reviewarticle - hindawi publishing...

Review ArticleGenetic Mutations and Epigenetic ModificationsDriving Cancer and Informing Precision Medicine

Krysta Mila Coyle1 Jeanette E Boudreau12 and Paola Marcato12

1Department of Pathology Dalhousie University Halifax NS Canada2Department of Microbiology amp Immunology Dalhousie University Halifax NS Canada

Correspondence should be addressed to Paola Marcato paolamarcatodalca

Received 7 December 2016 Revised 6 April 2017 Accepted 10 May 2017 Published 8 June 2017

Academic Editor Wen-Hwa Lee

Copyright copy 2017 Krysta Mila Coyle et al This is an open access article distributed under the Creative Commons AttributionLicense which permits unrestricted use distribution and reproduction in any medium provided the original work is properlycited

Cancer treatment is undergoing a significant revolution from ldquoone-size-fits-allrdquo cytotoxic therapies to tailored approaches thatprecisely target molecular alterations Precision strategies for drug development and patient stratification based on the molecularfeatures of tumors are the next logical step in a long history of approaches to cancer therapy In this review we discuss the historyof cancer treatment from generic natural extracts and radical surgical procedures to site-specific and combinatorial treatmentregimens which have incrementally improved patient outcomes We discuss the related contributions of genetics and epigeneticsto cancer progression and the response to targeted therapies and identify challenges and opportunities for the success of precisionmedicine The identification of patients who will benefit from targeted therapies is more complex than simply identifying patientswhose tumors harbour the targeted aberration and intratumoral heterogeneity makes it difficult to determine if a precision therapyis successful during treatment This heterogeneity enables tumors to develop resistance to targeted approaches therefore therational combination of therapeutic agents will limit the threat of acquired resistance to therapeutic success By incorporating theview of malignant transformation modulated by networks of genetic and epigenetic interactions molecular strategies will enableprecision medicine for effective treatment across cancer subtypes

1 Putting Precision Medicine in Context

All cancer treatment is patient-centric and could reasonablybe considered to be personalized or precision medicine Forthe context of this paper we have used ldquoprecision medicinerdquoto refer to the specific targeting of molecular abnormalitiesfor the stratification of patients to increase responses tospecific drugs (Box 1) ldquoPersonalized medicinerdquo is within theumbrella of precision medicine however these are the mostindividualized therapies tailored uniquely for each patientPrecision medicine encompasses drugs that can be usedldquooff the shelfrdquo (eg tamoxifen for the treatment of estrogenreceptor- (ER-) positive breast tumors) while personalizedtreatments may require specific engineering for each patient(eg chimeric antigen receptor (CAR) T-cells and adoptivetransfer of tumor-infiltrating lymphocytes) Both personal-ized and precision therapies require substantial analysis of

the patientrsquos tumor however precision therapies which dis-tribute the burden of development and licensing and testingbetween patients are more cost-effective and therefore arelikely to be available to a greater proportion of patients [1 2]With the expanding availability of high-throughput ldquoomicsrdquotechnologies and bioinformatic analysis precision therapy isbecoming available to an increasing number of patients Inthis paper we will provide historical context for precisionapproaches to cancer review a selection of related genetic andepigenetic contributions to precisionmedicine strategies anddiscuss the challenges and opportunities for the success ofprecision medicine in cancer therapy

2 Historical Evolution of Precision Medicine

Cancer therapy has historically used an ldquoeverything butthe kitchen sinkrdquo approach Both Hippocrates and Galen

HindawiBioMed Research InternationalVolume 2017 Article ID 9620870 18 pageshttpsdoiorg10115520179620870

2 BioMed Research International

Precision Medicine The specific targeting of molecular abnormalities and the stratification of patients who respond to specific drugsCan be used ldquooff the shelfrdquoPersonalized Medicine The most individualized form of precision therapy tailored uniquely for each patient Must be engineeredfor each patient

Box 1 Key terms

ancient physicians who have shaped the current practiceof medicine considered cancer as an incurable disease [3]Cancer treatments have developed substantially since theypracticedmedicine which is demonstrated by improvementsto patient health and survival

Treatment for those afflicted with cancers originallyused medicines such as extracts from chickpea adderwortstinging nettle and other plants [3] Surgical approaches totreat cancer have been described as early as the first centuryAD calling for removal of the affected part accompanied bythe now relatively obsolete practice of blood-letting in someindividuals [3] Cancer therapy through the 19th centuryand most of the 20th century did not deviate substantiallyfrom these ancient practices of medicine however improvedsurgical precision pain management and sanitation havesteadily improved patient outcomes

Surgical excision to debulk tumors remains a stalwartof cancer therapy and combinations of medicines naturalextracts chemicals and radiation have been introduced inan attempt to limit the rapid cellular growth associated withresidual tumor cells Cancer therapy experienced its firstmajor revolution in the mid-20th century with the use ofnitrogen mustards following the observation that mustardgas exposure correlated with depletion of lymphocytes in theblood of soldiers during World War II [4ndash6] This prompteda hypothesis that nitrogen mustard compounds could beused to inhibit the growth of white blood cells which isbeneficial to treat and cure leukemias and lymphomas Atthe same time Sidney Farber demonstrated that folic acidcould accelerate the growth of leukemia cells This led toclinical trials of methotrexate a folate antagonist to treatleukemia [6 7] A third project discovered antitumor effectsof the antibiotic actinomycin D which was used throughoutthe 1950s and 1960s in pediatric tumors [6 8] Finally amajor addition to the therapeutic regime of surgery andchemotherapy that Hippocrates and Galen could likely nothave envisioned is the use of ionizing radiation during the20th century Observed as early as 1903 Charles Leonardwrote that radiation therapy initially applied as palliativecare resulted in cures and restored patientsrsquo health [9]Although these approaches improved the survival of patientswith cancer they remained relatively unrefined with a highrisk of acute complications

Until the late 1900s cancer chemotherapy used genericcytotoxic drugs that aimed to inhibit rapid cellular prolifera-tion a characteristic hallmark of malignant cells The arsenalof cancer chemotherapies expanded to include 5-fluorouracilvinca alkaloids platinum agents and taxanes [10ndash13] whichthough effective at controlling malignant proliferation byinhibiting cellular division have little precision for specifictumors and often carry high-risk side effect profiles

Cancer is increasingly considered as a collection ofdiseases with characteristics derived from their tissues andcell types of origin and the mutations that drive themChemotherapy radiotherapy and surgical therapy are nowselected and combined based on their efficacy for particularcancers and histologies and the process for treating eachpatient is informed by their specific disease These strategiesto stratify cancer treatment based on the tissue of originand the specific type of transformed cell were the firstrefinement toward amore patient-centric treatment of cancer(Figure 1)

The next phase of cancer therapy precision therapy willleverage the ability to target specific molecular features totreat a cancer based on its characteristics rather than itstissue of origin alone More detailed understanding of tumorbiology has revealed that each individual tumor accumu-lates a unique set of alterations that allow it to escape thenormal checkpoints thatmaintain homeostasis Neverthelessindividual cancers harbour features that allow uncontrolledgrowth such as growth factor or receptor overexpression andloss of apoptosis and cell cycle control mechanisms whichmanifest as molecular features that can be targeted with agrowing arsenal of drugs Refining the description of cancerto a unique set of alterations describing each individual tumorwill enable precision medicine and inform the best treatmentapproach to target every tumor and limit the application ofineffective therapies (Figure 1)

Molecular understanding of tissue development hor-mones and required signals for cell proliferation pushedthe development of tamoxifen an estrogen receptor (ER)antagonist originally developed in an attempt to find newcontraceptives and cholesterol-lowering drugs (Table 1) [1415] Tamoxifen was licensed for use in the US for advancedbreast cancer patients in 1972 and its current success intreating patients with ER positive breast cancers has beencalled a catalyst for the precisionmedicine approach to cancertherapy [16] The 1990s and early 2000s saw the success ofother treatments aimed at molecular targets such as ima-tinib against the BCR-ABL translocation seen in chronicmyelogenous leukemia rituximab (anti-CD20) as a treatmentfor B-cell lymphomas and retinoic acid for treatment ofPML-RAR fusion acute promyelocytic leukemia (Table 1)[17ndash21] In the same decade trastuzumab was approved forthe treatment of breast cancer patients with amplification ofERBB2 (human epidermal growth factor receptor 2 alsoknown asHER2neu) [22]More recently checkpoint inhibit-ing antibodies anti-PD1 (nivolumab) and anti-CTLA-4 (ipil-imumab) (Table 1) are being systematically applied in clin-ical trials of particular cancer types [23ndash25] While thesetherapies illustrate the beginnings of cancer treatments that

BioMed Research International 3

(iii) Retrospective marker identication

(ii) Benecial outcomes

(i) Application of therapy

erapy based on tumor site

(a)

(i) Prospective target identication

(ii) Application of therapy

(iii) Benecial outcomes

erapy based on precise target

(b)

Figure 1 Retrospective and prospective identification of biomarkers and actionable targets can improve patient outcomes by allowing moreprecise therapeutic choices (a) Traditional treatment of cancers by site of origin (i) Patients with tumors from the same tissue of origin havetypically been treated with the same therapeutic agent (ii) Treatment outcomes from this type of therapy have been beneficial only in asubset of patients (iii) With increasing availability of molecular testing however we are now retrospectively identifying biomarkers thatcan predict the outcomes of treatment based on the characteristics of their tumor (b) Precise patient stratification considers the tumors andthe molecular characteristics to determine the best treatment approach (i) Molecular technologies can identify prospective biomarkers andactionable aberrations (ii) This allows patients to be given therapies most likely to foster beneficial treatment (iii) With patient stratificationand precise application of therapies beneficial outcomes are observed in a greater proportion of patients

target specific dependencies orweaknesses of cancer they stilllargely rely on a site-specific treatment modality (Figure 2)

It is essential to recognize that cancer therapy has his-torically been limited by our ability to collect and analyzeinformation about the tumorrsquos ontogeny driver mutationsand phenotype However the information we can now obtainfrom any one patient and any one tumor is ushering in adata-driven transformation of oncology which inspires preci-sion therapies Resources to curate and analyze data collectedin whole tumor genomic and transcriptomic analysis suchas the Cancer Genome Atlas (TCGA) and the InternationalCancer Genome Consortium (ICGC) are making massivecancer datasets available to researchers to test hypotheses andprobe genomic variants in primary datasets Precisionmedicine is limited by our understanding of cancer and theavailability of agents to treat key features of a tumor Anapplication of ldquoomicsrdquo approaches and novel models tounderstand the complex circuitry of cancer hijacked fromnormal cellular networks and pathways will accelerate im-provements in patient care

3 Precision Therapy Is Informed byGenetics and Epigenetics

Two key factors determining cell behaviour are geneticsthe study of heritable nucleotide sequences and epigeneticswhich has traditionally been defined as the study of heritable

changes to gene expression which do not involve changesof nucleotide sequences It is important to note that not allepigenetic modifications are heritable [26ndash28] and thus theterm is used more broadly in the context of this reviewCanonical epigenetic modifications can alter the transcrip-tion and translation of particular genes to increase or decreasetheir functional levels [29] Perhaps the most well-studiedmodification DNA methylation refers to the addition ofmethyl groups to CpG dinucleotides in DNA [30 31] andusually occurs at regions of the genome with a high densityof CpG dinucleotides (CpG islands) [32] Although DNAmethylation is canonically associated with gene silencingthe implications of DNA methylation vary significantly withgenomic context [33] Other epigenetic modifications thatcontribute to transcription and translational control of geneexpression include the posttranslational modification of his-tone proteins (by acetylation methylation phosphorylationubiquitylation or sumoylation) [34ndash36] and the interactionsof noncoding RNAs with proteins or other nucleic acids [37]These epigenetic processes function normally to provide aframework for development and differentiation contributingto tissue-specific gene expression inactivation of the X-chromosome and genomic imprinting [38ndash40] Epigeneticsalso contribute to aging and act in response to environmentalfactors [41 42]

As our understanding and treatment of cancer evolveselection of therapies for cancer patients must also be guidedby a molecular understanding of cancer (Figure 2) This


Table1Selected

listo

fpreciselytargeted

molecular

alteratio

nsin

cancer

Genes

ymbo

lGenen

ame

Effecto

falteratio

nMajor

associations

with

specifictum

ortypes

Implicated

therapy

Protooncogenesandoncogenes

BCR-ABL

Breakp

oint

cluste

rregion

Abelsonmurine

leuk

emiaviraloncogeneh

omolog

fusio

nprotein

Com

prom

isesfi

delityof

DNArepair

deregu

latesp

roliferation

impairs

apop

tosis

anddifferentiatio

nCh

ronicm

yelogeno

usleuk

emia

Imatinibdasatinib

HRA

SKR

AS

HarveyKr

isten

ratsarcomav

iraloncogene

homolog

Con

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gNon

-smallcelllun

gcancer

Salirasib

BRAF

v-Ra

fmurines

arcomav

iraloncogene

homolog

BCon

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gMelanom

aV60

0Eor

V60

0Kmutations

Vemurafenibdabrafenib

BCL2

B-celllymph

omaleuk

emia-2

Impairs

apop

tosis

Leuk

emialym

phom

amelanom

aVe

netocla

xTu

mor

suppresso

rgenes

BRCA

12Breastcancer

12Im

paire

dDNArepair

Breastandovariancancers

PARP

inhibitor(via

synthetic

lethality

)Ep

igeneticmodify

ingg

enes

IDH12lowastlowast

Isocitrated

ehydrogenase

DNAhyperm

ethylatio

ndisrup

tsdifferentiatio

nAc

utem

yeloid

leuk

emia(A

ML)

