Evolution's Clinical Guidebook: Translating Ancient Genes into Precision Medicine PDF
Preview Evolution's Clinical Guidebook: Translating Ancient Genes into Precision Medicine
Evolution’s Clinical Guidebook Evolution’s Clinical Guidebook Translating Ancient Genes into Precision Medicine Jules J. Berman AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom ©2019ElsevierInc.Allrightsreserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans,electronic ormechanical,includingphotocopying,recording,oranyinformationstorageandretrievalsystem, withoutpermissioninwritingfromthepublisher.Detailsonhowtoseekpermission,further informationaboutthePublisher’spermissionspoliciesandourarrangementswithorganizations suchastheCopyrightClearanceCenterandtheCopyrightLicensingAgency,canbefoundatour website:www.elsevier.com/permissions. Thisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightbythe Publisher(otherthanasmaybenotedherein). 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LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN978-0-12-817126-4 ForinformationonallAcademicPresspublications visitourwebsiteathttps://www.elsevier.com/books-and-journals Publisher:StacyMasucci AcquisitionEditor:RafaelTeixeira EditorialProjectManager:SandraHarron ProductionProjectManager:PunithavathyGovindaradjane CoverDesigner:ChristianBilbow TypesetbySPiGlobal,India Other Books by Jules J. Berman About the Author JulesJ.Bermanreceivedtwobaccalaureatedegreesfrom MITinMathematicsandinEarthandPlanetarySciences. HeholdsaPhDfromTempleUniversity,andanMD,from the University of Miami. His postdoctoral studies were completed at the US National Institutes of Health, and his residency was completed at the George Washington UniversityMedicalCenterinWashington,DC.Dr.Berman served as Chief of Anatomic Pathology, Surgical Patho- logy, and Cytopathology at the Veterans Administration Medical Center in Baltimore, Maryland, where he held jointappointmentsattheUniversityofMarylandMedical CenterandattheJohnsHopkinsMedicalInstitutions.In 1998, he was transferred to the US National Institutes of Health as a Medical Officer and as the Program Director for Pathology Informatics in the Cancer Diagnosis Program at the National Cancer Institute. Dr. Berman is a past presidentoftheAssociationforPathologyInformaticsandthe2011recipientoftheAsso- ciation’s Lifetime Achievement Award. He has first-authored more than 100 journal articles and has written numerous science books. His most recent titles, published by Elsevier, include: Taxonomic Guide to Infectious Diseases: Understanding the Biologic Classes of Pathogenic Organisms,1st edition (2012) PrinciplesofBigData:Preparing,Sharing,andAnalyzingComplexInformation(2013) Rare Diseases and Orphan Drugs: Keys to Understanding and Treating the Common Diseases (2014) Repurposing Legacy Data: Innovative Case Studies (2015) Data Simplification: Taming Information with Open SourceTools (2016) Precision Medicine and the Reinvention of Human Disease (2018) Principles and Practice of Big Data: Preparing, Sharing, and Analyzing Complex Information, 2nd edition (2018) Taxonomic Guide to Infectious Diseases: Understanding the Biologic Classes of Pathogenic Organisms,2nd edition (2019) xi Preface Everythinghasbeensaidbefore,butsincenobodylistenswehavetokeepgoingback and beginningall overagain. AndreGide In 1973, Theodosius Dobzhansky, a distinguished geneticist and the awardee of the US National Medal of Science, delivered an influential essay entitled “Nothing in biology makes sense except in the light of evolution” [1]. In this essay, he argued that we need the theory of evolution to explain paleontology, zoology, and the biomedical sciences. Thereasonforthisisthatalloftheobservablephenomenaofliving(oronce-living)organ- ismsdevelopedstepwise,overvaststretchesoftime.Itisthroughthetheoryofevolution thatscientistsunderstandbiologicalobservations.Withoutevolution,biologicalobserva- tions arereducedto merefactoids. AssumingthatDr.Dobzhanskywascorrectandthatallbiologicalobservationsmustbe interpreted within the framework