Liquid Biopsy: New Challenges in the era of Immunotherapy and Precision Oncology

252 Pages·2022·4.577 MB·English

by  Antonio Russo, Ettore Capoluongo, Antonio Galvano, Antonio Giordano

Liquid Biopsy
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Liquid Biopsy
New Challenges in the Era of
Immunotherapy and Precision
Oncology
Editedby
ANTONIO RUSSO
Department of Surgical,Oncological,and Oral Sciences,
University of Palermo,Palermo,Italy
ETTORE CAPOLUONGO
Department of Molecular Medicine and Medical
Biotechnology, University of Naples FedericoII,
Naples, Italy
CEINGE,Advances Biotecnologies,Naples, Italy
ANTONIO GALVANO
Department of Surgical,Oncological,and Oral Sciences,
University of Palermo,Palermo,Italy
ANTONIO GIORDANO
SbarroInstitute for Cancer Research and Molecular
Medicine, and Centerof Biotechnology, Collegeof
Science and Technology, Temple University,
Philadelphia, PA, United States
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Contents
Listofcontributors xi
Preface xv
1. What is precisionmedicine in oncology? 1
M.Arbitrio,A.Cordua,V.Uppolo,M.D’Apolito,D.Caracciolo,N.Staropoli,
O.Cuomo,L.Fiorillo,P.Tassone,M.T.DiMartinoandP.Tagliaferri
1.1 Introduction:whatdoesprecisionmedicinemean? 1
1.2 Theroleofbiomarkersinprecisionmedicine 2
1.3 Classificationofbiomarkers 2
1.4 Therationaleforthedefinitionoftumormutationalburden 4
1.5 Collectingsamplesformutationalanalysis:tissueorliquidbiopsy? 5
1.6 Pragmaticalaspectsofprecisionmedicine:howtobuildit? 7
1.7 Precisionmedicineandclinicaltrials:istheresomethingdifferent? 8
1.8 Precisionmedicineinoncology:whatisits“area-of-application”? 10
1.9 Pharmacogenomicsandprecisionmedicine 11
1.10 Determinationofprogrammeddeath-ligand1expressioninnon-smallcell
lungcarcinomainordertochoosepatientseligibleforimmunotherapy 12
1.11 Throughtheconceptofsyntheticlethality:polyADP-ribose
polymerases-inhibitorsandprecisionmedicine 16
1.12 Colorectalcanceremicrosatelliteinstability 18
1.13 Conclusions 22
Conflictofintereststatement 23
References 23
2. Liquid biopsy:a right tool in a right context? 31
M.LaMantia,S.Cutaia,V.Gristina,A.Galvano,E.Capoluongo,
C.Rolfo,U.Malapelle,L.Incorvaia,G.Badalamenti,A.RussoandV.Bazan
2.1 Liquid biopsy in NSCLC 31
Learningobjectives 31
2.1.1 Expertopinion 36
2.1.2 Keypoints 36
2.1.3 Summaryofclinicalrecommendations 36
Acknowledgments 37
References 37
Furtherreading 39
v
vi Contents
2.2 The role of mutatedctDNA in nonmalignant lesions:
challenging aspectsinliquid biopsy implementation 39
V.Gristina,U.Malapelle,P.Pisapia,M.LaMantia,R.Scalia,M.Greco,
L.Incorvaia,G.Badalamenti,A.Galvano,A.RussoandV.Bazan
Learningobjectives 39
2.2.1 Expertopinion 42
2.2.2 Keypoints 42
Acknowledgments 42
References 43
Furtherreading 45
3. Liquidbiopsy:newchallengesintheeraofimmunotherapyand
precisiononcologyNGSandtheotherfacesofmolecularbiology 47
F.Buttitta,A.Navicella,R.Rossetti,L.FelicioniandA.Marchetti
Learningobjectives 47
3.1 Tissueorliquidbiopsy? 47
3.2 Next-generationsequencingforidentificationofgene
alterationsinliquidbiopsy 50
3.3 Liquidbiopsyinmonitoringresponsetotherapy 53
3.4 Expertopinion 59
3.5 Keypoints 59
3.6 Hintsfordeeperinsight 59
References 59
Furtherreading 62
4. Current clinically validatedapplications of liquid biopsy 63
E.Capoluongo,C.Rolfo,A.Galvano,V.Gristina,A.Perez,N.Barraco,
M.LaMantia,L.Incorvaia,G.Badalamenti,A.RussoandV.Bazan
Learningobjectives 63
4.1 CirculatingtumorDNAinadvancednon-smallcelllungcancer 63
4.1.1 Treatment-naïveadvancednon-smallcelllungcancerpatients 64
4.1.2 Advancednon-smallcelllungcancerpatientsprogressing
duringtyrosinekinaseinhibitors 66
4.2 Emergingclinicalapplicationsofliquidbiopsy 67
4.2.1 Colorectalcancer 69
4.2.2 Breastcancer 71
4.2.3 Melanoma 73
4.3 Liquidbiopsyapplicationinclinicalresearch 74
Contents vii