AG120AG

221AG

881

EZH2

Enhancer

ofzeste

2po

lycombrepressiv

ecomplex

2subu

nit

Inhibitsapop

tosissilences

byH3K

27trim

ethylatio

nLymph

oma

Tazemetostat

DOT1L

DOT1-like

histo

neH3K

79methyltransfe

rase

Inhibitsdifferentiatio

nandapop

tosis

Mixed-lineageleukemia

Pino

metostat

DNMT

DNAmethyltransfe

rase

Disr

uptsno

rmalpatte

rnso

fDNAmethylatio

nBreastandcoloncancersgliomaAML

Azacytid

ine

decitabine

HDAC

Histon

edeacetylases

Disr

uptsno

rmalpatte

rnso

fhiston

eacetylatio

nGastricbreastcolorectalcancers

Vorin

ostatromidepsin

Othertargets

EREstro

genreceptor

Sustains

proliferativ

egrowth

signals


Tamoxifen

CD20

B-lymph

ocytea

ntigencluste

rof

differentiatio

n(C

D)2

0Supp

ortsB-cellactiv

ationandcellcycle

progression

B-celllymph

omas

Rituximab

ERBB

2(H

ER2neu)

Hum

anepidermalgrow

thfactor

receptor

2Sustains

proliferativ

egrowth

signals

Breast

ovarianuterineandlung

cancers

Trastuzumab

PD1

Programmed

celldeathprotein1(CD

279)

Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Nivolum

ab

CTLA

4Cy

totoxicT

-lymph

ocytea

ssociatedprotein

4Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Ipilimum

ab

AP-1

Activ

atingprotein1

Regu

lates

gene

expressio

ncontrolling

differentiatio

nproliferatio

nandapop

tosis

Colorectalcancer

casestu

dyIrbesartan

(ang

iotensin

IIreceptor

antagonist)

PML-RA

RProm

yelocytic

leuk

emiaretinoica

cid

receptor

alph

afusiongene

Inhibitsgranulocyticdifferentiatio

nAc

utep

romyelocytic

leuk

emia

Retin

oica

cid

Biom

arkersforclin

icalagents

APA

F1Ap

optotic

protease

activ

atingfactor

1Preventsapop

tosis

Melanom

aDoxorub

icin

MGMT

O6-m

ethylguanine-D

NA

methyltransfe

rase

Reverses

DNAdamage

Glio

ma

Alkylatingagents

lowastlowastAlth

ough

IDH12

aren

otepigeneticmod

ifyinggenesalteratio

nsin

theseg

enes

canhave

profou

ndeffectson

thee

pigeno

me


Site of originTemporal heterogeneity Uncontrolled proliferation

Spat

ial h

etero

gene

ity

Epigenetic modications

Specic gene mutation Presence or absence of specic genesGros

s chr

omos

omal

rear

rang

emen

tsAlready in use f

or clin

ical d

ecisi

on-m

akin

g

Inter

roga

ted by

emerg

ing tech

nologies

eg BRAFV600E

ER+minusPR+minus

middot middotmiddot

middotmiddotmiddot

middot middot middot

RX

Figure 2Emergingmolecular technologies provide important information for precision treatment strategies Treatment approaches have evolvedfrom a ldquoone-size-fits-allrdquo strategy based on the uncontrolled proliferation of cells and the site of a tumorrsquos origin Current approachesincorporate gross chromosomal rearrangements and the presence or absence of specific genes which can provide insight into the potentialfor therapeutic efficacy Limited precision strategies which target specific mutations are also in use Emerging technologies will provide acomprehensive view of cancer and allow clinical decision-making and drug development strategies to incorporate epigenetic modificationsspatial heterogeneity and temporal heterogeneity that can enable acquired resistance to targeted therapy

includes both genetic and epigenetic factors as they colludeto provide cancer with the required hallmark capabilities[43 44]

31Mutations and EpigeneticModificationsThatDrive CancerKey alterations including mutations are required for theinitiation and development of cancer Broadly these geneticaberrations enable growth-promoting signals to cancer genesandor destabilize the genome to allow continuousmalignanttransformation by facilitating increased rates of mutation[45ndash48] It is these mutations that drive cancer and alsoinform strategies for precision medicine in cancer (Table 1)

311 Inappropriate Activation of Oncogenes Oncogenes aremost often inappropriately activated by mutations but theremoval of epigenetic marks may also be responsible foractivating oncogenes and the rate of mutation varies signif-icantly across cancers of different tissues [49]The removal ofepigeneticmarksmay also be responsible for activating onco-genes Hypomethylation of the protooncogenes HRAS (Har-vey rat sarcoma viral oncogene homolog) and KRAS (Kirstenrat sarcoma viral oncogene homolog) was observed in pri-mary human tumors [50] Although lacking the mutationsthat would constitutively activate RAS signaling increasedexpression of these GTPases may contribute to the malignantphenotype observed in cancers [51] and can be targets of


precision medicine approaches (Table 1) Although earlierestimates suggested that 90 of the somatically mutatedoncogenes acted in a dominant manner [52] some mayinstead act in a recessive fashion (ie FOXP1 and MLLT4)[53] The emergence of candidate oncogenes from thecomprehensive data available through the TCGA and ICGCdatabases will likely provide further insight into the relativefrequency of somatic mutations in oncogenes and tumorsuppressor genes [54 55]

312 Genetic Inactivation or Epigenetic Silencing of TumorSuppressor and Genomic Stability Genes The majority oftumor suppressor genes require mutations on both alleles[52] resulting in the inactivation of a gene product thatcontrols excessive cell growth under healthy homeostaticconditions Typically loss of cellular integrity followed bypersistent and uncontrolled cellular division requires inacti-vation of protective cellular mechanisms (ie tumor suppres-sor genes) and mutations that facilitate tumor growth eitherdirectly (ie by activation of an oncogene) or indirectly (ieby enhancing sensitivity to growth factors) The ldquotwo-hitrdquohypothesis first described by Knudson in the 1970s [56 57]postulates that at least two mutations of a tumor suppressorgene are required for cancer to develop first loss of het-erozygosity and then subsequentmutation of its paired alleleleading to functional loss of the repression of cell divisionand cancer development While the classical definition ofa tumor suppressor includes the presence of truncatingmutations [58ndash60] there is evidence that tumor suppressorgenes are inactivated by nontypical mechanism such as hap-loinsufficiency or gain-of-function isoforms [58] Classicaltumor suppressor genes typically defined by inactivation bymutation may also be silenced by epigenetic mechanisms[61ndash64] We and others have posited that these ldquosilencedrdquotumor suppressors may make excellent drug targets as theycould potentially be reactivated by reversing these silencingmodifications [65 66] or may indicate the pathways anddownstream alterations that may be targeted by precisetherapeutics

Genomic instability is a key enabling characteristicunderlying carcinogenesis and continuous tumor progres-sion TP53 plays an essential role in this process as theldquoguardian of the genomerdquo [67] and is implicated in almostevery type of human tumor at varying rates [68] Broadlyinactivation of TP53 and other gene products responsible forprotecting the integrity of cellular DNA support a moremutable phenotype by preventing DNA repair or by allow-ing mutagenic molecules to damage DNA unchecked [44]Epigenetic aberrations can also impact the mutation rate ofcancer cells For example hypomethylation near guaninequadruplexes increases the rate of DNA breakage and acti-vation of homologous recombination and may act as amutagenic factor [69] There is also evidence that mutationrate varies near CpG islands and that histone methylationlevels may predict the loci of somatic mutations [70ndash72] Inaddition normal epigenetic regulation can impact the muta-tion frequency as highly expressed genes have been demon-strated to have higher mutation rates [73]

The effect of epigenetic modifiers on genomic stability ismost frequently observed in hematological malignancies Inacute myeloid leukemia (AML) and myelodysplasia muta-tions in isocitrate dehydrogenase (IDH) 1 or 2 disrupt cellulardifferentiation and drive leukemogenesis [74] Mutations inthe catalytic domain of EZH2 are found in diffuse large B-celland follicular lymphomas and disrupt H3K27 methylationpromoting cell survival (Table 1) [75 76] Similarly a commontarget of translocation in mixed-lineage leukemia is DOT1-like histone H3K79 methyltransferase (DOT1L) InhibitingDOT1L results in increased differentiation and apoptosis ofleukemia cells again suggesting that the abnormal epigeneticprogram is required for leukemic cell survival [77] Togetherthis evidence suggests that interactions between the genomeand epigenome occur throughout malignant transformation

Cancer is typically broadly characterized by genome-wideDNAhypomethylation and promoter hypermethylation[78ndash82] however the view and interpretation of epigeneticsin the context of precision medicine should be expandedbeyond a gene-centric view The epigenome is not just a sur-rogate for mutations and can have distal effects which rangebeyond canonical promoter methylation [72 83] Evidencesuggesting that methylation of distal regulatory elements isrelated to gene expression poses a complex question thatgenome-wide studies are now beginning to answer Thehypomethylation observed in cancer often occurs at satel-lite DNA the main component of functional centromeresand at other repeating sequences that do not functionas transcriptional units Hypomethylation in these DNAsequences is not likely to have a cis effect on gene expressionunless it spreads into neighbouring chromatin [78] Howevergene expression can be affected by nuclear positioning andhypomethylation near centromeres could affect gene expres-sion in trans Centromeric heterochromatin has been shownto act as a reservoir for transcriptional control proteins thatmay be disrupted by hypomethylation [78 84 85] Thishypomethylationmay also disrupt interactions between hete-rochromatin and euchromatin [86ndash88]With respect to gene-specific hypermethylation several studies have observed thatmost hypermethylated tumor suppressor gene-associatedCpG islands are not in gene promoters This hypermethy-lation is thus likely to be a consequence of another cancer-associated mechanism rather than a direct cause of tumordevelopment or progression [89ndash91] This necessitates thatcancer epigenetics step outside of a gene-centric focus andovercome the greater challenges associated with determiningthe effects of global epigenetic aberrations

4 Precision Approaches to Genetic andEpigenetic Events in Cancer

41 Targeting Genomic Drivers of Cancer Progression Ourknowledge of driver mutations and oncogene addiction inmany types of cancer has prompted development of cancertherapies targeted at molecular changes (Table 1) Althoughmany cancers have multiple genetic abnormalities drivermutations enable outgrowth of cancerous populationsChanges that foster cancer growth reflect an ldquooncogeneaddictionrdquo or reliance of some cancers on one gene or a few


genes to maintain a malignant phenotype Addiction toa specific alteration such as overexpression of growth factorreceptors may represent an ldquoAchilles heelrdquo a specific andidentifiable weakness which may be exploited by cancertherapies Indeed the addiction of folate receptor-positivetumors to folate and the success of the anti-HER2 antibodytrastuzumab have been described as ldquoconvincing and clini-cally relevant evidencerdquo for the theory of oncogene addiction[92 93]

In some tumors with high mutational load it can bechallenging to identify specificmutations as driver or passen-ger mutations Driver mutations are those which enable thecontinued development and evolution of a tumour passengermutations result from genomic instability and other tumor-associated factors but are dispensable for tumor progression[94] For instanceDNApolymerase regularly stutters in shorttandem repeats of mono- di- tri- or tetranucleotide repeats[95] When DNA repair is defective due to silencing of orpoint mutations in key DNA stability genes (such as MLH1MSH2MSH6 or PMS2) these mistakes cannot be repairedThis results in microsatellite instability and can lead to ahypermutable phenotype [96]

The boom in molecularly targeted drugs has yielded animpressive list of targeted drugs in clinical trials with manymore following behind in the development pipeline Morerecently emerging is the off-label use of drugs for thetreatment of cancers with specific alterations For exampleintegrative genomic analysis of a patient with metastaticcolorectal cancer revealed high expression of components ofthe activating protein-1 (AP1) complex (Table 1) Treat-ment with the angiotensin II receptor antagonist irbesartanresulted in a complete radiological response [97] This maybe an effective therapy against other tumors with a similarupregulation of the AP1 complex but it is unlikely to be effec-tive for any other alterations It is important to recognize thatthe components of AP1 were not mutated in this patient andwere revealed as outliers via gene expression analysis Thusthe repertoire of molecularly targeted drugs may need toencompass every possible gene product and not just those fre-quently mutated or rely on approaches to identify mutationsa priori in each patient This concept has driven the devel-opment of ldquobasket trialsrdquo based on the hypothesis that theindividual alterations in a patientrsquos tumor will dictate theresponse to therapy independent of the histology [98]

