & Jiang Liu & Meng Zhang & Tong Wang & Shi Huang & Scott T. Weiss & Yang-Yu Liu, 2023. "Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    6. Kaiyuan Zhu & Alejandro A. Schäffer & Welles Robinson & Junyan Xu & Eytan Ruppin & A. Funda Ergun & Yuzhen Ye & S. Cenk Sahinalp, 2022. "Strain level microbial detection and quantification with applications to single cell metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    7. Candice R. Gurbatri & Georgette A. Radford & Laura Vrbanac & Jongwon Im & Elaine M. Thomas & Courtney Coker & Samuel R. Taylor & YoungUk Jang & Ayelet Sivan & Kyu Rhee & Anas A. Saleh & Tiffany Chien , 2024. "Engineering tumor-colonizing E. coli Nissle 1917 for detection and treatment of colorectal neoplasia," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    8. Ziye Wang & Ronghui You & Haitao Han & Wei Liu & Fengzhu Sun & Shanfeng Zhu, 2024. "Effective binning of metagenomic contigs using contrastive multi-view representation learning," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    9. Quinn T. Easter & Bruno Fernandes Matuck & Germán Beldorati Stark & Catherine L. Worth & Alexander V. Predeus & Brayon Fremin & Khoa Huynh & Vaishnavi Ranganathan & Zhi Ren & Diana Pereira & Brittany , 2024. "Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis," Nature Communications, Nature, vol. 15(1), pages 1-23, December.

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