Scientific Reports (Nov 2022)

Parallel functional annotation of cancer-associated missense mutations in histone methyltransferases

  • Ashley J. Canning,
  • Susan Viggiano,
  • Martin E. Fernandez-Zapico,
  • Michael S. Cosgrove

DOI
https://doi.org/10.1038/s41598-022-23229-2
Journal volume & issue
Vol. 12, no. 1
pp. 1 – 13

Abstract

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Abstract Using exome sequencing for biomarker discovery and precision medicine requires connecting nucleotide-level variation with functional changes in encoded proteins. However, for functionally annotating the thousands of cancer-associated missense mutations, or variants of uncertain significance (VUS), purifying variant proteins for biochemical and functional analysis is cost-prohibitive and inefficient. We describe parallel functional annotation (PFA) of large numbers of VUS using small cultures and crude extracts in 96-well plates. Using members of a histone methyltransferase family, we demonstrate high-throughput structural and functional annotation of cancer-associated mutations. By combining functional annotation of paralogs, we discovered two phylogenetic and clustering parameters that improve the accuracy of sequence-based functional predictions to over 90%. Our results demonstrate the value of PFA for defining oncogenic/tumor suppressor functions of histone methyltransferases as well as enhancing the accuracy of sequence-based algorithms in predicting the effects of cancer-associated mutations.