One challenge to the concept of oncogene addiction andthe premise of molecular targeted therapies seen even inbasket trials is a maximal response rate of approximately50ndash60 [22 92] This suggests that the presence of a specificabnormality is not entirely responsible for the phenotype ofa cancer and supports an evolutionary model of cancerdevelopment where the initial transformation and subse-quent tumor growth foster further mutations and epigeneticalterations Integrative analysis of genetics and epigeneticsmay hold clues to this missing link

42 Epigenetic Therapies and Precision Epigenetic MedicineThe same qualities that make epigenetic heterogeneity dif-ficult to measure and model also make epigenetic modifi-cations excellent drug targets in particular the reversibility

of epigenetic modifications makes them attractive targets[99] The concept of oncogene addiction can be mirroredin several descriptions of the aberrant epigenetic landscapefound in cancer [100ndash102] Cancers may become dependenton the silencing of a few crucial tumor suppressor genes Forexample epigenetic silencing of a negative regulator of theWnt pathway results in constitutive activation of Wnt sig-naling driving proliferation [103 104] In another modelepigenetic silencing of HIC1 (hypermethylated in cancer 1)resulted in a partial loss of p53 function cooperating to drivetumor growth and progression [105]

Before exploring precision targeting of epigenetic aber-rations it is important to consider the conventional uses ofepigenetic therapy Epigenetic therapy is perhaps most wellknown for its effectiveness in treating myelodysplastic syn-dromes (MDS) MDS represents a heterogeneous group ofdisorders characterized by bone marrow failure Approxi-mately one-third of MDS patients progress to AML and thisshift is associated with accumulation of epigenetic modifi-cations within the cancerous cells Many genes have beendescribed as inappropriately silenced inMDS andAML how-ever the mechanisms by which hypermethylation of theseand other genes contributes to MDS or AML are not partic-ularly well characterized [106ndash108]

Azacytidine (5-azacytidine) has been shown to be effec-tive in approximately 50ndash60of patients withMDS [109 110]Azacytidine is a nucleoside analog which is incorporated intoRNA and DNA during transcription and DNA replicationWhen incorporated into DNA it acts as a DNA methyl-transferase (DNMT) inhibitor by binding DNMT leading toan irreversible loss of activity and its degradation [111ndash113]Additionally its structure prevents the addition of methylgroups to DNA [114] Azacytidine is also known to induceapoptosis and it is so far unclear if its efficacy in MDS isdue to demethylation or due to increased apoptosis [115 116]Decitabine (5-aza-21015840-deoxycytidine) can only be incorpo-rated into DNA and results in demethylation of DNA andapoptosis in a similar manner to that of azacytidine

Recent attempts to combine epigenetic therapies withconventional chemotherapies have shown promise It may bepossible to reverse epigenetic modifications that confer resis-tance to chemotherapy such as the silencing of APAF1 inmetastatic melanoma APAF1 is a downstream effector ofTP53 in DNA damage-induced apoptosis and a key mediatorof intrinsic apoptosis and it is frequently downregulated byDNAmethylation in malignant melanoma although it is notknown if this is a direct or indirect effect [117 118] Someantiapoptotic genes such as BCL2 have been observed to beoverexpressed contributing to chemoresistance While thesource of the aberration is not known it may be counteredby the use of venetoclax as in chronic lymphocytic leukemia[119]The impact of reversing the epigenetic alterationswhichdownregulate or upregulate specific genes contributing tochemoresistance (such as BCL2) has yet to be completelycharacterized however combinations of epigenetic agentswith chemotherapies have shown clinical benefit [120 121]

Epigenetic reprogramming in cancer also contributes tothe inappropriate expression of tissue-specific genes such asthe cancertestis antigen group These are so named because


their expression is limited in normal tissues to the testesThese are silenced in healthy cells as a result of DNAmethylation [122] but they can be found in numerous cancers[123 124] One group of these genes melanoma-associatedantigen genes (MAGEs) are found expressed at high levels inmelanoma and squamous cell lung cancers [125]The expres-sion of cancertestis antigens is an attractive target forimmune-mediated therapy as targeting antigens with limitedexpression profiles would result in limited off-target effectsAs intracellular proteins they are considered as targets forvaccines rather than antibody-based immunotherapy Re-sponses to MAGE peptide vaccines however have beenproven to be fairly limited and combination therapy withepigenetic modifiers which increase tumor expression ofMAGEs may be more effective [126]

The expression of cancertestis antigens allows spe-cific engineered T-cells to mediate an antitumor immuneresponse as has been seen in a clinical trial of personalizedmedicine for patients with myeloma [127] Additionally arecent study has illustrated that demethylation of DNA canupregulate hypermethylated endogenous retrovirus genesand induce the expression of double-stranded RNA whichcan mimic a viral response [128 129] These phenomena sig-nal that resetting the epigenome via pharmacological inhibi-tionmay sensitize cancer cells to other immunotherapies In apreclinical model DNMT inhibition sensitized melanoma totreatment with the anti-CTLA4 antibody an immune check-point inhibitor [128] and incidental findings in non-smallcell lung cancer support the addition of azacytidine to anti-PD1 checkpoint inhibitor therapy [130 131] The complexinteractions between the epigenome and the genome suggestthat this approach is a promising method to enhance theefficacy of existing precision therapies

One of the reasons that the epigenome is difficult toprecisely target is that it has been challenging to distinguishdriver alterations from passenger alterations While recentevolutionary tracing has contributed to our understanding ofdriver and passenger mutations in tumorigenesis [132 133]we are only beginning to identify the cancer-causing epige-netic changes among the many thousands of less-relevantalterations that are a consequence of cancer progression Onenotable study identified the gene promoters whose DNAmethylation is required for survival of somatic cells cancercells and cells in culture by examining promoter methylationafter disruption of DNAmethyltransferase activity [134]Thegenes identified as necessarily silenced for cancer cell survivalwere not known classical tumor suppressor genes This studydemonstrated that cancer cells can indeed be ldquoaddictedrdquoto specific epigenetic alterations and require silencing forsurvival [99] Additionally hypermethylation of some genesis required only in cell culture [134] providing further insightinto a culture-specific phenotype and offering reservationsabout epigenetic data collected only in culture Stable immor-talized and tumor cell lines displaymarked hypermethylationof CpG islands and studies of cultured cells risk revealingartefacts of the culturing process [135]

For themost part themechanisms behind the therapeuticbenefit of DNMT inhibition and HDAC inhibitors are notfully understood [99] It has been difficult to model and

measure the effects of histone modifications as the complexcombinatorial nature of the histone code means that eachmodification must be considered in context with othermodifications [35 136] Ongoing and future studies whichdiscriminate between driver and passenger alterations offerimportant insight into the specific alterations which must betargeted to enhance the clinical efficacy of epigenetic therapyDeveloping epigenetic inhibitors which target specific genesor groups of genes such as those genes identified by DeCarvalho et al (eg RAK3 P2RY14 CDO1 BCHE ESX1andARMCX1) would overcome the significant risks and sideeffects of the epigenetic agents currently in use which haveglobal effects [134]

Epigenetic information can also be used to predict clinicaloutcomes and patient responses to specific therapies [137]For example methylation of the DNA repair enzyme O6-methylguanine-DNA methyltransferase gene (MGMT) inglioma predicts a better response to alkylating agents com-monly used in therapy [138] When expressed MGMTrapidly reverses the damage caused by alkylating agents (egtemozolomide) and confers resistance to therapy (Table 1)[139 140] Other epigenetic profiles have been used to pri-oritize or exclude treatment strategies however they lack theclearmechanistic connection seen betweenMGMTand alky-lating agents For instance in non-small cell lung cancer anunmethylated IGFBP3 promoter is correlated to response tocisplatin-based chemotherapies [141] and methylation ofPITX2 predicts the outcomes of individuals with early-stagebreast cancer following adjuvant tamoxifen therapy [142]These and othermarkers have not shown a high degree of sen-sitivity or specificity perhaps because there is no clear mech-anism connecting the gene affected by methylation and theresponse to therapy The addition of methyl groups tocytosine is neither necessary nor sufficient to alter geneexpression thus the measurement of DNA methylation as asurrogate of gene expression or regulation may not be anaccurate tool to predict response to therapy [143]

In hematological cancers where mutations in epigeneticregulators are frequent targeted therapies show signifi-cant promise In EZH2-mutant lymphoma selective EZH2inhibitors have been shown to induce apoptosis with min-imal effects on EZH2 wild-type cells [75] The use of EZH2inhibitors decreases the global H3K27 trimethylation levelsand reactivates genes silenced as a result of mutant EZH2(Table 1) [144] Preliminary data from the use of an EZH2inhibitor tazemetostat in clinical trials of mutant and wild-type EZH2 lymphoma demonstrated a favorable safety andefficacy profile to warrant a phase II trial stratified by muta-tion status [145] Similar approaches have been seen to targetmutant IDH1 in MDS and AML and mutant DOT1L in MLL[77 146 147]While these agents have shown clinical successtheir use is challenged by the observation that epigeneticmodifiers exist in complexes and may target nonhistoneproteins

True epigenetic therapies have yet to cross the thresholdinto precision targetingThemajority of histonemodificationinhibitors are not yet specific enough to precisely targetspecific alterations [148] The resurgence of DNA editing andits clinical applications via the CRISPRCas9 system opens


the door to targeting DNA sequences which are permissive toepigenetic modifications [149ndash151] Deposition or removal ofDNA methylation marks or of chromatin modifications canhave a direct impact on gene expression (reviewed in [152])It remains to be seen how effective these strategies will be forprecision epigenetic targeting in animal or ex vivo models

5 Challenges and Opportunities for the Futureof Precision Medicine

The success of precision therapies regardless of their molec-ular targets depends on three key factors the identificationof patients who will benefit from targeted therapies theability to determine if a therapy is successful during thecourse of treatment and strategies to combat resistance totargeted therapies The study of exceptional responders theuse of ldquoomicsrdquo technologies and approaches to predict andrespond to therapeutic resistance are opportunities to addressthese significant challenges in the effective implementation ofprecision medicine

51 Patient Identification for Precision Approaches The iden-tification of patients who will benefit from therapy hasbeen an enormous challenge even for population-basedapproaches to cancer therapy Research has sought to moder-ate the use of aggressive therapies by identifying patients whosee no increased benefit from aggressive courses of ther-apy with tools such as Oncotype DX a tool for identi-fying precision approaches to treat breast cancer [153] orSnapShot a protocol for identifying driver mutations innon-small cell lung cancer [154] Another example of thisis the characterization of patients with medulloblastomawhere molecular characterization has revealed four distinctmolecular subtypes Wnt sonic hedgehog (Shh) and group3 and group 4 tumors [155] Patients with the Wnt subtypeexhibit long-term survival of approximately 90 makingthem ideal candidates for trials which reduce the intensity ofcurrent standard-of-care therapy [156] This is particularlyimportant asmedulloblastoma primarily affects children andthe side effects of chemotherapy and radiation therapy can bequite severe and have lasting impacts Identifying biomarkersand prognostic patient profileswill allowphysicians to choosethe most appropriate course of therapy to make the use ofexisting generic therapies more precise and minimize themorbidity associated with imprecise treatment approaches(Figure 1)

511 Exceptional Responders Perhaps the greatest oppor-tunity to identify patients who will benefit from currentprecision therapies is by study of exceptional responders It ishypothesized that most clinical trials showingmodest benefitdemonstrate substantial variability among patients (Figure 1)and could be separated into patients who respond exception-ally well to therapy and patients who fail to respond [157] Aprime example of this is the relative success of trastuzumabin treating HER2-positive breast cancer Roughly 25ndash30of all breast cancers are classified as HER2-positive andresponse rates to trastuzumab among this group range from15 to 80 (reviewed in [158]) Thus we could reasonably

hypothesize that a larger study which did not select patientswith HER2 amplifications and instead included all breastcancer patients would have concluded that approximately4ndash20 of patients (compared to 15ndash80 of HER2-positivepatients) would benefit from clinical use of trastuzumabThe same can be hypothesized for many clinical trials thatfail to show any statistically significant benefit there arepatients who demonstrate an objective clinical response [159160] These patients are deemed exceptional responders andnew initiatives aim to profile these individuals to determinewhat differentiates these outliers By definition exceptionalresponders are rare and studies of these outliers in the useof ineffective drugs or those with limited efficacy will lackstatistical power [161]This is a challenge that clinical trials ofthe most precise therapies and stratification approaches willface It will be difficult to determine signal from noiseeven through a comprehensive analysis of sequence dataexpression data epigenetic data and clinical outcomes [161]

