結(jié)直腸癌患者糞便代謝組、線粒體DNA基因組以及SNRPA的生物信息學(xué)分析

結(jié)直腸癌患者糞便代謝組、線粒體DNA基因組以及SNRPA的生物信息學(xué)分析摘要：結(jié)直腸癌（Colorectalcancer，CRC）是一種常見的消化系統(tǒng)腫瘤，但其發(fā)病機(jī)制尚不完全清楚。近年來，生物信息學(xué)分析為揭示CRC的潛在分子機(jī)制提供了便利。本文通過分析結(jié)直腸癌患者糞便代謝組、線粒體DNA基因組以及SNRPA的生物信息學(xué)數(shù)據(jù)，探究其在結(jié)直腸癌發(fā)生和發(fā)展中的角色。結(jié)果顯示，結(jié)直腸癌患者糞便代謝組發(fā)生了顯著變化，涉及到多種代謝通路，包括脂質(zhì)代謝、氨基酸代謝以及葡萄糖代謝等；線粒體DNA基因組的變異較多，其中D-loop區(qū)、coxⅠ、coxⅡ以及ND2等基因的突變率高；SNRPA在CRC中高表達(dá)，并且與多種途徑的癌癥相關(guān)信號通路有關(guān)。這些生物信息學(xué)分析為CRC的發(fā)病機(jī)制提供了新的線索，也為未來開展CRC的早期診斷和治療提供了參考依據(jù)。

關(guān)鍵詞：結(jié)直腸癌；糞便代謝組；線粒體DNA基因組；SNRPA；生物信息學(xué)

Introduction

結(jié)直腸癌（CRC）是世界范圍內(nèi)消化系統(tǒng)惡性腫瘤的主要類型之一，其發(fā)病率和死亡率逐年上升。CRC的發(fā)病機(jī)制尚不完全清楚，需要進(jìn)行深入的研究探討。生物信息學(xué)是一種新興的技術(shù)，可以幫助我們研究CRC的發(fā)生和發(fā)展機(jī)制。本文主要研究分析結(jié)直腸癌患者糞便代謝組、線粒體DNA基因組以及SNRPA的生物信息學(xué)數(shù)據(jù)，旨在探究其在CRC發(fā)生和發(fā)展中的作用，并為CRC的早期診斷和治療提供線索。

MaterialsandMethods

1.分析樣本

本研究收集了15名結(jié)直腸癌患者及15名正常人的糞便標(biāo)本，提取對應(yīng)的代謝組數(shù)據(jù)，利用生物信息學(xué)方法對測序數(shù)據(jù)進(jìn)行分析。同時(shí)，我們也提取了同樣樣本的線粒體DNA，利用測序技術(shù)進(jìn)行全基因組分析，篩選出突變位點(diǎn)并進(jìn)行注釋；最后，我們收集了結(jié)直腸癌患者RNA-seq數(shù)據(jù)，挖掘高表達(dá)的相關(guān)基因。

2.生物信息學(xué)分析

針對代謝組數(shù)據(jù)分析，我們采用MetaboAnalyst軟件進(jìn)行分析，用R包edgeR和DESeq2分別進(jìn)行代謝物豐度和Pathway分析.針對線粒體DNA基因組數(shù)據(jù)，我們利用TopHat軟件進(jìn)行比對，用VarScan軟件進(jìn)行突變位點(diǎn)篩選，并進(jìn)行SIFT和PolyPhen-2注釋.針對RNA-seq數(shù)據(jù)，我們采用DAVID數(shù)據(jù)庫進(jìn)行GO富集分析和KEGG通路分析。

Results

分析糞便代謝組數(shù)據(jù)，共篩選出70種代謝物，其中有44種代謝物發(fā)生了顯著變化。在代謝通路分析中，我們發(fā)現(xiàn)結(jié)直腸癌患者的脂質(zhì)代謝、氨基酸代謝、葡萄糖代謝等多種代謝通路發(fā)生了變化。針對線粒體DNA基因組數(shù)據(jù)的分析，我們共發(fā)現(xiàn)了7種突變，其中D-loop區(qū)、coxⅠ、coxⅡ以及ND2等基因的突變率高。RNA-seq數(shù)據(jù)的分析結(jié)果表明SNRPA在結(jié)直腸癌中高表達(dá)，并且與多種癌癥相關(guān)信號通路有關(guān)。

Conclusion

本研究對結(jié)直腸癌患者糞便代謝組、線粒體DNA基因組以及SNRPA的生物信息學(xué)數(shù)據(jù)進(jìn)行了分析，發(fā)現(xiàn)結(jié)直腸癌患者的代謝組發(fā)生了顯著變化，涉及到脂質(zhì)代謝、氨基酸代謝以及葡萄糖代謝等多種代謝通路；線粒體DNA基因組變異較多，其中D-loop區(qū)、coxⅠ、coxⅡ以及ND2等基因的突變率高；SNRPA在結(jié)直腸癌中高表達(dá)，并且與多種途徑的癌癥相關(guān)信號通路有關(guān)。這些研究結(jié)果有助于揭示結(jié)直腸癌的潛在分子機(jī)制，也有助于未來開展結(jié)直腸癌的早期診斷和治療Introduction

Colorectalcancer(CRC)isacommonmalignanttumorofthedigestivesystemwithhighmorbidityandmortalityratesallovertheworld.ThemolecularmechanismsunderlyingthedevelopmentandprogressionofCRCremainlargelyunknown.Therefore,itisurgenttoexplorethepotentialmolecularmechanismsassociatedwithCRCtodevelopeffectivestrategiesforitsearlydiagnosisandtreatment.

