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Biologie des LAL-B
Emmanuelle Clappier
Service d’Hématologie biologique, hôpital Saint-Louis, AP-HP
Equipe Génome et Cancer, UMR INSERM/CNRS 944/7212, IRSL
Université Paris-Diderot
DES Hématologie
12 avril 2019
Leucémies aiguës lymphoblastiques
✓ 800 cas/an en France, moitié enfant/adulte
✓ 80% des leucémies de l’enfant
✓ 4% des hémopathies malignes de l’adulte
Données GRAALL, Huguet, JCO 2009Hunger, NEJM 2015
LALA-94
GRAALL-2003/05
LAL-B de l’enfant LAL-B de l’adulte
Identifier des cibles thérapeutiques
Stratifier le traitement
Elucider les altérations génomiques des leucémies pour:
Comprendre les mécanismes oncogéniques
Identifier des marqueurs pronostiques
t(1;19) / E2A-PBX1
t(9;22) / BCR-ABL1Chromosome Philadelphie
Les débuts de la génomique des leucémies:anomalies cytogénétiques récurrentes dans les LAL-B
t(12;21) / ETV6-RUNX1 "cryptique" détectée par FISH
fusion
AML1
ES AML1TEL
6 7 8 9
1 2 3 4 5
10 11 12 X
13 14 15
16 17 18
19 20
21 22 Y
Hyperdiploïdie "standard " +X,+4,+6,+8,+10,+14,+17,+18,+21,+21
t(4;11) / MLL-AF4
Yeoh, Cancer Cell 2002
t(9;22) / BCR-ABL1
Ph1 Fusion TEL-AML1
AML1
Split AML1TEL
6 7 8 9
1 2 3 4 5
10 11 12 X
13 14 15
16 17 18
19 20
21 22 Y
t(1;19) / E2A-PBX1
MLL break-apart
Signatures transcriptionnelles associées aux altérations fondatrices
(years)
0 2 4 6 8 10 12
0
10
20
30
40
50
60
70
80
90
100
Logrank test: p<0.0001
t(12;21) ETV6-RUNX1
n=74 (23%)
Hyperdiploidy
n=109 (34%)
Others
n=122 (38%)
t(9;22) or t(4;11)
n=19 (6%)
% EFS
Données EORTC-CLG 58881, H. Cavé
Pronostic associé aux sous-types génétiques dans les LAL-B de l’enfantAnnées 1990-2000
Pronostic des altérations « classantes »
Hyperdiploidy30-35%
ETV6-RUNX120-25%
« B-other »25-30%
TCF3-PBX1
BCR-ABL1
iAMP21MLLt
Hypo/haploidy
< 5% chacun
Paysage génomique des LAL-B Ph-neg pédiatriques en 2010
years0 2 4 6 8 10
0
10
20
30
40
50
60
70
80
90
100Ev
ent
free
su
rviv
al
Cohorte EORTC-CLG 58951N = 1223
Lafage-Pochitaloff, Blood 2017
Cytogénétique des LAL-B Ph-nég de l’adulte
Données GRAALL-2003/05
Pronostic des altérations « classantes »
Pronostic des altérations « classantes »
Hyperdiploidy30-35%
ETV6-RUNX120-25%
« B-other »25-30%
TCF3-PBX1
BCR-ABL1
iAMP21MLLt
Hypo/haploidy
< 5% chacun
years0 2 4 6 8 10
0
10
20
30
40
50
60
70
80
90
100Ev
ent
free
su
rviv
al
Données EORTC-CLG 58951N = 1223 pts
B-other:~50% des rechutes
Paysage génomique des LAL-B Ph-neg pédiatriques en 2010
CGH/SNP-array et séquençage nouvelle génération (NGS):Multiplicité des lésions oncogéniques additionnelles
Roberts, NEJM 2014
Oncogenèse multi-étape +++
Mullighan, Nature 2007
Stigmates de recombinaison RAG-médiée :
• points de cassures clusterisés
• séquences RSS-like
• addition de nucléotides (région N)
Altérations secondaires/additionnelles
Paysage génomique des LAL-B pédiatriques
Altérations initiatrices et/ou classantes
Altérations secondaires/additionnelles
High hyperdiploidy
ETV6-RUNX1
TCF3-PBX1
ERGdel
iAMP21
Low hypo/near-haploidy
MLLt
B-Other
BCR-ABL1
Hyperdiploidy30-35%
« B-other »25-30%
TCF3-PBX1
BCR-ABL1< 5%
MLLt
Hypo/haploidy
< 5% each
ERGiAMP21
ETV6-RUNX120-25%
Frequency of IKZF1 deletions in distinct BCP-ALL genetic subtypes
0
10
20
30
40
50
60
70
80
90
100
BCR-ABL1 MLL / 11q23
abn.