One approach may be to view cancer as ldquoa disease ofpathwaysrdquo instead of examining specific distinct genetic orepigenetic alterations [48 161 162] An integrative network-based approach which includes all of the factors affectingcellular phenotypes (includingDNAandmitochondrialDNAsequencing DNA methylation histone modifications non-coding RNA gene expression protein expression and post-translational modifications) will not only inform precisiontreatment but also provide a framework of the hijackedcellular circuitry seen in cancer [163]

52 TumorHeterogeneity Is aChallenge for PrecisionMedicineMutations or other aberrations in the expression of genomicstability genes such as those involved in DNA repair orinduction of apoptosis can drive hypermutable phenotypesin tumors Some colorectal cancers have been found to haveupwards of 100 mutations per megabase of DNA similarfindings were reported in some uterine corpus endometrialcarcinomas and lung adenocarcinomas and squamous cellcarcinomas [49] A high number of mutations are similarlyfound in melanoma [164] Evolution within a particular can-cer rarely occurs as a process affecting a single increasinglyaggressive clone instead the theory of clonal evolution sug-gests evolutionary processes acting on divergent subcloneswhich evolve simultaneously [165ndash167] This divergent evo-lution can result in substantial intratumoral heterogeneitywhich presents a substantial challenge to molecular profilingof tumors It is a major challenge in cancer research to ensurethat minimal samples are taken from clinical specimenswhile still modelling the inherent heterogeneity with relativeaccuracy [168]

Epigenetic phenomena also contribute to tumor hetero-geneity however it is difficult to gain complete understand-ing of epigenetic heterogeneity and its distinct contributionsto cancer progression as the dynamic nature of epigeneticmodifications makes them more difficult to profile over timeand space The use of single-cell analytics and our abilityto analyze cell-free DNA have begun to unravel some ofthese complexities and are discussed below Genomic andepigenomic instability enabled by the processes of oncoge-nesis transformation progression and metastasis alter the


phenotypes of individual tumors While the study of clonalevolution in tumors has been mostly driven by a geneticframework recent evidence in prostate cancer demonstratesthat the epigenome may convergently evolve and contributeto tumor heterogeneity [169] Also findings in pancreaticductal adenocarcinoma have identified that while there islittle heterogeneity in driver mutations epigenetic hetero-geneity contributes to metastatic potential [170 171] Thecomplex interplay between genetics and epigenetics whichallows some tumors to become invasive and metastaticsupports the use of precision cancer medicine to target drivermutations and epigenetic modifications and the respectivechanges induced in cellular biology

Temporal and spatial molecular heterogeneity is a majorobstacle to biomarker discovery and our inability to accu-rately model and measure heterogeneity presents the greatestobstacle to successful precisionmedicine in cancer (Figure 2)For example breast tumors are classified as estrogen receptor-(ER-) positive based on a cut-off of 10 of cells expressingER however a response to therapy may be seen in patientsin whom as few as 1 of cells express ER [172] ER-positivitybased on the 10 cut-off does not accurately predict responseto selective ER modulators like tamoxifen thus it is plausiblethatmolecular heterogeneity affects the response of tumors totreatment [173ndash175] It is clear that the binary distinctionbetween ER-positive and ER-negative does not differentiatebetween those who will respond to tamoxifen and thosewho will not and molecular heterogeneity may help explainthis finding However the main challenge in modellingtumor heterogeneity is in obtaining appropriate samples fromtumors Studies have demonstrated that simultaneous evolu-tion takes place among different clones within a tumor andthese may exist within different spaces of the tumor Specifi-cally analysis of recurrent gliomas revealed that at least halfof the original driver mutations in classical driver genessuch as TP53 were undetectable at recurrence [176] Whilebiomarker discovery is limited by difficulties in appropriatelymeasuring each clone as it exists within a tumor techniquessuch as STAR-FISH that combine the detection of single-nucleotide and copy number alterations at a single-celllevel of resolution will support clinical decision-making forprecision therapies [177]

Accurately measuring and modelling intratumoralgenetic and epigenetic heterogeneity will help determinebiomarkers which will indicate if therapy is successful duringthe course of treatment One possible approach to determinetherapeutic response is by measuring circulating tumorDNA (ctDNA) In one study of melanoma ctDNA wasfound to be relatively consistent and informative as a blood-based biomarker [178] Levels of ctDNA corresponded toresponse and disease progression Similarly a study in breastcancer found that ctDNA predicted metastatic relapse forpatients with early-stage disease and was able to predict thegenetic events found in the metastatic relapse [179] Beyondpredicting relapse ctDNA may also offer insight intomechanisms of resistance For example RAS pathwaymutations have been detected by ctDNA as a mechanismof resistance in colorectal cancer to anti-EGFR therapies[180ndash182]

Measuring epigenetic alterations is also possible inctDNA Detecting methylated SEPT9 ctDNA identifiedapproximately 70 of colorectal cancers [183] Methylationof ctDNA may be a relatively noninvasive way to measure apatientrsquos response to therapy For example the presence ofmethylated GSTP1 DNA in plasma has been used to trackthe response of prostate cancer patients [184] and methy-lation of a panel of ten genes varied between breast cancerpatients achieving partial or complete response and thoseachieving no response to therapy [185] Many other methy-lated biomarkers have been established which correlate withdisease progression [186ndash190]

In addition to the growing sensitivity and specificity ofmeasuring cell-free DNA the advent of single-cell sequenc-ing as a diagnostic tool will improve our understanding ofthe contributions of genetics and epigenetics to spatial andtemporal heterogeneity [191 192] Whole-genome bisulfitesequencing [193 194] or other single-cell analytical tech-niques including single-cell DNase-sequencing [195] andsingle-cell chromosome conformation capture (Hi-C) [196197] will identify important epigenetic patterns which are rel-evant to the success of precision therapies In addition to pro-viding insight into the nature of genetic and epigenetic het-erogeneity these single-cell techniques hold great promise indetermining the role of specific subpopulations of tumorcells to cancer initiation and progression One example ofthis is the high degree of heterogeneity in expression of thehistone linker H10 which was demonstrated to supporttumor cell self-renewal an important consideration for thetumorigenicity of tumor cell subpopulations [198]

521 A Necessary Role for ldquoOmicsrdquo Technologies in MolecularPathology The current molecular pathology toolbox primar-ily detects major chromosomal abnormalities including geneamplifications and deletions Immunohistochemical (IHC)detection of HER2 expression fluorescent in situ hybridiza-tion (FISH) detection of the BCR-ABL translocation andRT-PCR detection of the PML-RARA translocation haveinformed clinical use of targeted agents such as trastuzumabimatinib and retinoic acid Our new understanding of canceras a phenotype influenced by gene expression andmodulatedby epigenetic factors on top of genetic sequences requiresa more detailed view to fully inform the development andselection of targeted therapies This requires use of moreprecise tools to determine both the presence and clinicalrelevance of point mutations and transcriptional modulation(Figure 2) Integrating the use of molecular ldquoomicsrdquo tech-nologies is essential to generate a more complete view ofthe behaviour of cancer and to visualize opportunities forintervention For example limited molecular assays such asPCR and Sanger sequencing have been used to detect knowncancer mutations such as V600E in the BRAF gene (Table 1)These higher-resolution diagnostic tools have guided theuse of specific BRAF inhibitors including vemurafenib anddabrafenib [199 200]Theuse of ldquoomicsrdquo technologies such ascomplete DNA and RNA sequencing and characterization ofprotein andmetabolite levels are beginning to provide amorecomprehensive view of cancer and the unique aberrations ineach occurrence (eg data emerging fromTCGAand ICGC)


Genetics and epigenetics are not two distinct processesthey are intertwined and interregulated at every step Withthis in mind it becomes clear that IHC markers and FISHalone cannot be reliably used for molecular classificationof cancer Molecular pathology that integrates data col-lected using historic and novel interrogative tools to explorepoint mutations epigenetic alterations gene expression andposttranslational modifications can provide the informationnecessary to inform precision therapy (Figure 2)

53 Resistance to Targeted Therapies The final challenge tothe success of precision medicine is the emergence of resis-tance to targeted therapies This is perhaps best modelled bythe series of TKIs developed against the BCR-ABL translo-cation [201] The success of imatinib was dampened by theemergence of resistant variants As a result second- andthird-generation tyrosine kinase inhibitors were developedagainst the BCR-ABL gene product [202ndash205] Finally anovel treatment for CML (omacetaxine) was developedacting independently of the BCR-ABL fusion protein Thishas been successful in patients who have failed treatmentwith earlier BCR-ABL-directed TKIs [206]We should expectthat continuous clonal evolution of cancer cells will enablegenetic and phenotypic variants to escape targeted precisiontherapies

Primary resistance to precision therapies has beenobserved with numerous targeted agents In lung cancerprimary resistance to EGFR- or ALK-targeted tyrosine kinaseinhibitors is a result of genetic alterations in or outside of theprimary target [207 208] The incorporation of genetic andepigenetic information using novel ldquoomicsrdquo technologies andcomputational methods will support the ongoing stratifica-tion of patients beyond the absence or presence of a specificalteration (Figure 2) Additionally in some cases false-positive results in diagnostics may contribute to observedresistance as has been documented for ALK rearrangementsin lung cancer [209] Improvements and advancements indiagnostics will eliminate these misinformed selections oftherapies Acquired or secondary resistance broadly resultsfrom alterations within the therapeutic target activation ofalternative or downstream signaling or phenotypic transfor-mation [210] One approach to combat this is by rationalcombination of therapeutic agents For example combiningthe small molecule venetoclax with the anti-CD20 rituximabmay prevent some acute myeloid leukemias from bypassingBCL2 inhibition [211]

We must attempt to fully map cancerrsquos complex circuitryto stay one step ahead of therapeutic resistance and thismust include ongoing observations of the genetic and epige-netic diversity before during and following treatment Theaccumulation of data from clinical trials of targeted therapiesalone or in combination with existing agents will continue toprovide insight into potential approaches to prevent acquiredresistance

6 Conclusion

The awareness of precision medicine in the public con-sciousness has brought out many questions which have yet

to be answered As we target molecular aberrations withincreasingly rare occurrences (Figure 1) the cost of drugdevelopment forces us to ask how much a cure for cancerperhaps an individual life in the foreseeable future is worthA precise approach rather than a personalized approach tocancer therapy is more cost-effective and is most likely to berealized in any system of socialized medicine As mentionedpreviously the small sample size for specific alterations willlimit statistical power and forces the acceptance of newclinical trial designs An innovative approach to existingmedical policy frameworks will strengthen the future forprecision medicine by accelerating the pipeline from drugdevelopment to approval and sharing information betweenmajor research centers conducting precision medicine trialswill similarly hasten the new age of cancer therapy

On 7 July 2016 US President Barack Obama made apowerful analogy to describe precision medicine stating ldquowewouldnrsquot buy a pair of glasses that doesnrsquot match our eyesightand though plenty of people break their arms everyone getsfitted for their own castrdquo [197] Research focused on exploringthe current threats to the success of precision medicinewill enable clinical oncology to enter what should be thegreatest revolution inmedical history a data-driven precisionapproach to curing cancer Our understanding of geneticsand epigenetics supports their continued investigation asmajor contributors to a malignant phenotype and holds thekey to unlocking the malignant transformation process sothat it can be stopped when it is found

Conflicts of Interest

The authors declare that there are no conflicts of interestregarding the publication of this paper

Acknowledgments

This work was supported by a grant from the CanadianInstitutes of Health Research (CIHR) to Paola Marcato(MOP-130304) Krysta Mila Coyle is an honorary KillamScholar and Scotia Scholar supported by aDoctoral ResearchAward fromCIHR by a DeWolfe Graduate Studentship fromtheDalhousieMedical Research Foundation (DMRF) and bya trainee award from the Beatrice Hunter Cancer ResearchInstitute (BHCRI) with funds provided by the CanadianImperial Bank of Commerce as part of the Terry Fox StrategicHealth Research Training Program in Cancer Research atCIHR Jeanette E Boudreau is the DMRF Cameron CancerScientist Chair and is additionally supported by the BantingResearch Foundation and the BHCRI

References

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[68] M Olivier M Hollstein and P Hainaut ldquoTP53 mutations inhuman cancers origins consequences and clinical userdquo ColdSpring Harbor Perspectives in Biology vol 2 no 1 Article IDa001008 2010

[69] S De and FMichor ldquoDNA secondary structures and epigeneticdeterminants of cancer genome evolutionrdquo Nature Structuraland Molecular Biology vol 18 no 8 pp 950ndash955 2011

[70] J Xia L Han and Z Zhao ldquoInvestigating the relationship ofDNA methylation with mutation rate and allele frequency inthe human genomerdquo BMC Genomics vol 13 article S7 2012

[71] B Schuster-Bockler and B Lehner ldquoChromatin organization isa major influence on regional mutation rates in human cancercellsrdquo Nature vol 488 no 7412 pp 504ndash507 2012

[72] W Timp and A P Feinberg ldquoCancer as a dysregulatedepigenome allowing cellular growth advantage at the expenseof the hostrdquo Nature Reviews Cancer vol 13 no 7 pp 497ndash5102013

