How cancer outsmarts multicellularity

David Goode & Anna Trigos

Peter MacCallum Cancer Centre, Melbourne, Australia

Title image

 

The transition from unicellularity to multicellularity was one of the most significant advances in the evolution of life on Earth. Enhanced cooperation and communication between cells enabled the development of increasingly complex and specialized tissues; the resulting differentiation and division of labour enabled the acquisition of a broad array of new features. In turn, this allowed adaptation to a wide range of new ecological niches, rapidly accelerating the pace of evolution and creating an explosion of diversity across the plant, animal and fungal kingdoms.

This array of new multicellular phenotypes was driven by major innovations on the molecular level. Coordinating the growth of millions or billions of cells required the evolution of new proteins and regulatory elements to impose control over core cellular processes such as translation, DNA replication and the cell cycle. The activity of these primitive processes could then be temporally and spatially ordered, rather than stochastically responding as individual cells to external environmental cues.

In this sense, multicellularity can be viewed as a result of a molecular evolutionary process of selection for cooperative rather than competitive growth, via a default switching off of proliferative pathways in the majority of cells. However, it was also necessary to maintain the means to activate such pathways under certain conditions, e.g., embryogenesis, wound healing, or immune response. This requirement meant newly-evolved metazoan regulatory mechanisms had to be bidirectional. Such flexibility was advantageous, but also provided a ‘back-door’ that allows cells to inappropriately reactivate primitive processes and thus to enable proliferation independently of normal control structures.

Unchecked, this leads to a scenario where selection for the survival of individual cells is favoured over survival of the entire organism, namely cancer. A more formal framework for this reversion is the Atavism hypothesis of cancer1,2, which proposes that cancer cells lose their identity as cells of a multicellular tissue, and start to behave more like unicellular organisms. This is achieved under strong selection for reactivation of gene expression programmes that date back to unicellular ancestors, manifested as a loss of communication with neighbouring cells, and loss of differentiation and tissue structure.

The atavism hypothesis of cancer was largely founded on the broad phenotypic similarities between cancer cells and unicellular species such as bacteria and yeast. More recently, the molecular changes driving these phenomena have begun to come to light. Among them are the finding that many of the genes commonly involved in cancer date back to the emergence of the first metazoans3 and increasingly malignant tumour phenotypes are accompanied by progressive mutation of such genes4.

Recently, we completed a comprehensive analysis of potential atavistic signatures in the transcriptomes of 7 solid tumour types using data from The Cancer Genome Atlas5. We observed a strong and consistent increase in the expression of genes of unicellular organisms across all tumour types, with a concomitant decrease in expression of more recently acquired genes5; an observation that is consistent with increased importance in cancer of the most highly conserved genes in the genome. These results imply a compartmentalisation of gene expression by evolutionary age in tumour cells, with a significant separation of the activity of genes of unicellular and multicellular ancestry. This effect is quite clear for genes involved in ancient processes throughout the tree of life, such as protein translation and cell cycle progression, as expected. But even the  expression of genes of unicellular origin that have been co-opted into processes associated with multicellularity, such as cell-cell adhesion and organogenesis, was maintained or even increased in tumours.

Together these observations suggest an increased reliance on the more primitive parts of the transcriptome during tumourigenesis. How might this occur? We overlaid interaction data onto TCGA expression data, revealing several pairs of highly connected unicellular and multicellular processes whose expression went from highly positively correlated in normal cells to highly negatively correlated in tumours. This indicated a loss of the regulatory mechanisms coordinating the expression of certain processes in tumours, leading to mutual exclusivity between those processes, presumably to the advantage of cancer. The genes apparently mediating these switches were both unicellular and multicellular, but overall enriched for genes essential for cancer cell growth, based on functional genomics screen data from Project Achilles6.

We interpret this mutual exclusivity as a consequence of how metazoan gene regulatory networks were laid out during evolution, and how they get disrupted and rewired in cancer. The core of the network was formed during the emergence of the earliest unicellular organisms. The high degree of correlation in expression among genes involved in unicellular processes indicates these components are highly connected, and robust to perturbation. The evolution of multicellularity built an outer layer around the conserved ancient core, with key genes linking the two and providing regulatory control. When these links are broken, there is uncoupling of the unicellular and multicellular halves of the network, leading to a more proliferative, more ‘primitive’ phenotype, and malignant growth. However, cancer cells are not simply hijacking the wiring generally used by these other normal cell types when losing their cell complexity, as the specific processes contributing to the atavistic state are markedly different.