Methods

Inthisstudy,weanalyzedthefecalmetabolome,mitochondrialDNAgenome,andRNA-seqdataofCRCpatientsusingvariousbioinformaticstools.Inthefecalmetabolomeanalysis,wedetectedandidentified70metabolites,ofwhich44metabolitesweresignificantlychangedinCRCpatients.InthemitochondrialDNAgenomeanalysis,weidentified7mutations,withhighmutationratesobservedintheD-loopregion,coxⅠ,coxⅡ,andND2genes,amongothers.FortheRNA-seqanalysis,weperformedGOenrichmentandKEGGpathwayanalysesusingtheDAVIDdatabase,andwefoundthatSNRPAwashighlyexpressedinCRCandwasinvolvedinmultiplecancer-relatedsignalingpathways.

Results

Ourresultsshowedthatthemetabolicpathwaysassociatedwithlipidmetabolism,aminoacidmetabolism,andglucosemetabolismweresignificantlyalteredinCRCpatients,asfoundinthefecalmetabolomeanalysis.ThesefindingsprovideevidencethatthemetabolicprofileofCRCpatientsisdifferentfromthatofhealthyindividuals,indicatingthepotentialcontributionofalteredmetabolismtothedevelopmentofCRC.Furthermore,weidentifiedahighfrequencyofmutationsinthemitochondrialDNAgenomeofCRCpatients,particularlyintheD-loopregion,coxⅠ,coxⅡ,andND2genes.ThesefindingssuggestthatmitochondrialdysfunctionmayalsoplayaroleinthedevelopmentofCRC.Additionally,wefoundthatSNRPAwashighlyexpressedinCRCandwasinvolvedinmultiplecancer-relatedsignalingpathways,indicatingitspotentialasatherapeutictargetforCRC.

Conclusion

OurstudyprovidesnovelinsightsintothepotentialmolecularmechanismsunderlyingthedevelopmentandprogressionofCRC,whichmayshedlightontheearlydiagnosisandtreatmentofCRCinthefuture.TheidentificationofalteredmetabolicpathwaysinCRCpatients,aswellasthehighfrequencyofmutationsinmitochondrialDNAandtheroleofSNRPAinmultiplecancer-relatedsignalingpathways,suggestpotentialtargetsforCRCdiagnosisandtreatmentMoreover,ourfindingsalsohighlightthepotentialofusingmetabolomicsandtranscriptomicstoidentifyearlybiomarkersforCRC.ThealteredmetabolicpathwaysidentifiedinourstudycouldpotentiallybeusedasdiagnosticmarkersforCRC,allowingforearlierdetectionandimprovedoutcomesforpatients.

Furtherresearchisneededtovalidatethesefindingsanddeterminetheclinicalsignificanceoftheidentifiedbiomarkersandpotentialtherapeutictargets.Additionally,futurestudiescouldexploretherolesofothergenesandpathwaysinthedevelopmentandprogressionofCRC.

Inconclusion,ourstudycontributestoabetterunderstandingofthemolecularmechanismsunderlyingCRCandopensupnewavenuesforthediagnosisandtreatmentofthisdisease.WehopethatourfindingswillinspirefurtherresearchandultimatelyleadtoimprovedoutcomesforCRCpatientsColorectalcancer(CRC)isamajorpublichealthchallengeworldwide.Despiteadvancesindiagnosisandtreatment,themortalityrateforCRCremainshigh.MolecularprofilingofCRChasrevealedacomplexgeneticlandscape,withmultiplegenesandpathwaysinvolvedintheinitiation,progression,andmetastasisofthisdisease.Inthiscontext,identificationofbiomarkersandtherapeutictargetsisimportantforimprovingtheclinicalmanagementofCRC.

Ourstudyaimedtoidentifydifferentiallyexpressedgenes(DEGs)andenrichedpathwaysassociatedwithCRCusingbioinformaticstools.WeanalyzedgeneexpressiondatafromCRCtissuesandnormaltissuesobtainedfrompubliclyavailabledatabases.Weidentifiedatotalof941DEGs,ofwhich471wereupregulatedand470weredownregulatedinCRCtissuescomparedtonormaltissues.GeneontologyandpathwayanalysisrevealedthattheseDEGsweremainlyinvolvedincellularprocessessuchascellcycleregulation,DNArepair,andimmuneresponse.

FurtheranalysisidentifiedseveralkeygenesandpathwaysassociatedwithCRC.OneofthemostsignificantlydownregulatedgeneswasGATAbindingprotein5(GATA5),whichhasrecentlyemergedasapotentialtumorsuppressorinCRC.GATA5regulatesseveralgenesinvolvedincelldifferentiation,proliferation,andapoptosis,anditslossoffunctionhasbeenshowntopromotethedevelopmentandprogressionofCRC.OthersignificantDEGsidentifiedinourstudyincludedTSPAN8,CDH17,andTFF3,whichhavebeenimplicatedinCRCpathogenesisandmayserveaspotentialbiomarkersforearlydetectionandprognosis.

PathwayanalysisrevealedthatseveralsignalingpathwaysweredysregulatedinCRC,includingtheWnt/β-cateninpathway,JAK-STATsignalingpathway,andPI3K-Aktsignalingpathway.Thesepathwaysplayimportantrolesincellproliferation,differentiation,andsurvival,andtheirdysregulationhasbeenlinkedtothedevelopmentofCRC.Ourfindingssuggestthattargetingthesepathwaysmayhavetherapeu