low hypo /
near-haploidy
iAMP21 TCF3-PBX1 ERGdel ETV6-RUNX1 High
hyperdiploidy
B-other
IKZF1
15%
% of IKZF1del in each genetic subtype
4-7
telo centro1 2 3 4 5 6 7 8
7p12.2
2-3, 2-7, D2-8, D4-8…
Whole deletion (including 7p-)
Délétions d’IKZF1
Impact pronostique des délétions d’IKZF1
86.5%
67.7%
HR = 2.41 (1.75, 3.32)
p<0.0001
(years)
0 2 4 6 8 10 12 14
0
10
20
30
40
50
60
70
80
90
100
O N Number of patients at risk : IKZF1 deletion134 1044 984 771 511 303 129 10
52 179 159 118 84 49 13 1
Negative
Positive
92.4%
86.7%
HR = 1.67 (1.03, 2.72)
p<0.035
(years)
0 2 4 6 8 10 12 14
0
10
20
30
40
50
60
70
80
90
100
O N Number of patients at risk : IKZF1 deletion73 1044 1010 833 567 339 152 15
21 179 172 137 105 69 21 1
Negative
Positive
Even
t-fr
ee s
urv
ival
(%)
8-y EFS
No IKZF1del
IKZF1del
n = 1223 Ph-negative BCP-ALL in childrentreated in EORTC-CLG 58951 trial (1998-2008)
Beldjord, Blood 2014;123:3739-49
N= 216 Ph-negative BCP-ALL in adultstreated in GRAALL 03/05 trials (2003-2011)
IKZF1del
No IKZF1del
Clappier E, et al. Leukemia 2015;29:2154–61
IKZF1 deletion is a marker of poor outcome in B-other ALL
Forest-plot analysis
EORTC-CLG 58951 study
Clappier E, et al. Leukemia2015;29:2154–61
B-other
87/354 IKZF1del (25%)
HR=2.22 (1.45, 3.39)
p=0.0002
79.0%
56.4%
years0 2 4 6 8 10 12 14
0
10
20
30
40
50
60
70
80
90
100
O N Number of patients at risk : IKZF1 deletion
51 264 240 176 119 75 37 336 90 74 55 40 24 6 1
NegativePositive
8-y EFS
IKZF1 intragenic deletionBP-PCR +/- CGH
Risk classification in GRAALL-2014
MRD1 ≥ 10-4 et <10-3
Oncogenetics
TP1
TP2
High risk criteria
Very High Risk criteria
MRD2 ≥ 10-4
MRD1 ≥ 10-3
MLL/KMT2A rearrangementKaryo, FISH, bio mol
MRD
High hyperdiploidy
ETV6-RUNX1
TCF3-PBX1
ERGdel
iAMP21
Low hypo/near-haploidy
MLLt
B-Other
BCR-ABL1
Hyperdiploidy30-35%
« B-other »25-30%
TCF3-PBX1
BCR-ABL1< 5%
MLLt
Hypo/haploidy
< 5% each
ERGiAMP21
ETV6-RUNX120-25%
Hyperdiploidy5-10%
ETV6-RUNX1
« B-other »~50%
TCF3-PBX1
BCR-ABL1~25%
iAMP21
MLLt~10%
Hypo/haploidy
< 5% each
LAL-B pédiatriques LAL-B adultes
Groupes génétiques des LAL-B de l’adulte et de l’enfant
LAL Ph-like (BCR-ABL1-like) : un groupe de mauvais pronostic
Den Boer, Lancet Oncology 2009
Den Boer, Lancet Oncology 2009Harvey, Blood 2010
ProB signatureFrequent IKZF1 deletions (40-90%)
Mutations JAK
Shochat, J Exp Med 2011
Altérations génétiques ciblant l’axe CRLF2-IL7R-JAK2-STAT5
Translocations IGH@-CRLF2t(X;14)(p22;q32) ou
t(Y;14)(p11;q32)
Délétion interstitielle PAR1 fusion P2RY8-CRLF2
Mutations IL7R
Dérégulation CRLF2Russel LJ, et al. Blood 2009
Yoda A, et al. Proc Natl Acad Sci 2010
➢ Signalisation dérégulée potentiellement « ciblable » par des inhibiteurs de JAK, PI3kinase, mTOR
Russel LJ, et al. Blood 2009
Mullighan CG, et al. Proc Natl Acad Sci 2009
ruxolitinib
rapamycine
Peeters P et al., Blood 1997Reiter A et al., Cancer Res 2005De Braekeleer E et al., Leukemia 2007Poitras JL et al., Chromosomes & Cancer 2008Hidalgo-Curtis C et al., Genes, Chrom & Cancer 2008Soler G et al., Leukemia 2008Ernst E et al., British Journal of Haematology 2011Kakadia PM et al., Leukemia 2011Kobayashi K et al., British J of Haematology 2014Lilljebjorn U et al., Leukemia 2014Roberts KG, et al. N Engl J MedKawamura M et al., Genes, Chrom & Cancer 2015Yano M et al., British J of Haematology 2015…