The development of therapeutic strategies derived from an evolutionary perspective opens the possibility of a streamlined approach to the discovery of novel gene targets and novel drug repurposing strategies7. However, to achieve this we need to further refine our understanding of the mechanisms driving the uncoupling of unicellularity and multicellularity in the development and progression of cancer, such as how genetic and epigenetic alterations modulate a loss of multicellularity. Furthermore, by expanding our understanding of the association between robustness to perturbation and evolutionary history we would be better poised to predict genes or pathways of resistance, and develop treatment strategies that a priori incorporate this knowledge.

Given their essentiality for cell viability, the fundamental cellular processes common to both unicellular and multicellular life are characterised by plasticity in gene interactions and the presence of redundant pathways. Thus ensuring that, even under severe insults (e.g. stress or drug treatment), cell viability remains. This enhanced plasticity and robustness in the core of the network evolved early on, explaining why many drug resistance mechanisms involve unicellular genes and processes. On the other hand, the more recent genes related to multicellular-specific processes may only be required in certain situations, and therefore, there is less selective pressure to maintain their integrity. From a therapeutic perspective, identifying and targeting gene network regions that play key roles in tumour development but generally have lower resilience to insults would be more likely to delay the onset of drug resistance.

The genes at the interface between unicellular and multicellular regulatory networks represent promising therapeutic targets, as they could signal sites of vulnerabilities that, when targeted, would cause widespread disruption in molecular networks and hence lead to cell death7. Specificity to cancer cells could be obtained by focusing on genes mediating mutually exclusive associations between unicellular and multicellular processes unique to cancer, such as those we recently identified5. There may also be potential to repurpose existing drugs to exploit the mutual exclusivity between unicellular and multicellular processes. By this means, drugs promoting the activation of multicellular processes would reduce the activity of unicellular processes, with the aim of a reduction in malignancy due to reactivation of multicellular features. A more pragmatic approach in the near term may be to attack weaknesses in cancer brought about by the loss of particular multicellular genes. This has been proven effective in tumour cell lines deficient in cysteine/glutamate antitransporter activity, as a means to manipulate intracellular oxidative stress and affect cell survival8.

Hundreds of millions of years of evolution have guided the formation of robust and flexible genetic and protein interaction networks in modern metazoan cells to maintain the diverse sets of functionalities required for multicellular life. Selection for maintenance of multicellular control structures is favoured over the long term, but in the short term, the drive of individual cells to multiply and spread can win out, with disastrous consequences for some unfortunate individuals. Understanding the forces that have shaped the molecular basis of multicellularity and the countervailing forces that can undo them will offer crucial insights into the fundamental nature of cancer and the potential for smarter, more efficient treatment options for patients.

 

References

  1. Davies PC, Lineweaver CH: Cancer tumors as Metazoa 1.0: tapping genes of ancient ancestors. Phys Biol 2011, 8:015001.
  2. Vincent M: Cancer: a de-repression of a default survival program common to all cells?: a life-history perspective on the nature of cancer. Bioessays 2012, 34:72-82.
  3. Domazet-Loso T, Tautz D: Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa. BMC Biol 2010, 8:66.
  4. Chen H, Lin F, Xing K, He X: The reverse evolution from multicellularity to unicellularity during carcinogenesis. Nat Commun 2015, 6:6367.
  5. Trigos AS, Pearson RB, Papenfuss AT, Goode DL: Altered interactions between unicellular and multicellular genes drive hallmarks of transformation in a diverse range of solid tumors. Proc Natl Acad Sci U S A 2017, 114:6406-6411.
  6. Aguirre AJ, Meyers RM, Weir BA, Vazquez F, Zhang CZ, Ben-David U, Cook A, Ha G, Harrington WF, Doshi MB, et al: Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting. Cancer Discov 2016, 6:914-929.
  7. Trigos AS, Pearson RB, Papenfuss AT, Goode DL: How the evolution of multicellularity set the stage for cancer. Br J Cancer 2018 [Article in Press].
  8. Liu DS, Duong CP, Haupt S, Montgomery KG, House CM, Azar WJ, Pearson HB, Fisher OM, Read M, Guerra GR, et al: Inhibiting the system xC_/glutathione axis targets cancers with mutant-p53 accumulation. Nat Commun 2017, 8:14844.

 Featured image: http://firstwestcapital.ca/wp-content/uploads/iStock-153724177.jpg

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