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

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

ous.research.no
from ous.research.no More from this publisher
11.07.2015 Views

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

TARGET GENES OF MSI COLORECTAL CANCEReven sole criterion for target gene detection, and to treat any involvement of afrequently mutated gene in, e.g., apoptosis or cell cycle control as a bonus. Anotherpotentially complicating factor is that, however detrimental frameshiftsusually are, mutations in the repetitive tracts of target genes do not invariablycause complete inactivation. This appears to be the case for AXIN2, where themutated product is more stable than wild type and may have a dominant negativeeffect, 68 and also for the mutated isoform of TCF4. 162 Both mutated gene productsencourage inappropriate WNT signaling activation, which is cancerpromoting.164The very fact that so many different mutational constellations exist suggeststhat the are few, if any, truly key genes for carcinogenesis among the target genes,TGFRII being the only one to have been accorded such status. 44,55,159 Rather, thecumulative effect of many different and interchangeable mutations may drivetumorigenesis, with very few of the total being decisive in themselves. 159 Nor isit likely that all the relevant microsatellite-containing genes have as yet beentested for mutations in MSI tumors, or even necessarily characterized in anyDNA sequence database. Several studies have used genome-wide sequence databasesearches for genes containing cMNRs as a basis for potential target gene selection.44,53,55,105,119 Such a search * currently yields well over 1000 protein-codinggenes containing the most promising (N)8 repeats, the figure rising more thantenfold when the range is expanded to include (N)6-7. Even allowing for unpublishednegative data, it may be seen from the number of genes in Table I thatfundamental target genes may still lurk in the unplumbed depths of the humangenome.VII. PERSPECTIVESIn addition to the mutational frequency and association studies of small numbersof target genes, future work will hopefully determine the prognostic values ofdistinct combinations of target genes—the prognostic value of any target genemutations is at present unclear. None of the studies examining the matter consistentlycorroborate each other, despite being almost solely concerned with BAXand TGFRII mutations and their inferred effect on patient survival ranges froma poor prognosis through prognostically irrelevant to improved survival.108,154,161,166,167* Scanning for monorepeats in human genes. The 41,030 coding sequences in the transcripts of 20,484 humanprotein-coding genes were downloaded using the BioMart service at www.biomart.org 165 on March 13, 2007. APerl script was written to scan the sequences for repeats. For each gene, only the longest coding sequence wasconsidered. The script identified all mononucleotide repeats of length six and over, and also produced summaryinformation about the repeats in each gene (longest repeat, number of repeats, sum of length of repeats).241

RØYRVIK ET AL.gene must be validated by functional suppressor studies <strong>in</strong> <strong>in</strong> vivo or <strong>in</strong> vitromodels. These criteria have been criticized as excessively narrow: 160 (1) Inactivationevents are <strong>no</strong>t the only functionally important types of mutation, for example,AXIN2 <strong>and</strong> TCF4 are ack<strong>no</strong>wledged target genes but the mutations to which theyare subject are <strong>no</strong>t expected to be <strong>in</strong>activat<strong>in</strong>g. (2) Biallelic <strong>in</strong>activation need <strong>no</strong>tbe a requirement <strong>in</strong> the case of haplo<strong>in</strong>sufficiency (see below), c.f. the dearth ofbiallelic TAF1B <strong>in</strong>activation. 44 To be truly useful, 3 <strong>and</strong> 4 would have to entailcomplete k<strong>no</strong>wledge both of all possible growth suppressor pathways <strong>and</strong> ofevery gene or pathway <strong>in</strong>volved mismatch repair proficient cancers, <strong>and</strong> 4 <strong>in</strong>cludesthe assumption that the molecular pathway to MSS <strong>and</strong> MSI tumors areessentially equivalent, which is <strong>no</strong>t necessarily the case. Nor do all ack<strong>no</strong>wledgedtarget genes participate <strong>in</strong> growth suppressor pathways, most <strong>no</strong>tablyMSH3/6. 159 Regard<strong>in</strong>g criterion 5, such studies are lack<strong>in</strong>g for most target genes,<strong>and</strong> furthermore, it is unsuitable for several types of potential target genes. Thetransformed phe<strong>no</strong>type, for example, will <strong>no</strong>t be reversed <strong>in</strong> the event of re<strong>in</strong>troductio<strong>no</strong>f a wild-type mutator target gene to a system, 160 <strong>and</strong> a gene with <strong>no</strong>k<strong>no</strong>wn functional significance <strong>in</strong> tumor progression may yet be of prog<strong>no</strong>sticcl<strong>in</strong>ical significance. Among the genes which have been subject to functionalstudies are AXIN2, BAX, E2F4, RIZ, TCF4, <strong>and</strong> TGFRII. 45,68,111,156,161,162Duval <strong>and</strong> Hamel<strong>in</strong> proposed a fourfold, functional classification of affectedgenes <strong>in</strong>to survivor genes, hibernator genes, cooperator genes <strong>and</strong> transformatorgenes. 159Survivor genes encode vital products <strong>and</strong> whose <strong>in</strong>activation should exert anegative selection pressure. Hibernator genes are <strong>no</strong>nvital <strong>and</strong> downregulated,<strong>and</strong> should have a mutation rate <strong>in</strong> the background range. Cooperator genes designatesets of genes with the same term<strong>in</strong>al effect, e.g., promotion of apoptosis,which have a synergistic effect without any one gene requir<strong>in</strong>g a high mutationfrequency. Transformator genes are those which, upon mutation, <strong>in</strong>dependentlyconfer a selection advantage to the cells concerned, <strong>and</strong> therefore should have thehighest mutation frequency. These categories are thought to be mutated <strong>in</strong> a preferentialorder, with the transformator TGFRII be<strong>in</strong>g among the earliest. 49,16352The statistical regression model presented by Woerner et al. takes <strong>in</strong>to considerationthe fact that longer repetitive tracts are more mutable (see below), i.e.the background rate for them is higher, <strong>and</strong> a gene with a mutation frequencyabove the 95% prediction <strong>in</strong>terval for any given repeat length is considered a realtarget gene. TGFRII, BAX, TCF4, MSH3, ACVR2, PTHL3, HT001, <strong>and</strong>SLC23A1 are, by this method, considered genu<strong>in</strong>e positive targets for MSI colorectalcancer, while the authors ack<strong>no</strong>wledge the <strong>in</strong>applicability of the model asregards target pathways, c.f. cooperator genes above.Due to the difficulties of implement<strong>in</strong>g clear-cut qualitative criteria—functional aspects of s<strong>in</strong>gle <strong>genetic</strong> products <strong>and</strong> their <strong>in</strong>teractions are often <strong>in</strong>sufficientlyelucidated, likewise signal<strong>in</strong>g pathways <strong>and</strong> cascades—it has beenmost common to use the unmanipulated mutation frequency as the primary or240

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!