Partenaires
ATF7IPBCREBF1ETV6FOXP1LSM14AMEF2DNUMA1NUP214PAX5PCM1RANBP2RCSD1SFPQSHIP1SNX2SSBP2STRN3SPTBN1ZC3HAV1ZMIZ1ZMYM2 … Roberts KG, et al. Cancer Cell 2012
Kinases
ABL1
ABL2
PDGFRB
PDGFRA
CSF1R
JAK2
NTRK3
LYN
SYK
FLT3
FGFR1…
Fusions impliquant des kinases: partenaires variés +++
Pronostic des LAL Ph-like chez l’adulte
Jain, Blood 2017
Roberts, JCO 2017
0.00
0.20
0.40
0.60
0.80
1.00
Ove
rall
Sur
viva
l
13 10 5 4 3 1 1 1 0 0 Number at risk
0 1 2 3 4 5 6 7 8 9Time(years)
Hunger, Blood 2015
Jain, Blood 2017
GRAALL, unpublished data
Peeters P et al., Blood 1997Reiter A et al., Cancer Res 2005De Braekeleer E et al., Leukemia 2007Poitras JL et al., Chromosomes & Cancer 2008Hidalgo-Curtis C et al., Genes, Chrom & Cancer 2008Soler G et al., Leukemia 2008Ernst E et al., British Journal of Haematology 2011Kakadia PM et al., Leukemia 2011Kobayashi K et al., British J of Haematology 2014Lilljebjorn U et al., Leukemia 2014Roberts KG, et al. N Engl J MedKawamura M et al., Genes, Chrom & Cancer 2015Yano M et al., British J of Haematology 2015…
Partenaires
ATF7IPBCREBF1ETV6FOXP1LSM14AMEF2DNUMA1NUP214PAX5PCM1RANBP2RCSD1SFPQSHIP1SNX2SSBP2STRN3SPTBN1ZC3HAV1ZMIZ1ZMYM2 … Roberts KG, et al. Cancer Cell 2012
Kinases
ABL1
ABL2
PDGFRB
PDGFRA
CSF1R
JAK2
NTRK3
LYN
SYK
FLT3
FGFR1…
Fusions impliquant des kinases: partenaires variés +++
Kinases de classe ABL
-> sensibilité aux inhibiteurs
de type imatinib
BCR-ABL1High hyperdiploidyLow hypodiploidyMLL fusionsiAMP21 ERGdel (DUX4)CRLF2 deregulationTCF3-PBX1ETV6-RUNX1TCF3-HLF ABL1 fusionsJAK2 fusionsPDGFRB fusionsPAX5 fusionsZNF384 fusions
… all known fusion beeing detected by RT-MLPA
KaryotypeFISH
RNA-seq
BP-PCR IKZF1del , ERGdel
RQ-PCR CRLF2, EPOR
CGH-arrayRT-MLPA
No classifying lesion identifiedand
Poor treatment response
Stratégie de diagnostic prospectif centralisé des altérations génétiques Ph-like pour une prise en charge thérapeutique précoce
Search for fusion genes
Reads
LSM14A ex6 TGATAACAAGAGACAAGTAGGTGAAAAGCTCCGGGTCTTAG ABL1 ex3
SPTBN1 ex9 TCATCTCTGACATCAACAAGAAGCCACGTTACGAGATCCAG PDGFRB ex12
NRF1 ex10 TGGAGTCCAAGATGCTAATGTTATGAACTATTAACAGAAAA JAK2 ex19
ZNF566 ex4 AACAAGAGGCCAGTGGCCAGTTGAACTTAGCTCATTAAGGG JAK2 ex9
ZEB2 ex10 ACATAAATACGAACACACAGATTATGAACTATTAACAGAAA JAK2 ex19
ETV6 ex4 GCATCAGAACCATGAAGAAGATGTGCAGCACATTAAGAGGA NTRK3 ex15
CREBBP ex14 AAGGGGAGCCCAGGTCTGAGGTAGAATGGAAGAATCTCACT ZNF384 ex3
EP300 ex6 GCGGCCCATGAGCAACATGAAAAGTTCAGGAGCCCTGGAAA ZNF384 ex3
RNA-seq analysis for « B-other » ALL cases
Efficacy of Tyrosine Kinase Inhibitors therapy in patients with Philadelphia-like Acute Lymphoblastic Leukemia harboring ABL-class fusions
Lengliné, et al., Haematological2013Duployez et al., Haematologica 2016Tanensi et al. , manuscript in preparation
Retrospective study on 24 patientsTreated with TKI firstline (n=19) or at relapse (n=5)
Retrospective study on 24 patientsTreated with TKI firstline (n=19) or at relapse (n=5)
Lengliné, et al., Haematological2013Duployez et al., Haematologica 2016Tanensi et al. , manuscript in preparation
Efficacy of Tyrosine Kinase Inhibitors therapy in patients with Philadelphia-like Acute Lymphoblastic Leukemia harboring ABL-class fusions
