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

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Discussiongenes. One is based on mutation frequency and suggests that genes with mutationfrequencies below 12% are considered likely to have no functional consequence on tumordevelopment, and therefore entitled by-stander genes[204]. The second scheme is to dividegenes into four categories: survivor genes, hibernator genes, cooperator genes andtransformator genes[205]. Transformator genes confer a positive selection to the cells, havethe highest mutation frequencies, and are most likely to be genes driving tumorigenesis[205].Prior to Paper IV a literature survey was performed[90] and only genes passing certaincriteria, amongst others a mutation frequency exceeding the aforementioned 12% wereincluded. As we aimed to identify prognostic markers we wanted ensure that we did notanalyze mere background artifacts.In the field of epigenetics, genome-wide studies have been performed suggesting that 100-600 genes are subject to promoter hypermethylation in a random tumor[206-208]. Mostlikely, methylation instability, such as CIMP, causes a large number of genes to behypermethylated, and similar to the MSI-tumors, only some of the affected genes exerttumorigenic effects.Whether passenger mutations are just relics of some sort of genome instability andcompletely irrelevant for tumorigenesis or if they apply some minor effect on tumor growthis still questioned. A recent paper argues that for any trait, there will be only a few genes withlarge phenotypic effects, but many associated genes having small effects, although theircombined effect may be substantial[209]. This may be important to keep in mind whendescribing a phenotype, but whether or not the passenger mutations have phenotypic effectsis irrelevant in the case of identifying diagnostic and maybe also prognostic markers, asillustrated by VIM and MAL. Indeed, subsequent to our identification of MAL as apotential biomarker, it has been shown that hypermethylation of MAL is significantlyassociated with improved disease-free survival in gastric cancer[210]. Hence, MAL can berelevant both for diagnosing colorectal cancer and determining prognosis in gastric cancereven though its impact on tumorigenesis is unresolved.62

DiscussionDifferent origins of colorectal cancer contribute to a non-uniform diseaseAs mentioned earlier there is increasing evidence that CRC is not a uniform disease, and thatthere are at least two distinct routes causing it, the traditional adenoma-carcinoma pathwayand the newer pathway through HPs and sessile serrated adenomas (page 25-26). There areseveral indications also in the present studies supporting the theory that MSI tumorsoriginate from sessile serrated adenomas and not traditional adenomas. If adenomas gaverise to both MSS and MSI tumors one would expect close to a similar frequency of MSIadenomasas MSI-carcinomas (~12-15%). In paper II, 63 adenomas were included in whichonly 2 were MSI (3%). In addition, the majority of sporadic MSI tumors are caused byMLH1 hypermethylation. None of the adenomas in our study, not even the two with MSIcontained hypermethylation of this gene. Also, the 5 genes almost exclusively methylated inMSI-tumors (CRABP1, MLH1, NR3C1, RUNX3 and SCGB3A1) displayed very low, orabsent, methylation frequencies in adenomas, supporting the fact that MSI tumors areunlikely to originate from adenomas. In parallel, we have analyzed the same genes as in paperII for promoter hypermethylation in 12 hyperplastic polyps (HPs) as well as determinedmutation status of BRAF (data not included). The HPs were significantly more frequentlymethylated than the adenomas, and when comparing HPs and MSI tumors, similarmethylation frequencies were observed across all genes. Also, 50% of the HPs carried aV600E mutation in BRAF. Only one of the HPs displayed MSI, consistent with the sessileserrated pathway theory in which mutation in BRAF is the initiating event while MSI is a lateevent[71]. Together these data show that the HPs already carry alterations typical for MSItumors,while the adenomas do not, hence supporting the aforementioned theory.63

DiscussionDifferent orig<strong>in</strong>s of colorectal cancer contribute to a <strong>no</strong>n-uniform diseaseAs mentioned earlier there is <strong>in</strong>creas<strong>in</strong>g evidence that CRC is <strong>no</strong>t a uniform disease, <strong>and</strong> thatthere are at least two dist<strong>in</strong>ct routes caus<strong>in</strong>g it, the traditional ade<strong>no</strong>ma-carc<strong>in</strong>oma pathway<strong>and</strong> the newer pathway through HPs <strong>and</strong> sessile serrated ade<strong>no</strong>mas (page 25-26). There areseveral <strong>in</strong>dications also <strong>in</strong> the present studies support<strong>in</strong>g the theory that MSI tumorsorig<strong>in</strong>ate from sessile serrated ade<strong>no</strong>mas <strong>and</strong> <strong>no</strong>t traditional ade<strong>no</strong>mas. If ade<strong>no</strong>mas gaverise to both MSS <strong>and</strong> MSI tumors one would expect close to a similar frequency of MSIade<strong>no</strong>masas MSI-carc<strong>in</strong>omas (~12-15%). In paper II, 63 ade<strong>no</strong>mas were <strong>in</strong>cluded <strong>in</strong> whichonly 2 were MSI (3%). In addition, the majority of sporadic MSI tumors are caused byMLH1 hypermethylation. None of the ade<strong>no</strong>mas <strong>in</strong> our study, <strong>no</strong>t even the two with MSIconta<strong>in</strong>ed hypermethylation of this gene. Also, the 5 genes almost exclusively methylated <strong>in</strong>MSI-tumors (CRABP1, MLH1, NR3C1, RUNX3 <strong>and</strong> SCGB3A1) displayed very low, orabsent, methylation frequencies <strong>in</strong> ade<strong>no</strong>mas, support<strong>in</strong>g the fact that MSI tumors areunlikely to orig<strong>in</strong>ate from ade<strong>no</strong>mas. In parallel, we have analyzed the same genes as <strong>in</strong> paperII for promoter hypermethylation <strong>in</strong> 12 hyperplastic polyps (HPs) as well as determ<strong>in</strong>edmutation status of BRAF (data <strong>no</strong>t <strong>in</strong>cluded). The HPs were significantly more frequentlymethylated than the ade<strong>no</strong>mas, <strong>and</strong> when compar<strong>in</strong>g HPs <strong>and</strong> MSI tumors, similarmethylation frequencies were observed across all genes. Also, 50% of the HPs carried aV600E mutation <strong>in</strong> BRAF. Only one of the HPs displayed MSI, consistent with the sessileserrated pathway theory <strong>in</strong> which mutation <strong>in</strong> BRAF is the <strong>in</strong>itiat<strong>in</strong>g event while MSI is a lateevent[71]. Together these data show that the HPs already carry <strong>alterations</strong> typical for MSItumors,while the ade<strong>no</strong>mas do <strong>no</strong>t, hence support<strong>in</strong>g the aforementioned theory.63

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