[73] C ParkW Qian and J Zhang ldquoGenomic evidence for elevatedmutation rates in highly expressed genesrdquo EMBO Reports vol13 no 12 pp 1123ndash1129 2012

[74] H Yang D Ye K-L Guan and Y Xiong ldquoIDH1 and IDH2mutations in tumorigenesis mechanistic insights and clinicalperspectivesrdquoClinical Cancer Research vol 18 no 20 pp 5562ndash5571 2012

[75] S K Knutson T J Wigle N M Warholic et al ldquoA selectiveinhibitor of EZH2 blocks H3K27 methylation and kills mutantlymphoma cellsrdquo Nature Chemical Biology vol 8 no 11 pp890ndash896 2012

[76] J K Shen G M Cote Y Gao et al ldquoTargeting EZH2-mediatedmethylation of H3K27 inhibits proliferation and migration of


Synovial Sarcoma in vitrordquo Scientific Reports vol 6 Article ID25239 2016

[77] E M Stein G Garcia-Manero D A Rizzieri M Savona RTibes and J K Altman ldquoThe DOT1L Inhibitor EPZ-5676safety and Activity in RelapsedRefractory Patients with MLL-Rearranged Leukemiardquo Blood vol 124 p 387 2014

[78] M Ehrlich ldquoDNAmethylation in cancer toomuch but also toolittlerdquo Oncogene vol 21 no 35 pp 5400ndash5413 2002

[79] A De Capoa A Musolino S Della Rosa et al ldquoDNA demethy-lation is directly related to tumour progression Evidence innormal pre-malignant and malignant cells from uterine cervixsamplesrdquo Oncology Reports vol 10 no 3 pp 545ndash549 2003

[80] B Cadieux T-T Ching S R VandenBerg and J F CostelloldquoGenome-wide hypomethylation in human glioblastomas asso-ciated with specific copy number alteration methylenetetrahy-drofolate reductase allele status and increased proliferationrdquoCancer Research vol 66 no 17 pp 8469ndash8476 2006

[81] H-H Seifert V Schmiemann M Mueller et al ldquoIn situdetection of global DNA hypomethylation in exfoliative urinecytology of patients with suspected bladder cancerrdquo Experimen-tal and Molecular Pathology vol 82 no 3 pp 292ndash297 2007

[82] M Ehrlich ldquoDNA hypomethylation in cancer cellsrdquo Epige-nomics vol 1 no 2 pp 239ndash259 2009

[83] D Aran S Sabato and A Hellman ldquoDNAmethylation of distalregulatory sites characterizes dysregulation of cancer genesrdquoGenome Biology vol 14 no 3 article R21 2013

[84] B S Cobb S Morales-Alcelay G Kleiger K E Brown A GFisher and S T Smale ldquoTargeting of Ikaros to pericentromericheterochromatin by direct DNA bindingrdquo Genes and Develop-ment vol 14 no 17 pp 2146ndash2160 2000

[85] P Sabbattini M Lundgren A Georgiou C-M Chow GWarnes and N Dillon ldquoBinding of Ikaros to the 1205825 promotersilences transcription through a mechanism that does notrequire heterochromatin formationrdquoEMBO Journal vol 20 no11 pp 2812ndash2822 2001

[86] K E Brown J Baxter D Graf M Merkenschlager and AG Fisher ldquoDynamic repositioning of genes in the nucleus oflymphocytes preparing for cell divisionrdquo Molecular Cell vol 3no 2 pp 207ndash217 1999

[87] S M Gasser ldquoPositions of potential Nuclear organization andgene expressionrdquo Cell vol 104 no 5 pp 639ndash642 2001

[88] M Ehrlich K L Buchanan F Tsien et al ldquoDNA methyltrans-ferase 3B mutations linked to the ICF syndrome cause dysregu-lation of lymphogenesis genesrdquoHumanMolecular Genetics vol10 no 25 pp 2917ndash2931 2001

[89] K Hosoya S Yamashita T Ando T Nakajima F Itoh andT Ushijima ldquoAdenomatous polyposis coli 1A is likely to bemethylated as a passenger in human gastric carcinogenesisrdquoCancer Letters vol 285 no 2 pp 182ndash189 2009

[90] D Levanon Y Bernstein V Negreanu et al ldquoAbsence ofRunx3 expression in normal gastrointestinal epithelium callsinto question its tumour suppressor functionrdquoEMBOMolecularMedicine vol 3 no 10 pp 593ndash604 2011

[91] T H Bestor ldquoUnanswered questions about the role of promotermethylation in carcinogenesisrdquoAnnals of theNewYorkAcademyof Sciences vol 983 pp 22ndash27 2003

[92] I B Weinstein and A K Joe ldquoMechanisms of Disease Onco-gene addiction - A rationale for molecular targeting in cancer

therapyrdquo Nature Clinical Practice Oncology vol 3 no 8 pp448ndash457 2006

[93] M G Vander Heiden ldquoTargeting cancer metabolism a thera-peutic window opensrdquo Nature Reviews Drug Discovery vol 10no 9 pp 671ndash684 2011

[94] A H Shain I Yeh I Kovalyshyn et al ldquoThe genetic evolutionof melanoma from precursor lesionsrdquo New England Journal ofMedicine vol 373 no 20 pp 1926ndash1936 2015

[95] S T Henderson and T D Petes ldquoInstability of simple sequenceDNA in Saccharomyces cerevisiaerdquo Molecular and CellularBiology vol 12 no 6 pp 2749ndash2757 1992

[96] C R Boland and A Goel ldquoMicrosatellite instability in colorec-tal cancerrdquoGastroenterology vol 138 no 6 pp 2073ndash2087 2010

[97] M R Jones K A Schrader Y Shen et al ldquoResponseto angiotensin blockade with irbesartan in a patient withmetastatic colorectal cancerrdquo Annals of Oncology vol 27 no 5Article ID mdw018 pp 801ndash806 2016

[98] A J Redig and P A Janne ldquoBasket trials and the evolution ofclinical trial design in an era of genomic medicinerdquo Journal ofClinical Oncology vol 33 no 9 pp 975ndash977 2015

[99] T K Kelly D D De Carvalho and P A Jones ldquoEpigeneticmodifications as therapeutic targetsrdquoNature Biotechnology vol28 no 10 pp 1069ndash1078 2010

[100] S B Baylin and J E Ohm ldquoEpigenetic gene silencing incancermdasha mechanism for early oncogenic pathway addictionrdquoNature Reviews Cancer vol 6 no 2 pp 107ndash116 2006

[101] Y Ying and Q Tao ldquoEpigenetic disruption of the WNT120573-catenin signaling pathway in human cancersrdquo Epigenetics vol4 no 5 pp 34ndash39 2009

[102] B Mair S Kubicek and S M B Nijman ldquoExploiting epigeneticvulnerabilities for cancer therapeuticsrdquo Trends in Pharmacolog-ical Sciences vol 35 no 3 pp 136ndash145 2014

[103] H Suzuki D N Watkins K-W Jair et al ldquoEpigenetic inac-tivation of SFRP genes allows constitutive WNT signaling incolorectal cancerrdquo Nature Genetics vol 36 no 4 pp 417ndash4222004

[104] M M Taketo ldquoShutting down Wnt signal-activated cancerrdquoNature Genetics vol 36 no 4 pp 320ndash322 2004

[105] Y C Wen D H Wang C Y RayWhay J Luo W Gu andS B Baylin ldquoTumor suppressor HIC1 directly regulates SIRT1to modulate p53-dependent DNA-damage responsesrdquo Cell vol123 no 3 pp 437ndash448 2005

[106] J Ihalainen S Pakkala E-R Savolainen S-E Jansson andA Palotie ldquoHypermethylation of the calcitonin gene in themyelodysplastic syndromesrdquo Leukemia vol 7 no 2 pp 263ndash267 1993

[107] T Shimamoto J H Ohyashiki and K Ohyashiki ldquoMethylationof p15INK4b and E-cadherin genes is independently correlatedwith poor prognosis in acute myeloid leukemiardquo LeukemiaResearch vol 29 no 6 pp 653ndash659 2005

[108] H Cechova P Lassuthova L Novakova et al ldquoMonitoring ofmethylation changes in 9p21 region in patients with myelodys-plastic syndromes and acutemyeloid leukemiardquoNeoplasma vol59 no 2 pp 168ndash174 2012

[109] S K Sadashiv CHilton CKhan et al ldquoEfficacy and tolerabilityof treatment with azacitidine for 5 days in elderly patients withacute myeloid leukemiardquo Cancer Medicine vol 3 no 6 pp1570ndash1578 2014


[110] K Raj and G J Mufti ldquoAzacytidine (Vidaza) in the treatmentof myelodysplastic syndromesrdquo Therapeutics and Clinical RiskManagement vol 2 no 4 pp 377ndash388 2006

[111] F Creusot G Acs and J K Christman ldquoInhibition of DNAmethyltransferase and induction of Friend erythroleukemia celldifferentiation by 5-azacytidine and 5-aza-21015840-deoxycytidinerdquoJournal of Biological Chemistry vol 257 no 4 pp 2041ndash20481982

[112] J K Christman ldquo5-Azacytidine and 5-aza-21015840-deoxycytidine asinhibitors of DNA methylation mechanistic studies and theirimplications for cancer therapyrdquo Oncogene vol 21 no 35 pp5483ndash5495 2002

[113] K Ghoshal J Datta S Majumder et al ldquo5-Aza-deoxycytidineinduces selective degradation of DNA methyltransferase 1 bya proteasomal pathway that requires the KEN box bromo-adjacent homology domain and nuclear localization signalrdquoMolecular and Cellular Biology vol 25 no 11 pp 4727ndash47412005

[114] P A Jones and S M Taylor ldquoHemimethylated duplexDNAs prepared from 5-azacytidine-treated cellsrdquo Nucleic AcidsResearch vol 9 no 12 pp 2933ndash2947 1981

[115] T Murakami X Li J Gong U Bhatia F Traganos and ZDarzynkiewicz ldquoInduction of Apoptosis by 5-Azacytidine drugConcentration-dependent Differences in Cell Cycle SpecificityrdquoCancer Research vol 55 no 14 pp 3093ndash3098 1995

[116] RKhan J Schmidt-MendeMKarimi et al ldquoHypomethylationand apoptosis in 5-azacytidine-treated myeloid cellsrdquo Experi-mental Hematology vol 36 no 2 pp 149ndash157 2008

[117] M S Soengas P Capodieci and D Polsky ldquoInactivation of theapoptosis effector Apaf-1 in malignant melanomardquo Nature vol409 no 6817 pp 207ndash211 2001

[118] A P Bird and A P Wolffe ldquoMethylation-induced repressionmdashbelts braces and chromatinrdquo Cell vol 99 no 5 pp 451ndash4541999

[119] A W Roberts M S Davids J M Pagel et al ldquoTargeting BCL2with venetoclax in relapsed chronic lymphocytic leukemiardquoNew England Journal of Medicine vol 374 no 4 pp 311ndash3222016

[120] S S Ramalingam R A Parise R K Ramananthan et al ldquoPhaseI and pharmacokinetic study of vorinostat a histone deacetylaseinhibitor in combination with carboplatin and paclitaxel foradvanced solid malignanciesrdquo Clinical Cancer Research vol 13no 12 pp 3605ndash3610 2007

[121] S S RamalingamM LMaitland P Frankel et al ldquoCarboplatinand paclitaxel in combination with either vorinostat or placebofor first-line therapy of advanced non-small-cell lung cancerrdquoJournal of Clinical Oncology vol 28 no 1 pp 56ndash62 2010

[122] B Yang J Wu N Maddodi Y Ma V Setaluri and B JLongley ldquoEpigenetic control of MAGE gene expression by theKIT tyrosine kinaserdquo Journal of Investigative Dermatology vol127 no 9 pp 2123ndash2128 2007

[123] P van der Bruggen C Traversari P Chomez et al ldquoA geneencoding an antigen recognized by cytolytic T lymphocytes ona human melanomardquo Science vol 254 no 5038 pp 1643ndash16471991

[124] M Sang LWang C Ding et al ldquoMelanoma-associated antigengenesmdashan updaterdquo Cancer Letters vol 302 no 2 pp 85ndash902011

[125] S J Jang J C Soria L Wang K A Hassan R C Morice andG L Walsh ldquoActivation of melanoma antigen tumor antigensoccurs early in lung carcinogenesisrdquo Cancer Research vol 61pp 7959ndash7963 2001

[126] M Sang Y Lian X Zhou and B Shan ldquoMAGE-A familyAttractive targets for cancer immunotherapyrdquo Vaccine vol 29no 47 pp 8496ndash8500 2011

[127] A P Rapoport E A Stadtmauer G K Binder-Scholl OGoloubevaD TVogl and S F Lacey ldquoNY-ESO-1-specificTCR-engineeredT cellsmediate sustained antigen-specific antitumoreffects in myelomardquo Nature Medicine vol 21 pp 914ndash921 2015