Tanensi et al. , manuscript in preparation
Efficacy of Tyrosine Kinase Inhibitors therapy in patients with Philadelphia-like Acute Lymphoblastic Leukemia harboring ABL-class fusions
Retrospective study on 24 patientsTreated with TKI firstline (n=19) or at relapse (n=5)
3-years OS 77%
Tanensi et al. , manuscript in preparation
Efficacy of Tyrosine Kinase Inhibitors therapy in patients with Philadelphia-like Acute Lymphoblastic Leukemia harboring ABL-class fusions
Retrospective study on 24 patientsTreated with TKI firstline (n=19) or at relapse (n=5)
3-years OS 77%
-> Recommendation for the treatment of patients with Ph-like ALL ABL-class in the GRAALL 2014 trial:Imatinib 600 mg in association with chemo
ZD
+
321
0-1-2-3
Classifying alterations
BCR-ABL1-likeKMT2A
B_
SL
06
7B
_S
L0
61
B_
SL
05
0B
_S
L0
52
B_
SL
13
8B
_S
L1
69
B_
SL
03
2B
_S
L0
60
B_
SL
09
3B
_S
L0
23
B_
SL
06
3B
_S
L0
76
B_
SL
01
1B
_S
L0
06
B_
SL
03
1B
_S
L0
37
B_
SL
11
1B
_S
L0
13
B_
SL
15
5B
_S
L0
42
B_
SL
10
7B
_S
L1
28
B_
SL
07
4B
_S
L1
08
B_
SL
16
5B
_S
L0
46
B_
SL
00
2B
_S
L1
27
B_
SL
02
2B
_S
L1
09
B_
SL
06
9B
_S
L0
71
B_
SL
11
8B
_S
L1
40
B_
SL
12
3B
_S
L0
98
B_
SL
14
5B
_S
L1
46
B_
SL
10
3B
_S
L0
21
B_
SL
01
4B
_S
L0
30
B_
SL
05
3B
_S
L1
35
B_
SL
08
6B
_S
L1
14
B_
SL
05
5B
_S
L1
61
B_
SL
05
8B
_S
L0
09
B_
SL
01
5B
_S
L1
53
B_
SL
03
6B
_S
L1
42
B_
SL
04
4B
_S
L1
34
B_
SL
12
1B
_S
L0
16
B_
SL
04
7B
_S
L1
20
B_
SL
15
2B
_S
L0
99
B_
SL
13
7B
_S
L1
43
B_
SL
08
7B
_S
L0
51
B_
SL
06
2B
_S
L0
88
B_
SL
13
0B
_S
L0
27
B_
SL
07
0B
_S
L0
96
B_
SL
09
4B
_S
L1
10
B_
SL
09
7B
_S
L1
06
B_
SL
01
0B
_S
L1
67
B_
SL
06
4B
_S
L1
31
B_
SL
03
8B
_S
L0
80
B_
SL
11
7B
_S
L0
25
B_
SL
08
5B
_S
L0
54
B_
SL
06
6B
_S
L1
16
B_
SL
02
8B
_S
L0
03
B_
SL
04
5B
_S
L0
04
B_
SL
13
3B
_S
L0
84
B_
SL
02
0B
_S
L1
12
B_
SL
01
8B
_S
L0
17
B_
SL
02
4B
_S
L0
34
B_
SL
00
5B
_S
L0
68
B_
SL
07
7B
_S
L0
75
B_
SL
11
9B
_S
L0
08
B_
SL
05
7B
_S
L1
36
B_
SL
16
6B
_S
L1
49
B_
SL
07
8B
_S
L1
25
B_
SL
10
5B
_S
L0
29
B_
SL
15
4B
_S
L0
33
B_
SL
14
7B
_S
L1
70
B_
SL
08
9B
_S
L1
64
B_
SL
04
0B
_S
L0
95
B_
SL
05
6B
_S
L1
48
B_
SL
03
5B
_S
L1
59
B_
SL
17
2B
_S
L1
56
B_
SL
01
2B
_S
L0
91
B_
SL
12
6B
_S
L1
29
B_
SL
05
9B
_S
L1
32
B_
SL
00
1B
_S
L0
90
B_
SL
06
5B
_S
L0
26
B_
SL
04
8B
_S
L1
68
B_
SL
08
2B
_S
L0
19
B_
SL
14
1B
_S
L1
57
B_
SL
16
0B
_S
L1
39
B_
SL
10
0B
_S
L0
79
B_
SL
04
9B
_S
L0
07
B_
SL
03
9B
_S
L0
73
B_
SL
12
2B
_S
L1
63
B_
SL
10
1B
_S
L1
51
B_
SL
14
4B
_S
L1
50
B_
SL
17
4B
_S
L0
43
B_
SL
09
2B
_S
L1
02
B_
SL
12
4B
_S
L1
71
B_
SL
17
3B
_S
L1
04
B_
SL
08
3B
_S
L1
13
B_
SL
11
5B
_S
L0
72
USP32P1G PM 6BCO L6A3CXCL12HLA- DRB6HLA- DQ A2ZNF516FAM 171A1B3G NT5CREB5DI RAS1PLK2RG S16SPRY1SO CS3G PR183RG S1RG S2HSPA1BI TG A9SERPI NE1SNAI 1EFNB1XI RP1PER1EG R1EG R2EG R3BHLHE40FO SBDLL1HBEG FSI K1ATF3G RASPM AFFNR4A1BRE- AS1FO SL2NR4A2NR4A3PVRL2RTP5ELL2SG K1I FI T2SNX9DUSP8SYTL3PELI 1ERM NTNFPTG S2CXCL8ADMI ER3PLI N2UNC13BCEBPAADG RE2M YRI PFLT3ABHD17CEM P1SPRY2ADM 2N4BP3ETV5PDG FAI RX1LAM B2CACNA2D4CSF1RCCNA1M M P14NI NLCLEC11AAI F1LCO L5A1DDR1STAG 3CLEC14ANO S2BCL6BFLT4CD9S100A16HSPG 2PALMHTRA3UG T3A2LO C101928841LG R6LO C728175ZNF185CYG BM N1LCN8I FI 44LCPAM D8CO BLTM CC3ANKRD33BKI AA1462FAM 101BWDFY3LPAR6DO