Corals, Cancer, and Colonial Fusion

Gratuitous Coral Images

source: reefbuilders

Watermelon Discoma - credit: Tidal Gardens

Tree of Life - Metazoans

Part 1: Is it worthwhile to look at cancer?

  1. Voolstra, et al. 2011 reported 3.7% of orthologs unique to scleractinians were involved in immunity.
  2. Scweinsburg et al., identified that genotypic mosaicism (arises from somatic mutation) and chimerism (arises from genome fusion event as an embryo) was a common occurrence among 5 different species of coral-- 69 cases of 222 tested colonies, primarily mosaicism.
  • Moreover, this observation found to be associated with tissue loss and was more commonly found in certain environments.
  • Cancer most commonly arises from somatic mutation and finds various ways to avoid immune detection.

Colonial Chimerism

Credit: SA Coralfarm

Functional Clustering Among Corals and Predicted Human Orthologs

Method:

  • Obtained whole transcriptomes of the 5 Acropora species. (Bhattacharya, et al. 2016)
  • Run all species with the OrthoVenn webservice tool against the human proteome.

Protein clustering among Homo sapien

and five species within the Acropora genus

Transcriptome Stats and Clustering results

GOEnrichment findings: Most related to metabolism

Part 2: Looking

Using BLASTx to identify human orthologs in rapidly evolving Acropora orthologs

Acropora millepora

Credit: MDC Seamarc Maldives - Own work

Acropora palmata

Credit: NOAA's Florida Keys National Marine Sanctuary

Methods:

  • Obtain transcripts of A. millepora and A. palmata orthologs (2606 entries) with corresponding dN/dS values from "Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment" (Voolstra, et al. 2011)
  • Perform BLASTx search with these orthologs against the reviewed entries in Uniprot human proteome (20402), with all available isoforms.
  • Take match from each query, identify the coral orthologs from the study that show rapid evolution (nonsynonymous rate/synonymous rate > 1)
  • Parse the CanProVar database containing human genes with known somatic mutations in human cancer, compare with BLAST top hits.

This is as far as I got, but next steps:

  • For coral orthologs that show rapid evolution (nonsynonymous rate/synonymous rate > 1), inspect human orthologs in whole-transcript samples of cancer patients vs non-cancer patients.
  • Perform similar analyses using human cancer transcript variants against all 20 coral species with publicly available transcriptomes to find if any somatic mutations are evolutionarily set in related coral species.
  • Hopefully we find whether rapidly evolving proteins in corals have orthologs that contribute to cancer in humans, whether it be related to immune function or environmental response.