Identification and analysis of mutational hotspots in oncogenes and tumour suppressors

Abstract

Background: The key to interpreting the contribution of a disease-associated mutation in the development and progression of cancer is an understanding of the consequences of that mutation both on the function of the affected protein and on the pathways in which that protein is involved. Protein domains encapsulate function and position-specific domain based analysis of mutations have been shown to help elucidate their phenotypes.

Results: In this paper we examine the domain biases in oncogenes and tumour suppressors, and find that their domain compositions substantially differ. Using data from over 30 different cancers from whole-exome sequencing cancer genomic projects we mapped over one million mutations to their respective Pfam domains to identify which domains are enriched in any of three different classes of mutation; missense, indels or truncations. Next, we identified the mutational hotspots within domain families by mapping small mutations to equivalent positions in multiple sequence alignments of protein domainsWe find that gain of function mutations from oncogenes and loss of function mutations from tumour suppressors are normally found in different domain families and when observed in the same domain families, hotspot mutations are located at different positions within the multiple sequence alignment of the domain.

Conclusions: By considering hotspots in tumour suppressors and oncogenes independently, we find that there are different specific positions within domain families that are particularly suited to accommodate either a loss or a gain of function mutation. The position is also dependent on the class of mutation.We find rare mutations co-located with well-known functional mutation hotspots, in members of homologous domain superfamilies, and we detect novel mutation hotspots in domain families previously unconnected with cancer. The results of this analysis can be accessed through the MOKCa database (http://strubiol.icr.ac.uk/extra/MOKCa).

Keywords: cancer; mutation; oncogene; tumour suppressor.

Figure 1. Distribution of molecular function for the 44 domains types found in both oncogenes and tumour suppressors

The outer ring shows each Pfam domain type. The inner ring groups the Pfam domains by function.

Figure 2. Domains enriched in mutations in oncogenes and tumour suppressors

The number of domains in the dataset is plotted against the estimated mutational enrichment for that domain. Only domains with significant mutational enrichment (see methods) are shown. Missense, truncation and indel mutational enrichments are calculated independently for tumour suppressors and oncogenes. Enrichments in tumour suppressors are coloured in blue, those found in oncogenes in red. (A) Missense mutations in tumour suppressors, (B) truncation mutations in tumour suppressors (C) indel mutations in tumour suppressors, (D) missense mutations in oncogenes, (E) truncation mutations in oncogenes, (F) indel mutations in oncogenes.

Figure 3. Domain hotspots

To calculate a domain hotspot all the members of the domain family were aligned using MUSCLE. The position of the mutation was mapped to the multiple sequence alignment, and the number of mutations at that position summed. For the position to be considered a hotspot, at least two mutations of the same class (missense, truncation or indel) had to be recorded at the same position.

Figure 4. WD40 domain

This illustrates the WD40 domain of FBXW7. Threonine 385 is located on the first propeller blade of the WD40, (shown in blue) forming a hydrogen bond with arginine 674 in the final propeller blade (shown in red) via a water molecule (shown as a green ball) helping to stabilise the propeller structure. Replacing the side chain with arginine would mean this hydrogen bond could not be formed destabilisation of the internal water structure of the WD40 and hence the overall fold.

Figure 5. Positional analysis of domain hotspots

Analysis of the overlap in the positions of the significant hotspots in oncogenes and tumour suppressors compared with those found within the whole genome. (A–C) These venn diagrams illustrate that significant hotspots can occur in the same domain family in oncogenes (pink), tumour suppressors (blue) and in the whole genome (purple). Each circle represents the number of domains that contains a hotspot mutation, intersections illustrate when the same domain is found in more than one data set. (A) missense mutations (B) truncation mutations and (C) indels mutations. (D–F) These venn diagrams illustrate that significant hotspots that occur in the same position in domain families in oncogenes, tumour suppressors and within the whole genome; (D) missense mutations, (E) truncations (F) indels mutations.