[128] K B Chiappinelli P L Strissel A Desrichard et al ldquoInhibitingDNAMethylation Causes an Interferon Response in Cancer viadsRNA Including Endogenous Retrovirusesrdquo Cell vol 162 no5 pp 974ndash986 2015

[129] D Roulois H Loo Yau R Singhania et al ldquoDNA-demeth-ylating agents target colorectal cancer cells by inducing viralmimicry by endogenous transcriptsrdquo Cell vol 162 no 5 pp961ndash973 2015

[130] R A Juergens J Wrangle F P Vendetti et al ldquoCombinationepigenetic therapy has efficacy in patients with refractoryadvanced non-small cell lung cancerrdquo Cancer Discovery vol 1no 7 pp 598ndash607 2011

[131] J Wrangle W Wang A Koch et al ldquoAlterations of immuneresponse of non-small cell lung cancer with AzacytidinerdquoOncotarget vol 4 no 11 pp 2067ndash2079 2013

[132] S P Shah A Roth R Goya A Oloumi G Ha and Y Zhaoldquohe clonal andmutational evolution spectrumof primary triple-negative breast cancersrdquo Nature vol 486 pp 395ndash399 2012

[133] A Bashashati G Ha A Tone et al ldquoDistinct evolutionary tra-jectories of primary high-grade serous ovarian cancers revealedthrough spatial mutational profilingrdquo Journal of Pathology vol231 no 1 pp 21ndash34 2013

[134] D De Carvalho S Sharma J S You et al ldquoDNA methylationscreening identifies driver epigenetic events of cancer cellsurvivalrdquo Cancer Cell vol 21 no 5 pp 655ndash667 2012

[135] M F Paz M F Fraga S Avila et al ldquoA systematic profile ofDNAmethylation in human cancer cell linesrdquo Cancer Researchvol 63 no 5 pp 1114ndash1121 2003

[136] K E Gardner C D Allis and B D Strahl ldquoOperating onchromatin a colorful language where context mattersrdquo Journalof Molecular Biology vol 409 no 1 pp 36ndash46 2011

[137] M Zhang S Zhang Y Wen et al ldquoDNA methylation patternscan estimate nonequivalent outcomes of breast cancer with thesame receptor subtypesrdquo PLoS ONE vol 10 no 11 Article IDe0142279 2015

[138] M Esteller J Garcia-Foncillas and E Andion ldquoInactivationof the DNA-repair gene MGMT and the clinical response ofgliomas to alkylating agentsrdquo The New England Journal ofMedicine vol 343 no 19 pp 1350ndash1354 2000

[139] A E Pegg M E Dolan and R C Moschel ldquoStructureFunction and Inhibition of O6-Alkylguanine-DNAAlkyltrans-feraserdquo Progress in Nucleic Acid Research andMolecular Biologyvol 51 pp 167ndash223 1995

[140] D B Ludlum ldquoDNA alkylation by the haloethylnitrosoureasNature of modifications produced and their enzymatic repairor removalrdquo Mutation Research - Fundamental and MolecularMechanisms of Mutagenesis vol 233 no 1-2 pp 117ndash126 1990


[141] I I de Caceres M Cortes-Sempere C Moratilla et al ldquoIGFBP-3 hypermethylation-derived deficiency mediates cisplatin resis-tance in non-small-cell lung cancerrdquo Oncogene vol 29 no 11pp 1681ndash1690 2010

[142] S Maier I Nimmrich T Koenig et al ldquoDNA-methylation ofthe homeodomain transcription factor PITX2 reliably predictsrisk of distant disease recurrence in tamoxifen-treated node-negative breast cancer patients - Technical and clinical valida-tion in amulti-centre setting in collaborationwith the EuropeanOrganisation for Research and Treatment of Cancer (EORTC)PathoBiology grouprdquo European Journal of Cancer vol 43 no 11pp 1679ndash1686 2007

[143] P A Jones and P W Laird ldquoCancer epigenetics comes of agerdquoNature Genetics vol 21 no 2 pp 163ndash167 1999

[144] M T McCabe H M Ott G Ganji et al ldquoEZH2 inhibition asa therapeutic strategy for lymphoma with EZH2-activatingmutationsrdquo Nature vol 491 no 7427 pp 108ndash112 2012

[145] V Ribrag J-C Soria J-M Michot et al ldquoPhase 1 Study ofTazemetostat (EPZ-6438) an Inhibitor of Enhancer of Zeste-Homolog 2 (EZH2) Preliminary Safety andActivity inRelapsedor Refractory Non-Hodgkin Lymphoma (NHL) PatientsrdquoBlood vol 126 p 473 2015

[146] F Wang J Travins B DeLaBarre et al ldquoTargeted inhibition ofmutant IDH2 in leukemia cells induces cellular differentiationrdquoScience vol 340 no 6132 pp 622ndash626 2013

[147] D Rohle J Popovici-Muller N Palaskas et al ldquoAn inhibitorof mutant IDH1 delays growth and promotes differentiation ofglioma cellsrdquo Science vol 340 no 6132 pp 626ndash630 2013

[148] A C West and R W Johnstone ldquoNew and emerging HDACinhibitors for cancer treatmentrdquoThe Journal of Clinical Investi-gation vol 124 no 1 pp 30ndash39 2014

[149] S Yao Z He and C Chen ldquoCRISPRCas9-mediated genomeediting of epigenetic factors for cancer therapyrdquo Human GeneTherapy vol 26 no 7 pp 463ndash471 2015

[150] I B Hilton A M DrsquoIppolito C M Vockley et al ldquoEpigenomeediting by a CRISPR-Cas9-based acetyltransferase activatesgenes from promoters and enhancersrdquo Nature Biotechnologyvol 33 no 5 pp 510ndash517 2015

[151] A Vojta P Dobrinic V Tadic et al ldquoRepurposing the CRISPR-Cas9 system for targeted DNA methylationrdquo Nucleic AcidsResearch vol 44 no 12 pp 5615ndash5628 2016

[152] G Kungulovski and A Jeltsch ldquoEpigenome Editing State of theArt Concepts and Perspectivesrdquo Trends in Genetics vol 32 no2 pp 101ndash113 2016

[153] S Paik G Tang S Shak et al ldquoGene expression and bene-fit of chemotherapy in women with node-negative estrogenreceptor-positive breast cancerrdquo Journal of Clinical Oncologyvol 24 no 23 pp 3726ndash3734 2006

[154] R S Heist and J A Engelman ldquoSnapShot non-small cell lungcancerrdquo Cancer Cell vol 21 no 3 pp 448ndashe2 2012

[155] P A Northcott A Korshunov HWitt et al ldquoMedulloblastomacomprises four distinct molecular variantsrdquo Journal of ClinicalOncology vol 29 no 11 pp 1408ndash1414 2011

[156] S E S Leary and J M Olson ldquoThe molecular classification ofmedulloblastoma Driving the next generation clinical trialsrdquoCurrent Opinion in Pediatrics vol 24 no 1 pp 33ndash39 2012

[157] D K Chang S M Grimmond T R J Evans and A VBiankin ldquoMining the genomes of exceptional respondersrdquoNature Reviews Cancer vol 14 no 5 pp 291-292 2014

[158] R Bartsch C Wenzel and G G Steger ldquoTrastuzumab inthe management of early and advanced stage breast cancerrdquoBiologics Targets andTherapy vol 1 pp 19ndash31 2007

[159] G Iyer A J Hanrahan M I Milowsky et al ldquoGenomesequencing identifies a basis for everolimus sensitivityrdquo Sciencevol 338 no 6104 p 221 2012

[160] N Wagle B C Grabiner E M Van Allen et al ldquoResponse andacquired resistance to everolimus in anaplastic thyroid cancerrdquoThe New England Journal of Medicine vol 371 no 15 pp 1426ndash1433 2014

[161] V Marx ldquoCancer a most exceptional responserdquo Nature vol520 no 7547 pp 389ndash393 2015

[162] M Xu M-C J Kao J Nunez-Iglesias J R Nevins M Westand X J Jasmine ldquoAn integrative approach to characterizedisease-specific pathways and their coordination A case studyin cancerrdquo BMC Genomics vol 9 no 1 article S12 2008

[163] S Volinia M Galasso S Costinean et al ldquoReprogramming ofmiRNA networks in cancer and leukemiardquo Genome Researchvol 20 no 5 pp 589ndash599 2010

[164] B Vogelstein N Papadopoulos V E Velculescu S Zhou LA Diaz Jr and K W Kinzler ldquoCancer genome landscapesrdquoScience vol 340 no 6127 pp 1546ndash1558 2013

[165] R A Burrell and C Swanton ldquoRe-evaluating clonal dominancein cancer evolutionrdquo Trends in Cancer vol 2 no 5 pp 263ndash2762016

[166] MGerlinger S Horswell J Larkin et al ldquoGenomic architectureand evolution of clear cell renal cell carcinomas defined bymultiregion sequencingrdquo Nature Genetics vol 46 no 3 pp225ndash233 2014

[167] D A Landau S L Carter P Stojanov et al ldquoEvolution andimpact of subclonal mutations in chronic lymphocytic leu-kemiardquo Cell vol 152 no 4 pp 714ndash726 2013

[168] D F Ransohoff ldquoBias as a threat to the validity of cancermolecular-marker researchrdquo Nature Reviews Cancer vol 5 no2 pp 142ndash149 2005

[169] D Brocks Y Assenov S Minner et al ldquoIntratumor DNAmethylation heterogeneity reflects clonal evolution in aggres-sive prostate cancerrdquo Cell Reports vol 8 no 3 pp 798ndash8062014

[170] A P Makohon-Moore M Zhang J G Reiter et al ldquoLim-ited heterogeneity of known driver gene mutations amongthe metastases of individual patients with pancreatic cancerrdquoNature Genetics vol 49 no 3 pp 358ndash366 2017

[171] O G McDonald X Li T Saunders et al ldquoEpigenomic repro-gramming during pancreatic cancer progression links anabolicglucose metabolism to distant metastasisrdquo Nature Genetics vol49 no 3 pp 367ndash376 2017

[172] CM Lin J Jaswal T Vandenberg A Tuck andM BrackstoneldquoWeakly hormone receptor- positive breast cancer and use ofadjuvant hormonal therapyrdquo Current Oncology vol 20 no 6pp e612ndashe613 2013

[173] P J McDonald R Carpenter G T Royle and I Taylor ldquoPoorresponse of breast cancer to tamoxifenrdquo Postgraduate MedicalJournal vol 66 no 782 pp 1029ndash1031 1990

[174] NHarbeck andA Rody ldquoLost in translation Estrogen receptorstatus and endocrine responsiveness in breast cancerrdquo Journal ofClinical Oncology vol 30 no 7 pp 686ndash689 2012


[175] F Lumachi A Brunello M Maruzzo U Basso and S M MBasso ldquoTreatment of estrogen receptor-positive breast cancerrdquoCurrent Medicinal Chemistry vol 20 no 5 pp 596ndash604 2013

[176] B E Johnson T Mazor C Hong et al ldquoMutational analysisreveals the origin and therapy-driven evolution of recurrentgliomardquo Science vol 343 no 6167 pp 189ndash193 2014

[177] M Janiszewska L Liu V Almendro et al ldquoIn situ single-cell analysis identifies heterogeneity for PIK3CA mutation andHER2 amplification in HER2-positive breast cancerrdquo NatureGenetics vol 47 no 10 pp 1212ndash1219 2015

[178] S Chang-Hao Tsao J Weiss C Hudson et al ldquoMonitoringresponse to therapy in melanoma by quantifying circulatingtumour DNA with droplet digital PCR for BRAF and NRASmutationsrdquo Scientific Reports vol 5 article 11198 2015

[179] I Garcia-Murillas G Schiavon B Weigelt et al ldquoMutationtracking in circulating tumor DNA predicts relapse in earlybreast cancerrdquo Science Translational Medicine vol 7 no 302Article ID 302ra133 2015

[180] L A Diaz Jr R T Williams J Wu et al ldquoThe molecularevolution of acquired resistance to targeted EGFR blockade incolorectal cancersrdquoNature vol 486 no 7404 pp 537ndash540 2012

[181] S Misale R Yaeger S Hobor et al ldquoEmergence of KRASmutations and acquired resistance to anti-EGFR therapy incolorectal cancerrdquoNature vol 486 no 7404 pp 532ndash536 2012

[182] SMisale S Arena S Lamba et al ldquoBlockade of EGFRandMEKintercepts heterogeneous mechanisms of acquired resistance toanti-EGFR therapies in colorectal cancerrdquo Science TranslationalMedicine vol 6 no 224 Article ID 224ra26 2014

[183] T deVos R Tetzner F Model et al ldquoCirculating methylatedSEPT9 DNA in plasma is a biomarker for colorectal cancerrdquoClinical Chemistry vol 55 no 7 pp 1337ndash1346 2009