of their evolutionary origins, then we would surmise thatanyoneinterestedinbiologywouldbehighlyencouragedtostudythefieldofevolu- tion, as well as the complementary fields in which the steps of evolution are directly expressedinanimals(i.e.,embryology,histology,anatomy,microbiology,andphysiology). Thesefivefields,theformermainstaysofmedicaleducation,havefallenbehindthetwo relatively new fields of molecular biology and bioinformatics. Progress in the fields of molecular biology and bioinformatics, over the past three decades, has been so rapid andsoexcitingthatwecanhardlyfaultstudentswhochoosetoconcentratetheiratten- tion on these twonew areas. Asapointoffact,advancesinthegeneticsofhumandiseaseshavevastlyoutpacedour abilitytoanalyzeandunderstandourdata.Wehavenowidentifiedthousandsofgenevar- iants that arethe putative root causes of rarediseases, without achieving a deep under- standing of the biological mechanism whereby the variant gene leads to the clinical expression of disease [2]. In the case of the common diseases of humans, particularly in the case of cancers, we have collected thousands of gene variants that are associated withsubsetsofaffectedindividuals,butweseldomhaveaclearunderstandingofthebio- logical roles these genes play in the development or progression ofdisease[3]. Wenowknowthatdiseasesdevelopthroughasequenceofbiologicalstepsthateven- tuallyleadtotheappearanceofaspecificclinicalphenotype(i.e.,cellularpathologyand consequentsymptoms).Aspecificdefectinaparticulargenemaylieattherootcauseof the disease, but identifying a “causal” gene seldom tells us much about the subsequent stepsthatoccuroverdaysormonthsoryears,leadingtodisease.Inmanycases,knowing xiii xiv PREFACE those steps may be more important than simply identifying the root causal gene; the reason being that the most effective way to prevent, diagnose, or treat a disease may involve targeting those subsequent events and pathways. Furthermore, knowledge of theeventsandpathwaysthatleadtothedevelopmentofaspecificdiseasemaybedirectly applicable to otherdiseases, including subsets of common diseases[4]. At this point, you might be wondering how issues concerning disease development mightrelatetothetopicofevolution.Asithappens,thepathwaysleadingtothedevelop- mentofdiseaseareconservedcellularpathways,allofwhichcameintoexistencethrough evolution, at particular moments in the development of ancestral species. If we want to understandthepathwaysthatleadtodisease,wemightwanttolookathowandwhythese pathwaysevolved,thefunctionstheyserveatparticularstagesinanorganism’sdevelop- ment, and the particularcellsin which those pathways areexpressed. Now we come to the premise of this book. We’ll take Dobzhansky at his word, that “Nothing in biology makes sense except in the light of evolution,” and we’ll extend it to assert that “nothing in the field of Precision Medicine makes sense except in the light of evolution.” Evolution’s Clinical Guidebook: Translating Ancient Genes into Precision Medicine is an exploration ofthisassertion. Howto read this book This book is primarily written for anyone who is searching for a clear, logical, and informedexplanationoftherelationshipbetweenevolutionaryprocessesandthescience of modern medicine.On a verysimplistic level, evolutionarytheorycan be coveredin a fewparagraphsofamiddleschooltextbook,leavingstudentswithacredibleaccounting ofhowancientanimalsmayhavegivenrisetoallthespeciesofanimalsthatinhabitour planettoday.Ifwewanttounderstandexactlyhowparticulardiseasesmayhaveevolved andhowwemightuseourunderstandingofevolutionaryhistorytodevelopandtestnew and effective treatments for human diseases, then we must be prepared to think very deeplyandtointegratetheseeminglyunrelateddisciplinesofembryology,biochemistry, paleontology, comparative anatomy,molecular biology, bioinformatics, and pathology. Needless to say, it is impossible for anyone to absorb all the subjects covered in this book.Settingasidethemanynewconceptsthatwillbediscussed,theburdenofmastering theterminologiesofhalfadozenscientificfieldsistoooneroustobear.Accordingly,the