1. An miRNA-Signature Profiling Approach to Treatment Management in CLL
and AML
CLL is notoriously heterogeneous, notonlyinthe clinical course of individualswiththe disease,but
alsothe geneticlesionspresentinthe DNA of CLL B cells. In2000, fludarabine becamethe preferred
first-linetreatmentforCLL. Itis relativelycommonhowever,forindividualstodevelopresistance to
fludarabine-basedfirst-line treatment. Aswell asthis,the utilisationof intensive
chemoimmunotherapiesinrecent years,hasledtoa group of individualswhodevelopresistance to
first-linefludarabine-basedregimesafter6 months(Zenz etal., 2010). Although50% of these cases
are associatedwithp53 defectsor11q deletion(Stilgenbauer etal.,2009; Zenzet al., 2008), half of
relapse casesoccur independentlyof these aberrations.
AML isa similarlyheterogeneous leukaemia,andpatientsare againsusceptible todrugresistance as
well asrelapse. AML treatmentcommonlyinvolvesaninitialphase of remission initiation,followed
by post-remissionchemotherapy orallogeneicstemcell transplantation. People whorelapse with6
monthsof diagnosishave alowrate of achievingacomplete secondremissionandoverallsurvival,
and 10% to 40% of patientsare resistanttoconventionaltherapyanddonot achieve complete
remission(Thol etal.,2015). It is alsoclearthat moleculardetectionof minimalresidual disease
(MRD) inhigh-riskAMLpatientsfollowingsupposedremission,wouldbe invaluableindirecting
consolidationandsalvage therapy. Due tothe heterogeneousnature of AMLhowever,apatient-
tailoredapproachtargetinganindividual'sspecificgeneticaberrationswouldbe required.
MicroRNAs(miRNAs) are highlyspeciesconservednon-codingRNAs. DifferentialmiRNA expression
profilesbetweencancerphenotypesandnormal phenotypes,have beenshowntooccur
haematological malignancies(Calin etal.,2002). Aswell asthis,miRNA targetshave consistently
beenoncogenes andtumoursuppressorgenes,andtheirtranscripts(Volinia etal.,2006). It has
beenobservedthatdysregulationof miRNAsisassociatedwithfludarabine-resistance (Moussay et
al., 2010), as well aschemo-sensitivityin AML(Bhise etal., 2016).
It isplausible thatthe detectionof cell-freemiRNA inplasmacouldrepresentanattractive non-
invasive meanstostratifythese diseasesintermsof treatmentresponse,andmayrepresent
sensitivebiomarkersforearlydiagnosisandrelapse (Moussay etal., 2011).

2. The proposedresearchwill involveinvestigatingthe value of miRNA expressionsignaturesusedina
clinical settingtodirecttreatmentof AMLand CLL, particularly inthe absence of traditional
prognosticmarkers. Itwill explore the potential of usingmultiplex qRT-PCRinconjunctionwith
microfluidicarraycards and characterisedmiRNA signaturesinplasmaorserumsamples,asthis
wouldrepresentacost-effective platform withanappealingease-of-use,sensitivity,andnon-
invasive nature.
I propose twostudyareas:
Study 1 wouldexplorethe use of cost-effective miRNA expressionarraysina CLL treatmentsetting
and consistof twophases.
Phase1; Explore whetherlevelsof circulatingmiRNAsinpatientplasma/serumcanbe usedto
identifyfludarabine resistantphenotypes,withthe use of commerciallyavailablearrayscoveringa
comprehensive range of miRNAs.
Phase2; Developthese signaturesintoarefinedcost-effective customassay(coveringasmall
number(11) of miRNAs) thatiseffectiveinidentifyingresistantpatientsbefore orshortlyafter
treatmentinitiation,aswell asdetectingresistance developedthroughlong-termtreatment.
Study 2 wouldexplorethe use of patient-specificmiRNA signaturestodirecttreatmentinAML,and
explore twoquestions:
1; Can circulatingpatient-specificsignaturesof miRNA expression accuratelydetecttumourburden,
as well asidentifyresistantorearlyrelapse patients andpredicttreatmentresponse?
2; Isthe assaysensitive enoughtodetect minimal residual diseaseanddirectconsolidation
treatment(andminimise relapse)orinitiate salvagetreatmentatan earlystage of relapse?
These toolscouldbe usedtoidentifyindividualsforinclusioninclinicaltrialsforemergingnovel
agents(particularlyinthe treatmentof the frail andelderly), aswell as helpdirectcytoreduction
priorto allogeneicstemcell transplant andaidinthe developmentof miRNA-targetedtherapeutics.