Corals, Cancer, and Colonial Fusion
Gratuitous Coral Images
Watermelon Discoma - credit: Tidal Gardens
Tree of Life - Metazoans
Part 1: Is it worthwhile to look at cancer?
- Voolstra, et al. 2011 reported 3.7% of orthologs unique to scleractinians were involved in immunity.
- 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.
Credit: SA Coralfarm
Functional Clustering Among Corals and Predicted Human Orthologs
- 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
Credit: MDC Seamarc Maldives - Own work
Credit: NOAA's Florida Keys National Marine Sanctuary
- 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.