book is organized to eliminate the need for rote memorization, while permitting the readerto focus onthe fundamentalconceptsexplained in each sectionofeach chapter. Insomesense,thebookisacollectionoflogicalarguments.Thefactsinthebookappear forthesolepurposeoflegitimizingthearguments.Ifyouareacuriouslayman,thecon- ceptsthataredevelopedthroughoutthebookwillsatisfyyourcuriosity.Ifyouareamed- ical researcher, then you can always returnto the book and readit a second time for its factualcontent. Thereareabout800referencesincludedwiththetextandthisshouldkeeptheserious scholaroccupiedforyearstocome.Inaddition,eachchapterisaccompaniedbyaglos- sarycontainingmanyofthediscipline-specifictermsappearinginthetext.Thereare,in toto, over 300 glossary terms. Along with term definitions, most of the glossary items Preface xv expand upon the concepts covered in the text, providing additional references and instructiveexamples.Readerswholackastrongbackgroundinthebiologicalormedical sciences are encouraged to read the chapter glossaries, before proceeding to the subse- quent chapters. References [1] Dobzhansky T. Nothing in biology makes sense except in the light of evolution. Am Biol Teach 1973;35125–9. [2] Berman JJ.Rarediseasesandorphandrugs:keystounderstandingand treatingcommondiseases. Cambridge,MA:AcademicPress;2014. [3] BermanJJ.Neoplasms:principlesofdevelopmentanddiversity.Sudbury:Jones&Bartlett;2009. [4] Berman JJ. Precision medicine, and the reinvention of human disease. Cambridge, MA: Academic Press;2018. 1 Evolution, From the Beginning OUTLINE Section1.1IntheBeginning ...........................................................................................................1 Section1.2BootstrappingParadoxes .............................................................................................5 Section1.3OurGenes,fortheMostPart,ComeFromAncestralSpecies .................................12 Section1.4HowdoMetabolicPathwaysEvolve? .......................................................................15 Section1.5CambrianExplosion ....................................................................................................21 Section1.6AftertheCambrian:CoexistenceandCoevolution ..................................................25 Glossary ..........................................................................................................................................29 References ......................................................................................................................................44 Section 1.1 In the Beginning The beginningsandendings of all human undertakings are untidy. JohnGalsworthy Every story has a beginning. Inthe case of life on planetEarth, thereis no one who can speakwithanygreatauthorityonthesubject.Ithappenedtoolongago,onaworldthat wasverydifferentfromtheworldwelivein.Nonetheless,thebeginningoflifeonEarthisa topic that invites thoughtful speculation. The purpose of this chapter is to discuss how biological processes begin, in general terms. If nothing else, the chapter provides us an opportunity to explore fundamental concepts that will surface throughout the book: enzymes, pathways, natural selection, and evolution. Abiogenesis Abiogenesisisthecreationoflifefromnonlivingmatter.Forthousandsofyears,themys- teryoftheoriginoflivingorganismshaschallengedphilosophers,theologists,andscien- tists.Inthissection,we’lltrytoshowthatlifeisverysimpletocreate,ifwejustacceptthe following threeassumptions: –1. Alllivingthingsarecomposed ofnonliving things. Lifeonearthconsistsofcells,andcellsarejustbagsofchemicals.Ithappensthatthese bagsofchemicalscanreplicatethemselves(i.e.,self-replicate),accountingforwhythere aresomanycellsontheplanet.Becausealllivingmatteriscomposedentirelyofnonliving matter, we can guess that life may have gotten its start from some process involving nonlife. 1 Evolution’sClinicalGuidebook.https://doi.org/10.1016/B978-0-12-817126-4.00001-1 ©2019ElsevierInc.Allrightsreserved.
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