CK6CNN3NXNC6or f 25M M P17RASD1FAM 69BCALN1SI PA1L2SM AD1NPR1WFS1EG FL7ERGSHANK3I TG A6CD34DAPK1TDRD9PTPRDFRM D4ATTC28SPP1RG S18VNN1ATP9ASALL4G ATA3TFPIPCDH10ESAMM AST4VASH2CASC15DEF8H1F0FSCN1AG AP3NPDC1CDH11M ACRO D2PPM 1HPVRL1CSM D1ARHG AP24BTNL9KLF11LO C729737TNS1CYBBPADI 2M POCEACAM 6TUBB6SYTL2I G LL5SEL1L3M CO LN2M ARCKSKI AA0125ANXA5M S4A1TTNLTBTESSH2D1AAHNAKG PRI N3FCRL1M TSS1S100A10FCG R3AG NLYPRF1G ZM BTCF7CD6RO RAI TKVCANI TG A2BPPBPLG ALS1LM NACRI P1SELLM PEG 1THBS1I FI TM 1JCHAI NBM P3PTCH1F13A1ARHG EF12M YH10SPATS2LALDH1A1FLT1DCHS1AASSLO C284581G NG 11KLF4FAT1UNC79VLDLRSERI NC2LI NC01226DDI T4LHS3ST4SO X7G LDCLO C613266LO C728989HDG FRP3PCDH9STAP1CHST2PTPRMAG AP1CLEC12ALHFPL2M PPED2RG M BSDK1PCDH17SHRO O M 3SDC2M LLT4FM NL2APBB2M TCL1SNX25NETO 1FSTL4M DG A1PO U4F1KI AA0226LAKAP12LI NC01163LG R5PTG DRANKRD30BTM PRSS15CO L24A1CDH4NPR3SPO N1PLCB4TI NAG L1PREX2SETBP1TBC1D9SLI TRK4CYB5R2O VCH2G O LG A8AG O LG A8BM YEF2M CTP2I KZF2CRM P1SULF2LAM A3I G F2BP2SO X11ZNF711NRN1LI NC00689M YT1LDO CK1SCN3ACDC42BPBCECR2PLEKHG 4BRG S9M CAMM TSS1LCPXM 1KCNQ 5NFATC4ATP1A3DTX1RASAL1PTPN14NEG R1USP53SYNMCD96EVPLNAV2M EG F10KI R3DX1PDG FRBKCNA5ABCA9PTPRKSYT1APBA1NPYFG FR1CO L27A1ARHG AP32PHG DHPARD3ADG RA3SLI T2I G F2BP3THSD7AI FNLR1VAT1LLAM P5CAM K2DI RF4EFEM P1TENM 4G PR176RPS17M AP1BPAX8- AS1USP6PRO M 1M YO 10G REM 1YES1CD109KCNK17LCN10LCN6FZD6PLCH1TI AM 2KLF8BAALCNEI L1STAB1SH3BP5DPEP1PLEKHG 1PFKFB2CDC42EP3I RX2RCAN1I D3EPHA7NT5EPO N2SO CS2PCLOCTG FLI NC01013CHST15BLACEP2RY14CYTL1PLVAPFAM 69CECM 1TSPAN7SLC2A5ELFN2LI NC00114M YO 1BTM EM 236VWA2NRXN3M UC4ADG RF1ADG RG 1DENND3PRXEPAS1ARHG EF17PALD1NRP1BM P2SEM A6ATP53I NP1M M ERI M S3ARPP21LRI G 1PEG 10RAPG EF5ARHG AP29KHDRBS3ATP10AAHRKCTD12KLF9SCM L1NKAI N4NPTX1M YO 7BCPNE7M YO 18BSDK2SCN4AFAM 150BAO X2PTCL6TCL1BLO C101927697RAG 1BAHCC1VPREB1TCL1ADNTTI G LL1VPREB3
Genetic alteration
PAX5 P80R
Other PAX5 mutations
PAX5 deletion
DDDD- - D- DD- DDD- - D- - DD- ZZ- ZZZZZ- ZZZ- ZZZZZZZZZ- ZZ- Z- - - - - - - - - - - - - - - - - KKKKKB- - - - - - - - HHBBBBBBBBBBBBBBBB- B- B- - - - - - - - - B- - - - - L - - P- - - L - PM- - - - - L - - - B- - - - - - - - - - - - - - P- Z- - MB- - - - - - - B- - B
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ++++++++++++++- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - + - - + - - - - - - - - - - - - - - - - - - - - - - - +++- - - - - - - - ++ - - - . - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + - - - - +++- - . - - - - - - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + - - - - - - - - - - - - -
. . . . - ++ - . + . . + - . - . + - - . . . . + . - . - . . . - + . . - - . - + . . - . . . - - - - - - - ++++++++- - . . . . . . - . . . . . + . . . - + - + . . . - . - - - . . - . + - - - - . - . - - - - + - - . . . ++++ . - . . . - - - - - - . . . . . - . . . . . . - + - - + . - . ++ . + . . . - . . . . . + . . . . . . .
-3.0 -2.9 -2.8 -2.7 -2.6 -2.5 -2.4 -2.3 -2.2 -2.1 -2.0 -1.9 -1.8 -1.7 -1.6 -1.4 -1.3 -1.2 -1.1 -1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0
ZNF384DUX4/ERG
Classifying alterations
ZNF384 fusion BCR-ABL1-like rearrangement Low hypodiploidy PAX5 fusionDUX4 rearrangement MLL/KMT2A rearrangement Hyperdiploidy MEF2D fusion
BK
-
LH
.
