Novel genetic and epigenetic alterations in ... - Ous-research.no

RØYRVIK ET AL.gene must be validated by functional suppressor studies in in vivo or in vitromodels. These criteria have been criticized as excessively narrow: 160 (1) Inactivationevents are not the only functionally important types of mutation, for example,AXIN2 and TCF4 are acknowledged target genes but the mutations to which theyare subject are not expected to be inactivating. (2) Biallelic inactivation need notbe a requirement in the case of haploinsufficiency (see below), c.f. the dearth ofbiallelic TAF1B inactivation. 44 To be truly useful, 3 and 4 would have to entailcomplete knowledge both of all possible growth suppressor pathways and ofevery gene or pathway involved mismatch repair proficient cancers, and 4 includesthe assumption that the molecular pathway to MSS and MSI tumors areessentially equivalent, which is not necessarily the case. Nor do all acknowledgedtarget genes participate in growth suppressor pathways, most notablyMSH3/6. 159 Regarding criterion 5, such studies are lacking for most target genes,and furthermore, it is unsuitable for several types of potential target genes. Thetransformed phenotype, for example, will not be reversed in the event of reintroductionof a wild-type mutator target gene to a system, 160 and a gene with noknown functional significance in tumor progression may yet be of prognosticclinical significance. Among the genes which have been subject to functionalstudies are AXIN2, BAX, E2F4, RIZ, TCF4, and TGFRII. 45,68,111,156,161,162Duval and Hamelin proposed a fourfold, functional classification of affectedgenes into survivor genes, hibernator genes, cooperator genes and transformatorgenes. 159Survivor genes encode vital products and whose inactivation should exert anegative selection pressure. Hibernator genes are nonvital and downregulated,and should have a mutation rate in the background range. Cooperator genes designatesets of genes with the same terminal effect, e.g., promotion of apoptosis,which have a synergistic effect without any one gene requiring a high mutationfrequency. Transformator genes are those which, upon mutation, independentlyconfer a selection advantage to the cells concerned, and therefore should have thehighest mutation frequency. These categories are thought to be mutated in a preferentialorder, with the transformator TGFRII being among the earliest. 49,16352The statistical regression model presented by Woerner et al. takes into considerationthe fact that longer repetitive tracts are more mutable (see below), i.e.the background rate for them is higher, and a gene with a mutation frequencyabove the 95% prediction interval for any given repeat length is considered a realtarget gene. TGFRII, BAX, TCF4, MSH3, ACVR2, PTHL3, HT001, andSLC23A1 are, by this method, considered genuine positive targets for MSI colorectalcancer, while the authors acknowledge the inapplicability of the model asregards target pathways, c.f. cooperator genes above.Due to the difficulties of implementing clear-cut qualitative criteria—functional aspects of single genetic products and their interactions are often insufficientlyelucidated, likewise signaling pathways and cascades—it has beenmost common to use the unmanipulated mutation frequency as the primary or240