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
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
- Page 12 and 13: Introduction“Epigenetic inheritan
- Page 14 and 15: Introductionamino acid change it is
- Page 16 and 17: Introductionmethylation during embr
- Page 18 and 19: IntroductionDNA is most of the time
- Page 20 and 21: IntroductionFigure 5. DNA methylati
- Page 22 and 23: IntroductionFigure 6. Incidence rat
- Page 24 and 25: IntroductionFigure 8. Tumor staging
- Page 26 and 27: Introductioninasmuch as 80% of colo
- Page 28 and 29: IntroductionInstabilities involved
- Page 30 and 31: Introductionthere seems to be a fid
- Page 32 and 33: Introductionsevere alterations are
- Page 34 and 35: Introductionpopulation-wide screeni
- Page 36 and 37: IntroductionFigure 12. Present and
- Page 38 and 39: RESULTS IN BRIEFPaper Ia. “DNA hy
- Page 40 and 41: Results in Briefinstability, and se
- Page 42 and 43: Results in BriefUnivariate survival
- Page 44 and 45: Discussionseveral factors, and full
- Page 46 and 47: Discussionlow threshold, we increas
- Page 48 and 49: DiscussionIt may seem like unnecess
- Page 50 and 51: Discussionthan 96% DHPLC do not sta
- Page 52 and 53: DiscussionFigure 13. Mutation detec
- Page 54 and 55: DiscussionClinical impact of molecu
- Page 56 and 57: Discussionmarkers with a very high
- Page 58 and 59: Discussionchromosomes in metaphase[
- Page 60 and 61: DiscussionThese examples underline
- Page 64 and 65: CONCLUSIONSWe have identified novel
- Page 66 and 67: Future PerspectivesMolecular risk a
- Page 68 and 69: REFERENCES1. Breasted J (1930) The
- Page 70 and 71: References29. Deng G, Chen A, Pong
- Page 72 and 73: References57. Al-Sukhni W, Aronson
- Page 74 and 75: References84. Kunkel TA (1993) Nucl
- Page 76 and 77: ReferencesLeggett B, Levine J, Kim
- Page 78 and 79: References133. Lind GE, Thorstensen
- Page 80 and 81: References156. Meling GI, Lothe RA,
- Page 82 and 83: ReferencesT, Song X, Day RH, Sledzi
- Page 84 and 85: References196. Honda S, Haruta M, S
- Page 86 and 87: ORIGINAL ARTICLESAPPENDIXAppendix I
- Page 89 and 90: GASTROENTEROLOGY 2007;132:1631-1639
- Page 91: Paper IbGuro E Lind, Terje Ahlquist
- Page 94 and 95: Journal of Translational Medicine 2
- Page 96 and 97: Journal of Translational Medicine 2
- Page 98 and 99: Journal of Translational Medicine 2
- Page 100 and 101: Journal of Translational Medicine 2
- Page 102 and 103: Journal of Translational Medicine 2
- Page 105: Paper IITerje Ahlquist, Guro E Lind
- Page 108 and 109: BackgroundMost cases of colorectal
- Page 110 and 111: ADAMTS1 CDKN2A CRABP1 HOXA9 MAL MGM
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