[184] K L Mahon W Qu J Devaney et al ldquoMethylated GlutathioneS-transferase 1 (mGSTP1) is a potential plasma free DNAepigenetic marker of prognosis and response to chemotherapyin castrate-resistant prostate cancerrdquo British Journal of Cancervol 111 no 9 pp 1802ndash1809 2014

[185] M J Fackler Z L Bujanda C Umbricht et al ldquoNovelmethylated biomarkers and a robust assay to detect circulatingtumor dna inmetastatic breast cancerrdquoCancer Research vol 74no 8 pp 2160ndash2170 2014

[186] H Fiegl S Millinger E Mueller-Holzner et al ldquoCirculatingtumor-specific DNA a marker for monitoring efficacy ofadjuvant therapy in cancer patientsrdquo Cancer Research vol 65no 4 pp 1141ndash1145 2005

[187] M Zurita P C Lara R del Moral et al ldquoHypermethylated14-3-3-120590 and ESR1 gene promoters in serum as candidatebiomarkers for the diagnosis and treatment efficacy of breastcancer metastasisrdquo BMC Cancer vol 10 article 217 2010

[188] G Sharma S Mirza R Parshad S D Gupta and R RalhanldquoDNA methylation of circulating DNA a marker for moni-toring efficacy of neoadjuvant chemotherapy in breast cancerpatientsrdquo Tumour Biology The Journal of the InternationalSociety for Oncodevelopmental Biology andMedicine vol 33 no6 pp 1837ndash1843 2012

[189] A A Ponomaryova E Y Rykova N V Cherdyntseva etal ldquoPotentialities of aberrantly methylated circulating DNAfor diagnostics and post-treatment follow-up of lung cancerpatientsrdquo Lung Cancer vol 81 no 3 pp 397ndash403 2013

[190] K Warton K L Mahon and G Samimi ldquoMethylated circu-lating tumor DNA in blood Power in cancer prognosis andresponserdquo Endocrine-Related Cancer vol 23 no 3 pp R157ndashR171 2016

[191] Y Hou H Guo C Cao et al ldquoSingle-cell triple omics sequenc-ing reveals genetic epigenetic and transcriptomic heterogene-ity in hepatocellular carcinomasrdquo Cell Research vol 26 no 3pp 304ndash319 2016

[192] F Schmidt and T Efferth ldquoTumor heterogeneity single-cellsequencing and drug resistancerdquo Pharmaceuticals vol 9 no 2article 33 2016

[193] S A Smallwood H J Lee C Angermueller et al ldquoSingle-cell genome-wide bisulfite sequencing for assessing epigeneticheterogeneityrdquo Nature Methods vol 11 no 8 pp 817ndash820 2014

[194] M Farlik N C Sheffield A Nuzzo et al ldquoSingle-Cell DNAmethylome sequencing and bioinformatic inference of epige-nomic cell-state dynamicsrdquo Cell Reports vol 10 no 8 pp 1386ndash1397 2015

[195] W Jin Q Tang M Wan et al ldquoGenome-wide detection ofDNase i hypersensitive sites in single cells and FFPE tissuesamplesrdquo Nature vol 528 no 7580 pp 142ndash146 2015

[196] N L van Berkum E Lieberman-Aiden L Williams et al ldquoHi-C a method to study the three-dimensional architecture ofgenomesrdquo Journal of Visualized Experiments JoVE no 39 2010

[197] T Nagano Y Lubling T J Stevens et al ldquoSingle-cell Hi-Creveals cell-to-cell variability in chromosome structurerdquoNaturevol 502 no 7469 pp 59ndash64 2013

[198] C M Torres A Biran M J Burney et al ldquoThe linkerhistone H10 generates epigenetic and functional intratumorheterogeneityrdquo Science vol 353 no 6307 p aaf1644 2016

[199] A Sharma S R Shah H Illum and J Dowell ldquoVemurafenibTargeted inhibition ofmutated BRAF for treatment of advancedmelanoma and its potential in other malignanciesrdquo Drugs vol72 no 17 pp 2207ndash2222 2012

[200] A M Menzies G V Long and R Murali ldquoDabrafenib and itspotential for the treatment of metastatic melanomardquo DrugDesign Development andTherapy vol 6 pp 391ndash405 2012

[201] K M Coyle M L Thomas M Sultan and P MarcatoldquoTargeting key stemness-related pathways in human cancersrdquo inCancer Stem Cells Emerg Concepts Future Perspect Transl Oncol[Internet] S Babashah Ed pp 393ndash443 Springer InternationalPublishing Cambridge UK 2015

[202] J M Golas K Arndt C Etienne et al ldquoSKI-606 a 4-anilino-3-quinolinecarbonitrile dual inhibitor of Src and Abl kinases is apotent antiproliferative agent against chronic myelogenousleukemia cells in culture and causes regression of K562xenografts in nude micerdquo Cancer Research vol 63 no 2 pp375ndash381 2003

[203] L J Lombardo F Y Lee P Chen et al ldquoDiscovery of N-(2-chloro-6-methylphenyl)-2-(6-(4-(2-hydroxyethyl)- piperazin-1-yl)-2-methylpyrimidin-4-ylamino)thiazole-5-carboxamide(BMS-354825) a dual SrcAbl kinase inhibitor with potentantitumor activity in preclinical assaysrdquo Journal of MedicinalChemistry vol 47 no 27 pp 6658ndash6661 2004

[204] E Weisberg P W Manley W Breitenstein et al ldquoCharacter-ization of AMN107 a selective inhibitor of native and mutantBcr-Ablrdquo Cancer Cell vol 7 pp 129ndash141 2005


[205] P Valent ldquoImatinib-resistant chronicmyeloid leukemia (CML)current concepts on pathogenesis and new emerging pharma-cologic approachesrdquo Biologics Targets andTherapy vol 1 no 4pp 433ndash448 2007

[206] P Perez-Galan G Roue N Villamor E Campo and DColomer ldquoThe BH3-mimetic GX15-070 synergizes with borte-zomib in mantle cell lymphoma by enhancing Noxa-mediatedactivation of Bakrdquo Blood vol 109 no 10 pp 4441ndash4449 2007

[207] G R Oxnard P C Lo M Nishino et al ldquoNatural history andmolecular characteristics of lung cancers harboring egfr exon20 insertionsrdquo Journal of Thoracic Oncology vol 8 no 2 pp179ndash184 2013

[208] A B Turke K Zejnullahu Y-L Wu et al ldquoPreexistence andclonal selection ofMETamplification inEGFRmutantNSCLCrdquoCancer Cell vol 17 no 1 pp 77ndash88 2010

[209] L M Sholl S Weremowicz S W Gray et al ldquoCombined useof ALK immunohistochemistry and FISH for optimal detectionof ALK-rearranged lung adenocarcinomasrdquo Journal of ThoracicOncology vol 8 no 3 pp 322ndash328 2013

[210] J J Lin and A T Shaw ldquoResisting resistance targeted therapiesin lung cancerrdquoTrends in Cancer vol 2 no 7 pp 350ndash364 2016

[211] AW Roberts S Ma DM Brander T J Kipps J C Barrientosand M S Davids ldquoDetermination of recommended phase 2dose of ABT-199 (GDC-0199) combined with Rituximab (R) inpatients with RelapsedRefractory (RR) chronic lymphocyticleukemia (CLL)rdquo Blood vol 124 p 325 2014

Submit your manuscripts athttpswwwhindawicom

Stem CellsInternational

Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014


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Behavioural Neurology

EndocrinologyInternational Journal of



Disease Markers


BioMed Research International

OncologyJournal of



Oxidative Medicine and Cellular Longevity


PPAR Research

The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014

Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014

Journal of

ObesityJournal of



Computational and Mathematical Methods in Medicine

OphthalmologyJournal of


Diabetes ResearchJournal of



Research and TreatmentAIDS


Gastroenterology Research and Practice


Parkinsonrsquos Disease

Evidence-Based Complementary and Alternative Medicine

Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom


Precision Medicine The specific targeting of molecular abnormalities and the stratification of patients who respond to specific drugsCan be used ldquooff the shelfrdquoPersonalized Medicine The most individualized form of precision therapy tailored uniquely for each patient Must be engineeredfor each patient

Box 1 Key terms

ancient physicians who have shaped the current practiceof medicine considered cancer as an incurable disease [3]Cancer treatments have developed substantially since theypracticedmedicine which is demonstrated by improvementsto patient health and survival

Treatment for those afflicted with cancers originallyused medicines such as extracts from chickpea adderwortstinging nettle and other plants [3] Surgical approaches totreat cancer have been described as early as the first centuryAD calling for removal of the affected part accompanied bythe now relatively obsolete practice of blood-letting in someindividuals [3] Cancer therapy through the 19th centuryand most of the 20th century did not deviate substantiallyfrom these ancient practices of medicine however improvedsurgical precision pain management and sanitation havesteadily improved patient outcomes

Surgical excision to debulk tumors remains a stalwartof cancer therapy and combinations of medicines naturalextracts chemicals and radiation have been introduced inan attempt to limit the rapid cellular growth associated withresidual tumor cells Cancer therapy experienced its firstmajor revolution in the mid-20th century with the use ofnitrogen mustards following the observation that mustardgas exposure correlated with depletion of lymphocytes in theblood of soldiers during World War II [4ndash6] This prompteda hypothesis that nitrogen mustard compounds could beused to inhibit the growth of white blood cells which isbeneficial to treat and cure leukemias and lymphomas Atthe same time Sidney Farber demonstrated that folic acidcould accelerate the growth of leukemia cells This led toclinical trials of methotrexate a folate antagonist to treatleukemia [6 7] A third project discovered antitumor effectsof the antibiotic actinomycin D which was used throughoutthe 1950s and 1960s in pediatric tumors [6 8] Finally amajor addition to the therapeutic regime of surgery andchemotherapy that Hippocrates and Galen could likely nothave envisioned is the use of ionizing radiation during the20th century Observed as early as 1903 Charles Leonardwrote that radiation therapy initially applied as palliativecare resulted in cures and restored patientsrsquo health [9]Although these approaches improved the survival of patientswith cancer they remained relatively unrefined with a highrisk of acute complications

Until the late 1900s cancer chemotherapy used genericcytotoxic drugs that aimed to inhibit rapid cellular prolifera-tion a characteristic hallmark of malignant cells The arsenalof cancer chemotherapies expanded to include 5-fluorouracilvinca alkaloids platinum agents and taxanes [10ndash13] whichthough effective at controlling malignant proliferation byinhibiting cellular division have little precision for specifictumors and often carry high-risk side effect profiles

Cancer is increasingly considered as a collection ofdiseases with characteristics derived from their tissues andcell types of origin and the mutations that drive themChemotherapy radiotherapy and surgical therapy are nowselected and combined based on their efficacy for particularcancers and histologies and the process for treating eachpatient is informed by their specific disease These strategiesto stratify cancer treatment based on the tissue of originand the specific type of transformed cell were the firstrefinement toward amore patient-centric treatment of cancer(Figure 1)

The next phase of cancer therapy precision therapy willleverage the ability to target specific molecular features totreat a cancer based on its characteristics rather than itstissue of origin alone More detailed understanding of tumorbiology has revealed that each individual tumor accumu-lates a unique set of alterations that allow it to escape thenormal checkpoints thatmaintain homeostasis Neverthelessindividual cancers harbour features that allow uncontrolledgrowth such as growth factor or receptor overexpression andloss of apoptosis and cell cycle control mechanisms whichmanifest as molecular features that can be targeted with agrowing arsenal of drugs Refining the description of cancerto a unique set of alterations describing each individual tumorwill enable precision medicine and inform the best treatmentapproach to target every tumor and limit the application ofineffective therapies (Figure 1)

Molecular understanding of tissue development hor-mones and required signals for cell proliferation pushedthe development of tamoxifen an estrogen receptor (ER)antagonist originally developed in an attempt to find newcontraceptives and cholesterol-lowering drugs (Table 1) [1415] Tamoxifen was licensed for use in the US for advancedbreast cancer patients in 1972 and its current success intreating patients with ER positive breast cancers has beencalled a catalyst for the precisionmedicine approach to cancertherapy [16] The 1990s and early 2000s saw the success ofother treatments aimed at molecular targets such as ima-tinib against the BCR-ABL translocation seen in chronicmyelogenous leukemia rituximab (anti-CD20) as a treatmentfor B-cell lymphomas and retinoic acid for treatment ofPML-RAR fusion acute promyelocytic leukemia (Table 1)[17ndash21] In the same decade trastuzumab was approved forthe treatment of breast cancer patients with amplification ofERBB2 (human epidermal growth factor receptor 2 alsoknown asHER2neu) [22]More recently checkpoint inhibit-ing antibodies anti-PD1 (nivolumab) and anti-CTLA-4 (ipil-imumab) (Table 1) are being systematically applied in clin-ical trials of particular cancer types [23ndash25] While thesetherapies illustrate the beginnings of cancer treatments that






(a)





(b)