4.3.1 Monitoringoftreatmentresponseinlungcancer 74
4.3.2 Monitoringoftreatmentresponseincolorectalcancer 76
4.4 Keypoints 77
Acknowledgments 77
References 77
5. Liquid biopsy and immunotherapy: is allthat glittergold? 83
L.Incorvaia,A.Perez,C.Brando,V.Gristina,M.LaMantia,M.Castiglia,
D.Fanale,A.Galvano,G.Badalamenti,A.RussoandV.Bazan
Learningobjectives 83
5.1 Background:theneedforpredictivebiomarkersforpatientselection 83
5.1.1 Circulatingtumorcells,cell-freeDNA,andexosomes 84
5.1.2 Circulatingtumorcells 86
5.1.3 Cell-freeDNAandcirculatingtumorDNA 98
5.1.4 Exosomes 101
5.1.5 T-lymphocytes(theT-cellreceptor)andcytokines 103
5.1.6 Thesolubleformofimmune-checkpointsandother
circulatingproteins 106
Abbreviations 108
Keypoints 108
Expertopinion 109
Acknowledgments 109
References 110
6. Which technology performsbetter?Fromsamplevolume
to extraction and molecular profiling 119
E.Capoluongo,P.Pisapia,U.MalapelleandG.Troncone
6.1 Molecular profiling 119
Learningobjectives 119
6.1.1 Expertopinion 122
6.1.2 Keypoints 122
References 122
Furtherreading 123
6.2 Biologicalfluid withdrawal: howmuch sample volume
is enough? 124
E.Capoluongo
Learningobjectives 124
6.2.1 Introduction 124
6.2.2 Otherbodyfluidsusedinliquidbiopsy-basedassays 128
viii Contents
6.2.3 Keypoints 130
References 130
Furtherreading 131
6.3 Methods for cf/ctDNA isolation 132
U.Malapelle,P.Pisapia,A.Galvano,V.Gristina,M.LaMantiaand
G.Troncone
Learningobjectives 132
6.3.1 Keypoints 134
Acknowledgments 135
References 135
Furtherreading 135
6.4 CTC andexosome: from the enrichment to the
characterization 136
E.Lianidou,M.CastigliaandS.Taverna
Learningobjectives 136
6.4.1 Introduction 136
6.4.2 Exosomeenrichment 138
6.4.3 Exosomescharacterization 139
6.4.3.1 Roleofexosomesinimmunotherapy 141
6.4.4 Circulatingtumorcellsenrichmentmethods 144
6.4.4.1 Roleofcirculatingtumorcellsinimmunotherapy 148
6.4.5 Keypoints 149
References 149
Furtherreading 154
6.5 CirculatingRNAs(miRNA, lncRNA, etc): from the
enrichment tothe characterization 155
D.Fanale,C.Brando,A.Fiorino,E.Pedone,A.Perez,M.Bono,
N.Barraco,M.LaMantia,M.DelRe,A.RussoandV.Bazan
Learningobjectives 155
6.5.1 Introduction 155
6.5.2 HousekeepingRNAs 156
6.5.3 RegulatoryncRNAs 158
6.5.4 Keypoints 162
6.5.5 Expertopinion 163
Acknowledgments 163
References 163
Furtherreading 167
Contents ix
6.6 Cell-free/circulating tumor DNA profiling:from
next-generation sequencing-basedto digital polymerase
chain reaction-based methods 168
A.Perez,C.Brando,M.LaMantia,V.Gristina,A.Galvano,L.Incorvaia,
G.Badalamenti,A.Giordano,E.Capoluongo,A.Russo,U.Malapelleand
V.Bazan
Learningobjectives 168
6.6.1 Introduction 169
6.6.2 Targetednext-generationsequencingmethods 171
6.6.3 Untargetednext-generationsequencingmethods 173
6.6.4 Dropletdigitalpolymerasechainreactionmethods 175
6.6.5 Keypoints 176
6.6.6 Expertopinion 177
Acknowledgments 177
References 177
6.7Standardizationandqualityassuranceinliquidbiopsy
testing 181
A.Perez,M.Bono,N.Barraco,C.Brando,D.Cancelliere,A.Pivetti,
A.Fiorino,E.Pedone,A.Giurintano,M.LaMantia,V.Gristina,A.Galvano,
L.Incorvaia,G.Badalamenti,U.Malapelle,A.RussoandV.Bazan
Learningobjectives 181
6.7.1 Introduction 182
6.7.2 Cell-freeDNAinliquidbiopsy:preanalyticallimitations 183
6.7.3 Thepreanalyticalphaseofcirculatingtumorcellsanalysis 185
6.7.4 Thepreanalyticalphaseofexosomesanalysis 187
6.7.4.1 Samplecollection,storage,andprocessing 187
6.7.4.2 Exosomesisolation 188
6.7.5 StandardizationinitiativesandISO/CEN/externalqualityassessment
developmentinliquidbiopsy 194
6.7.6 Keypoints 197
6.7.7 Expertopinion 197
Acknowledgments 198
References 198
Furtherreading 202
7. Early detection screening: mythor reality? 203
M.LaMantia,F.Iacono,S.Cutaia,V.Gristina,A.Perez,M.Greco,
K.Calcara,A.Galvano,V.BazanandA.Russo
References 207