PM
BCR-ABL1-likeDUX4/ERG ZNF384
Gene expression profiling
RNA-seq analysis for « B-other » ALL cases
ZD
+
321
0-1-2-3
Classifying alterations
BCR-ABL1-likeKMT2A
B_
SL
06
7B
_S
L0
61
B_
SL
05
0B
_S
L0
52
B_
SL
13
8B
_S
L1
69
B_
SL
03
2B
_S
L0
60
B_
SL
09
3B
_S
L0
23
B_
SL
06
3B
_S
L0
76
B_
SL
01
1B
_S
L0
06
B_
SL
03
1B
_S
L0
37
B_
SL
11
1B
_S
L0
13
B_
SL
15
5B
_S
L0
42
B_
SL
10
7B
_S
L1
28
B_
SL
07
4B
_S
L1
08
B_
SL
16
5B
_S
L0
46
B_
SL
00
2B
_S
L1
27
B_
SL
02
2B
_S
L1
09
B_
SL
06
9B
_S
L0
71
B_
SL
11
8B
_S
L1
40
B_
SL
12
3B
_S
L0
98
B_
SL
14
5B
_S
L1
46
B_
SL
10
3B
_S
L0
21
B_
SL
01
4B
_S
L0
30
B_
SL
05
3B
_S
L1
35
B_
SL
08
6B
_S
L1
14
B_
SL
05
5B
_S
L1
61
B_
SL
05
8B
_S
L0
09
B_
SL
01
5B
_S
L1
53
B_
SL
03
6B
_S
L1
42
B_
SL
04
4B
_S
L1
34
B_
SL
12
1B
_S
L0
16
B_
SL
04
7B
_S
L1
20
B_
SL
15
2B
_S
L0
99
B_
SL
13
7B
_S
L1
43
B_
SL
08
7B
_S
L0
51
B_
SL
06
2B
_S
L0
88
B_
SL
13
0B
_S
L0
27
B_
SL
07
0B
_S
L0
96
B_
SL
09
4B
_S
L1
10
B_
SL
09
7B
_S
L1
06
B_
SL
01
0B
_S
L1
67
B_
SL
06
4B
_S
L1
31
B_
SL
03
8B
_S
L0
80
B_
SL
11
7B
_S
L0
25
B_
SL
08
5B
_S
L0
54
B_
SL
06
6B
_S
L1
16
B_
SL
02
8B
_S
L0
03
B_
SL
04
5B
_S
L0
04
B_
SL
13
3B
_S
L0
84
B_
SL
02
0B
_S
L1
12
B_
SL
01
8B
_S
L0
17
B_
SL
02
4B
_S
L0
34
B_
SL
00
5B
_S
L0
68
B_
SL
07
7B
_S
L0
75
B_
SL
11
9B
_S
L0
08
B_
SL
05
7B
_S
L1
36
B_
SL
16
6B
_S
L1
49
B_
SL
07
8B
_S
L1
25
B_
SL
10
5B
_S
L0
29
B_
SL
15
4B
_S
L0
33
B_
SL
14
7B
_S
L1
70
B_
SL
08
9B
_S
L1
64
B_
SL
04
0B
_S
L0
95
B_
SL
05
6B
_S
L1
48
B_
SL
03
5B
_S
L1
59
B_
SL
17
2B
_S
L1
56
B_
SL
01
2B
_S
L0
91
B_
SL
12
6B
_S
L1
29
B_
SL
05
9B
_S
L1
32
B_
SL
00
1B
_S
L0
90
B_
SL
06
5B
_S
L0
26
B_
SL
04
8B
_S
L1
68
B_
SL
08
2B
_S
L0
19
B_
SL
14
1B
_S
L1
57
B_
SL
16
0B
_S
L1
39
B_
SL
10
0B
_S
L0
79
B_
SL
04
9B
_S
L0
07
B_
SL
03
9B
_S
L0
73
B_
SL
12
2B
_S
L1
63
B_
SL
10
1B
_S
L1
51
B_
SL
14
4B
_S
L1
50
B_
SL
17
4B
_S
L0
43
B_
SL
09
2B
_S
L1
02
B_
SL
12
4B
_S
L1
71
B_
SL
17
3B
_S
L1
04
B_
SL
08
3B
_S
L1
13
B_
SL
11
5B
_S
L0
72
USP32P1G PM 6BCO L6A3CXCL12HLA- DRB6HLA- DQ A2ZNF516FAM 171A1B3G NT5CREB5DI RAS1PLK2RG S16SPRY1SO CS3G PR183RG S1RG S2HSPA1BI TG A9SERPI NE1SNAI 1EFNB1XI RP1PER1EG R1EG R2EG R3BHLHE40FO SBDLL1HBEG FSI K1ATF3G RASPM AFFNR4A1BRE- AS1FO SL2NR4A2NR4A3PVRL2RTP5ELL2SG K1I FI T2SNX9DUSP8SYTL3PELI 1ERM NTNFPTG S2CXCL8ADMI ER3PLI N2UNC13BCEBPAADG RE2M YRI PFLT3ABHD17CEM P1SPRY2ADM 2N4BP3ETV5PDG FAI RX1LAM B2CACNA2D4CSF1RCCNA1M M P14NI NLCLEC11AAI F1LCO L5A1DDR1STAG 3CLEC14ANO S2BCL6BFLT4CD9S100A16HSPG 2PALMHTRA3UG T3A2LO C101928841LG R6LO C728175ZNF185CYG BM N1LCN8I FI 44LCPAM D8CO BLTM CC3ANKRD33BKI AA1462FAM 101BWDFY3LPAR6DO CK6CNN3NXNC6or f 25M M P17RASD1FAM 69BCALN1SI PA1L2SM AD1NPR1WFS1EG FL7ERGSHANK3I TG A6CD34DAPK1TDRD9PTPRDFRM D4ATTC28SPP1RG S18VNN1ATP9ASALL4G ATA3TFPIPCDH10ESAMM AST4VASH2CASC15DEF8H1F0FSCN1AG AP3NPDC1CDH11M ACRO D2PPM 1HPVRL1CSM D1ARHG AP24BTNL9KLF11LO C729737TNS1CYBBPADI 2M POCEACAM 6TUBB6SYTL2I G LL5SEL1L3M CO LN2M