Table1Selected

listo

fpreciselytargeted

molecular

alteratio

nsin

cancer

Genes

ymbo

lGenen

ame

Effecto

falteratio

nMajor

associations

with

specifictum

ortypes

Implicated

therapy


BCR-ABL

Breakp

oint

cluste

rregion

Abelsonmurine

leuk

emiaviraloncogeneh

omolog

fusio

nprotein

Com

prom

isesfi

delityof

DNArepair

deregu

latesp

roliferation

impairs

apop

tosis

anddifferentiatio

nCh

ronicm

yelogeno

usleuk

emia

Imatinibdasatinib

HRA

SKR

AS

HarveyKr

isten

ratsarcomav

iraloncogene

homolog

Con

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gNon

-smallcelllun

gcancer

Salirasib

BRAF

v-Ra

fmurines

arcomav

iraloncogene

homolog

BCon

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gMelanom

aV60

0Eor

V60

0Kmutations


BCL2

B-celllymph

omaleuk

emia-2

Impairs

apop

tosis

Leuk

emialym

phom

amelanom

aVe

netocla

xTu

mor

suppresso

rgenes

BRCA

12Breastcancer

12Im

paire

dDNArepair


PARP

inhibitor(via

synthetic

lethality

)Ep

igeneticmodify

ingg

enes

IDH12lowastlowast

Isocitrated

ehydrogenase

DNAhyperm

ethylatio

ndisrup

tsdifferentiatio

nAc

utem

yeloid

leuk

emia(A

ML)

AG120AG

221AG

881

EZH2

Enhancer

ofzeste

2po

lycombrepressiv

ecomplex

2subu

nit

Inhibitsapop

tosissilences

byH3K

27trim

ethylatio

nLymph

oma

Tazemetostat

DOT1L

DOT1-like

histo

neH3K

79methyltransfe

rase


nandapop

tosis


Pino

metostat

DNMT

DNAmethyltransfe

rase

Disr

uptsno

rmalpatte

rnso

fDNAmethylatio


Azacytid

ine

decitabine

HDAC

Histon

edeacetylases

Disr

uptsno

rmalpatte

rnso

fhiston

eacetylatio


Vorin

ostatromidepsin

Othertargets

EREstro

genreceptor

Sustains

proliferativ

egrowth

signals


Tamoxifen

CD20

B-lymph

ocytea

ntigencluste

rof

differentiatio

n(C

D)2

0Supp

ortsB-cellactiv

ationandcellcycle

progression

B-celllymph

omas

Rituximab

ERBB

2(H

ER2neu)

Hum

anepidermalgrow

thfactor

receptor

2Sustains

proliferativ

egrowth

signals

Breast


cancers

Trastuzumab

PD1

Programmed


279)

Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Nivolum

ab

CTLA

4Cy

totoxicT

-lymph

ocytea

ssociatedprotein

4Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Ipilimum

ab

AP-1

Activ

atingprotein1

Regu

lates

gene

expressio

ncontrolling

differentiatio

nproliferatio

nandapop

tosis

Colorectalcancer

casestu

dyIrbesartan

(ang

iotensin

IIreceptor

antagonist)

PML-RA

RProm

yelocytic

leuk

emiaretinoica

cid

receptor

alph

afusiongene


nAc

utep

romyelocytic

leuk

emia

Retin

oica

cid

Biom

arkersforclin

icalagents

APA

F1Ap

optotic

protease

activ

atingfactor

1Preventsapop

tosis

Melanom

aDoxorub

icin

MGMT

O6-m

ethylguanine-D

NA

methyltransfe

rase

Reverses

DNAdamage

Glio

ma

Alkylatingagents

lowastlowastAlth

ough

IDH12

aren

otepigeneticmod


nsin

theseg

enes

canhave

profou

ndeffectson

thee

pigeno

me



Spat

ial h

etero

gene

ity



s chr

omos

omal

rear

rang

emen

tsAlready in use f

or clin

ical d

ecisi

on-m

akin

g

Inter

roga

ted by

emerg

ing tech

nologies

eg BRAFV600E

ER+minusPR+minus

middot middotmiddot

middotmiddotmiddot


RX























































6 Conclusion






Acknowledgments


References



































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of





















(a)





(b)









Table1Selected

listo

fpreciselytargeted

molecular

alteratio

nsin

cancer

Genes

ymbo

lGenen

ame

Effecto

falteratio

nMajor

associations

with

specifictum

ortypes

Implicated

therapy


BCR-ABL

Breakp

oint

cluste

rregion

Abelsonmurine

leuk

emiaviraloncogeneh

omolog

fusio

nprotein

Com

prom

isesfi

delityof

DNArepair

deregu

latesp

roliferation

impairs

apop

tosis

anddifferentiatio

nCh

ronicm

yelogeno

usleuk

emia

Imatinibdasatinib

HRA

SKR

AS

HarveyKr

isten

ratsarcomav

iraloncogene

homolog

Con

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gNon

-smallcelllun

gcancer

Salirasib

BRAF

v-Ra

fmurines

arcomav

iraloncogene

homolog

BCon

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gMelanom

aV60

0Eor

V60

0Kmutations


BCL2

B-celllymph

omaleuk

emia-2

Impairs

apop

tosis

Leuk

emialym

phom

amelanom

aVe

netocla

xTu

mor

suppresso

rgenes

BRCA

12Breastcancer

12Im

paire

dDNArepair


PARP

inhibitor(via

synthetic

lethality

)Ep

igeneticmodify

ingg

enes

IDH12lowastlowast

Isocitrated

ehydrogenase

DNAhyperm

ethylatio

ndisrup

tsdifferentiatio

nAc

utem

yeloid

leuk

emia(A

ML)

AG120AG

221AG

881

EZH2

Enhancer

ofzeste

2po

lycombrepressiv

ecomplex

2subu

nit

Inhibitsapop

tosissilences

byH3K

27trim

ethylatio

nLymph

oma

Tazemetostat

DOT1L

DOT1-like

histo

neH3K

79methyltransfe

rase


nandapop

tosis


Pino

metostat

DNMT

DNAmethyltransfe

rase

Disr

uptsno

rmalpatte

rnso

fDNAmethylatio


Azacytid

ine

decitabine

HDAC

Histon

edeacetylases

Disr

uptsno

rmalpatte

rnso

fhiston

eacetylatio


Vorin

ostatromidepsin

Othertargets

EREstro

genreceptor

Sustains

proliferativ

egrowth

signals


Tamoxifen

CD20

B-lymph

ocytea

ntigencluste

rof

differentiatio

n(C

D)2

0Supp

ortsB-cellactiv

ationandcellcycle

progression

B-celllymph

omas

Rituximab

ERBB

2(H

ER2neu)

Hum

anepidermalgrow

thfactor

receptor

2Sustains

proliferativ

egrowth

signals

Breast


cancers

Trastuzumab

PD1

Programmed


279)

Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Nivolum

ab

CTLA

4Cy

totoxicT

-lymph

ocytea

ssociatedprotein

4Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Ipilimum

ab

AP-1

Activ

atingprotein1

Regu

lates

gene

expressio

ncontrolling

differentiatio

nproliferatio

nandapop

tosis

Colorectalcancer

casestu

dyIrbesartan

(ang

iotensin

IIreceptor

antagonist)

PML-RA

RProm

yelocytic

leuk

emiaretinoica

cid

receptor

alph

afusiongene


nAc

utep

romyelocytic

leuk

emia

Retin

oica

cid

Biom

arkersforclin

icalagents

APA

F1Ap

optotic

protease

activ

atingfactor

1Preventsapop

tosis

Melanom

aDoxorub

icin

MGMT

O6-m

ethylguanine-D

NA

methyltransfe

rase

Reverses

DNAdamage

Glio

ma

Alkylatingagents

lowastlowastAlth

ough

IDH12

aren

otepigeneticmod


nsin

theseg

enes

canhave

profou

ndeffectson

thee

pigeno

me



Spat

ial h

etero

gene

ity



s chr

omos

omal

rear

rang

emen

tsAlready in use f

or clin

ical d

ecisi

on-m

akin

g

Inter

roga

ted by

emerg

ing tech

nologies

eg BRAFV600E

ER+minusPR+minus

middot middotmiddot

middotmiddotmiddot


RX























































6 Conclusion






Acknowledgments


References



































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of

















Table1Selected

listo

fpreciselytargeted

molecular

alteratio

nsin

cancer

Genes

ymbo

lGenen

ame

Effecto

falteratio

nMajor

associations

with

specifictum

ortypes

Implicated

therapy


BCR-ABL

Breakp

oint

cluste

rregion

Abelsonmurine

leuk

emiaviraloncogeneh

omolog

fusio

nprotein

Com

prom

isesfi

delityof

DNArepair

deregu

latesp

roliferation

impairs

apop

tosis

anddifferentiatio

nCh

ronicm

yelogeno

usleuk

emia

Imatinibdasatinib

HRA

SKR

AS

HarveyKr

isten

ratsarcomav

iraloncogene

homolog

Con

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gNon

-smallcelllun

gcancer

Salirasib

BRAF

v-Ra

fmurines

arcomav

iraloncogene

homolog

BCon

stitutiv

elyactiv

ates

MEK

ERK

progrowth

signalin

gMelanom

aV60

0Eor

V60

0Kmutations


BCL2

B-celllymph

omaleuk

emia-2

Impairs

apop

tosis

Leuk

emialym

phom

amelanom

aVe

netocla

xTu

mor

suppresso

rgenes

BRCA

12Breastcancer

12Im

paire

dDNArepair


PARP

inhibitor(via

synthetic

lethality

)Ep

igeneticmodify

ingg

enes

IDH12lowastlowast

Isocitrated

ehydrogenase

DNAhyperm

ethylatio

ndisrup

tsdifferentiatio

nAc

utem

yeloid

leuk

emia(A

ML)

AG120AG

221AG

881

EZH2

Enhancer

ofzeste

2po

lycombrepressiv

ecomplex

2subu

nit

Inhibitsapop

tosissilences

byH3K

27trim

ethylatio

nLymph

oma

Tazemetostat

DOT1L

DOT1-like

histo

neH3K

79methyltransfe

rase


nandapop

tosis


Pino

metostat

DNMT

DNAmethyltransfe

rase

Disr

uptsno

rmalpatte

rnso

fDNAmethylatio


Azacytid

ine

decitabine

HDAC

Histon

edeacetylases

Disr

uptsno

rmalpatte

rnso

fhiston

eacetylatio


Vorin

ostatromidepsin

Othertargets

EREstro

genreceptor

Sustains

proliferativ

egrowth

signals


Tamoxifen

CD20

B-lymph

ocytea

ntigencluste

rof

differentiatio

n(C

D)2

0Supp

ortsB-cellactiv

ationandcellcycle

progression

B-celllymph

omas

Rituximab

ERBB

2(H

ER2neu)

Hum

anepidermalgrow

thfactor

receptor

2Sustains

proliferativ

egrowth

signals

Breast


cancers

Trastuzumab

PD1

Programmed


279)

Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Nivolum

ab

CTLA

4Cy

totoxicT

-lymph

ocytea

ssociatedprotein

4Preventsactiv

ationof

T-cells

Potentially

targetsa

llsolid

tumors

Ipilimum

ab

AP-1

Activ

atingprotein1

Regu

lates

gene

expressio

ncontrolling

differentiatio

nproliferatio

nandapop

tosis

Colorectalcancer

casestu

dyIrbesartan

(ang

iotensin

IIreceptor

antagonist)

PML-RA

RProm

yelocytic

leuk

emiaretinoica

cid

receptor

alph

afusiongene


nAc

utep

romyelocytic

leuk

emia

Retin

oica

cid

Biom

arkersforclin

icalagents

APA

F1Ap

optotic

protease

activ

atingfactor

1Preventsapop

tosis

Melanom

aDoxorub

icin

MGMT

O6-m

ethylguanine-D

NA

methyltransfe

rase

Reverses

DNAdamage

Glio

ma

Alkylatingagents

lowastlowastAlth

ough

IDH12

aren

otepigeneticmod


nsin

theseg

enes

canhave

profou

ndeffectson

thee

pigeno

me



Spat

ial h

etero

gene

ity



s chr

omos

omal

rear

rang

emen

tsAlready in use f

or clin

ical d

ecisi

on-m

akin

g

Inter

roga

ted by

emerg

ing tech

nologies

eg BRAFV600E

ER+minusPR+minus

middot middotmiddot

middotmiddotmiddot


RX























































6 Conclusion






Acknowledgments


References



































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of


















Spat

ial h

etero

gene

ity



s chr

omos

omal

rear

rang

emen

tsAlready in use f

or clin

ical d

ecisi

on-m

akin

g

Inter

roga

ted by

emerg

ing tech

nologies

eg BRAFV600E

ER+minusPR+minus

middot middotmiddot

middotmiddotmiddot


RX























































6 Conclusion






Acknowledgments


References



































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of


































































6 Conclusion






Acknowledgments


References



































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
















































































































































































































































of






Disease Markers



OncologyJournal of





PPAR Research



Journal of

ObesityJournal of
















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