Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution

Abstract

The presence and role of microbes in human cancers has come full circle in the last century. Tumors are no longer considered aseptic, but implications for cancer biology and oncology remain underappreciated. Opportunities to identify and build translational diagnostics, prognostics, and therapeutics that exploit cancer's second genome-the metagenome-are manifold, but require careful consideration of microbial experimental idiosyncrasies that are distinct from host-centric methods. Furthermore, the discoveries of intracellular and intra-metastatic cancer bacteria necessitate fundamental changes in describing clonal evolution and selection, reflecting bidirectional interactions with non-human residents. Reconsidering cancer clonality as a multispecies process similarly holds key implications for understanding metastasis and prognosing therapeutic resistance while providing rational guidance for the next generation of bacterial cancer therapies. Guided by these new findings and challenges, this Review describes opportunities to exploit cancer's metagenome in oncology and proposes an evolutionary framework as a first step towards modeling multispecies cancer clonality. Also see the video abstract here: https://youtu.be/-WDtIRJYZSs.

Keywords: cancer microbiome; clonal evolution; diagnostics; prognostics; therapeutic modulation.

FIGURE 1.

Illustration of opportunities to enhance clinical cancer diagnostics and prognostics using the cancer microbiome. Relevant references are listed in the title of each quadrant.

FIGURE 2.

Extracting and analyzing low-biomass microbiomes requires special care to control external and internal contamination.^[88,107,108] (A) Collection of environmental controls ideally begins in the operating room to account for non-patient environmental sources. (B) Post-operative tissues, if paraffin embedded, can have non-tissue paraffin controls taken to ensure the embedding process is not contaminated. Whole blood should ideally be collected with a skin swab to account for peri-needle contamination. (C) Negative reagent-only ‘blank’ controls and positive titrated controls should be processed simultaneously alongside nucleic acid extraction from biological and environmental samples. (D) Plating strategies should be considered to reduce cross-contamination; controls may include up to 40% of total samples. (E) Amplification steps may include PCR no-template controls and sequencing may include correction for cross-contamination or index swapping, although the latter remains challenging.

FIGURE 3.

Impacts of intratumoral microbes on cancer evolution and arguments for multispecies clonal evolution. Effects are summarized into three major categories: modulation of ecosystem effects, mechanisms of clonal diversity, and example disjoint and joint phylogenetic clonal evolution. Upper figure subpanels depict supported and hypothesized microbial counterparts to the host-specific clonal selection modes, mechanisms, and ecosystems originally described by McGranahan and Swanton.^[37]