ARCKSKI AA0125ANXA5M S4A1TTNLTBTESSH2D1AAHNAKG PRI N3FCRL1M TSS1S100A10FCG R3AG NLYPRF1G ZM BTCF7CD6RO RAI TKVCANI TG A2BPPBPLG ALS1LM NACRI P1SELLM PEG 1THBS1I FI TM 1JCHAI NBM P3PTCH1F13A1ARHG EF12M YH10SPATS2LALDH1A1FLT1DCHS1AASSLO C284581G NG 11KLF4FAT1UNC79VLDLRSERI NC2LI NC01226DDI T4LHS3ST4SO X7G LDCLO C613266LO C728989HDG FRP3PCDH9STAP1CHST2PTPRMAG AP1CLEC12ALHFPL2M PPED2RG M BSDK1PCDH17SHRO O M 3SDC2M LLT4FM NL2APBB2M TCL1SNX25NETO 1FSTL4M DG A1PO U4F1KI AA0226LAKAP12LI NC01163LG R5PTG DRANKRD30BTM PRSS15CO L24A1CDH4NPR3SPO N1PLCB4TI NAG L1PREX2SETBP1TBC1D9SLI TRK4CYB5R2O VCH2G O LG A8AG O LG A8BM YEF2M CTP2I KZF2CRM P1SULF2LAM A3I G F2BP2SO X11ZNF711NRN1LI NC00689M YT1LDO CK1SCN3ACDC42BPBCECR2PLEKHG 4BRG S9M CAMM TSS1LCPXM 1KCNQ 5NFATC4ATP1A3DTX1RASAL1PTPN14NEG R1USP53SYNMCD96EVPLNAV2M EG F10KI R3DX1PDG FRBKCNA5ABCA9PTPRKSYT1APBA1NPYFG FR1CO L27A1ARHG AP32PHG DHPARD3ADG RA3SLI T2I G F2BP3THSD7AI FNLR1VAT1LLAM P5CAM K2DI RF4EFEM P1TENM 4G PR176RPS17M AP1BPAX8- AS1USP6PRO M 1M YO 10G REM 1YES1CD109KCNK17LCN10LCN6FZD6PLCH1TI AM 2KLF8BAALCNEI L1STAB1SH3BP5DPEP1PLEKHG 1PFKFB2CDC42EP3I RX2RCAN1I D3EPHA7NT5EPO N2SO CS2PCLOCTG FLI NC01013CHST15BLACEP2RY14CYTL1PLVAPFAM 69CECM 1TSPAN7SLC2A5ELFN2LI NC00114M YO 1BTM EM 236VWA2NRXN3M UC4ADG RF1ADG RG 1DENND3PRXEPAS1ARHG EF17PALD1NRP1BM P2SEM A6ATP53I NP1M M ERI M S3ARPP21LRI G 1PEG 10RAPG EF5ARHG AP29KHDRBS3ATP10AAHRKCTD12KLF9SCM L1NKAI N4NPTX1M YO 7BCPNE7M YO 18BSDK2SCN4AFAM 150BAO X2PTCL6TCL1BLO C101927697RAG 1BAHCC1VPREB1TCL1ADNTTI G LL1VPREB3
Genetic alteration
PAX5 P80R
Other PAX5 mutations
PAX5 deletion
DDDD- - D- DD- DDD- - D- - DD- ZZ- ZZZZZ- ZZZ- ZZZZZZZZZ- ZZ- Z- - - - - - - - - - - - - - - - - KKKKKB- - - - - - - - HHBBBBBBBBBBBBBBBB- B- B- - - - - - - - - B- - - - - L - - P- - - L - PM- - - - - L - - - B- - - - - - - - - - - - - - P- Z- - MB- - - - - - - B- - B
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ++++++++++++++- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - + - - + - - - - - - - - - - - - - - - - - - - - - - - +++- - - - - - - - ++ - - - . - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + - - - - +++- - . - - - - - - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + - - - - - - - - - - - - -
. . . . - ++ - . + . . + - . - . + - - . . . . + . - . - . . . - + . . - - . - + . . - . . . - - - - - - - ++++++++- - . . . . . . - . . . . . + . . . - + - + . . . - . - - - . . - . + - - - - . - . - - - - + - - . . . ++++ . - . . . - - - - - - . . . . . - . . . . . . - + - - + . - . ++ . + . . . - . . . . . + . . . . . . .
-3.0 -2.9 -2.8 -2.7 -2.6 -2.5 -2.4 -2.3 -2.2 -2.1 -2.0 -1.9 -1.8 -1.7 -1.6 -1.4 -1.3 -1.2 -1.1 -1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0
ZNF384DUX4/ERG
Classifying alterations
ZNF384 fusion BCR-ABL1-like rearrangement Low hypodiploidy PAX5 fusionDUX4 rearrangement MLL/KMT2A rearrangement Hyperdiploidy MEF2D fusion
BK
-
LH
.
PM
RNA-seq analysis for « B-other » ALL cases
Gene expression profiling
-> PAX5 P80R mutation
PAX5 deletions
ZD
+
321
0-1-2-3
Classifying alterations
BCR-ABL1-like
PAX5 P80RPAX5 other mutations
KMT2A
B_
SL
06
7B
_S
L0
61
B_
SL
05
0B
_S
L0
52
B_
SL
13
8B
_S
L1
69
B_
SL
03
2B
_S
L0
60
B_
SL
09
3B
_S
L0
23
B_
SL
06
3B
_S
L0
76
B_
SL
01
1B
_S
L0
06
B_
SL
03
1B
_S
L0
37
B_
SL
11
1B
_S
L0
13
B_
SL
15
5B
_S
L0
42
B_
SL
10
7B
_S
L1
28
B_
SL
07
4B
_S
L1
08
B_
SL
16
5B
_S
L0
46
B_
SL
00
2B
_S
L1
27
B_
SL
02
2B
_S
L1
09
B_
SL
06
9B
_S
L0
71
B_
SL
11
8B
_S
L1
40
B_
SL
12
3B
_S
L0
98
B_
SL
14
5B
_S
L1
46
B_
SL
10
3B
_S
L0
21
B_
SL
01
4B
_S
L0
30
B_
SL
05
3B
_S
L1
35
B_
SL
08
6B
_S
L1
14
B_
SL
05
5B
_S
L1
61
B_
SL
05
8B
_S
L0
09
B_
SL
01
5B
_S
L1
53
B_
SL
03
6B
_S
L1
42
B_
SL
04
4B
_S
L1
34
B_
SL
12
1B
_S
L0
16
B_
SL
04
7B
_S
L1
20
B_
SL
15
2B
_S
L0
99
B_
SL
13
7B
_S
L1
43
B_
SL
08
7B
_S
L0
51
B_
SL
06
2B
_S
L0
88
B_
SL
13
0B
_S
L0
27
B_
SL
07
0B
_S
L0
96
B_
SL
09
4B
_S
L1
10
B_
SL
09
7B
_S
L1
06
B_
SL
01
0B
_S
L1
67
B_
SL
06
4B
_S
L1
31
B_
SL
03
8B
_S
L0
80
B_
SL
11
7B
_S
L0
25
B_
SL
08
5B
_S
L0
54
B_
SL
06
6B
_S
L1
16
B_
SL
02
8B
_S
L0
03
B_
SL
04
5B
_S
L0
04
B_
SL
13
3B
_S
L0
84
B_
SL
02
0B
_S
L1
12
B_
SL
01
8B
_S
L0
17
B_
SL
02
4B
_S
L0
34
B_
SL
00
5B
_S
L0
68
B_
SL
07
7B
_S
L0
75
B_
SL
11
9B
_S
L0
08
B_
SL
05
7B
_S
L1
36
B_
SL
16
6B
_S
L1
49
B_
SL
07
8B
_S
L1
25
B_
SL
10
5B
_S
L0
29
B_
SL
15
4B
_S
L0
33
B_
SL
14
7B
_S
L1
70
B_
SL
08
9B
_S
L1
64
B_
SL
04
0B
_S
L0
95
B_
SL
05
6B
_S
L1
48
B_
SL
03
5B
_S
L1
59
B_
SL
17
2B
_S
L1
56
B_
SL
01
2B
_S
L0
91
B_
SL
12
6B
_S
L1
29
B_
SL
05
9B
_S
L1
32
B_
SL
00
1B
_S
L0
90
B_
SL
06
5B
_S
L0
26
B_
SL
04
8B
_S
L1
68
B_
SL
08
2B
_S
L0
19
B_
SL
14
1B
_S
L1
57
B_
SL
16
0B
_S
L1
39
B_
SL
10
0B
_S
L0
79
B_
SL
04
9B
_S
L0
07
B_
SL
03
9B
_S
L0
73
B_
SL
12
2B
_S
L1
63
B_
SL
10
1B
_S
L1
51
B_
SL
14
4B
_S
L1
50
B_
SL
17
4B
_S
L0
43
B_
SL
09
2B
_S
L1
02
B_
SL
12
4B
_S
L1
71
B_
SL
17
3B
_S
L1
04
B_
SL
08
3B
_S
L1
13
B_
SL
11
5B
_S
L0
72
USP32P1G PM 6BCO L6A3CXCL12HLA- DRB6HLA- DQ A2ZNF516FAM 171A1B3G NT5CREB5DI RAS1PLK2RG S16SPRY1SO CS3G PR183RG S1RG S2HSPA1BI TG A9SERPI NE1SNAI 1EFNB1XI RP1PER1EG R1EG R2EG R3BHLHE40FO SBDLL1HBEG FSI K1ATF3G RASPM AFFNR4A1BRE- AS1FO SL2NR4A2NR4A3PVRL2RTP5ELL2SG K1I FI T2SNX9DUSP8SYTL3PELI 1ERM NTNFPTG S2CXCL8ADMI ER3PLI N2UNC13BCEBPAADG RE2M YRI PFLT3ABHD17CEM P1SPRY2ADM 2N4BP3ETV5PDG FAI RX1LAM B2CACNA2D4CSF1RCCNA1M M P14NI NLCLEC11AAI F1LCO L5A1DDR1STAG 3CLEC14ANO S2BCL6BFLT4CD9S100A16HSPG 2PALMHTRA3UG T3A2LO C101928841LG R6LO C728175ZNF185CYG BM N1LCN8I FI 44LCPAM D8CO BLTM CC3ANKRD33BKI AA1462FAM 101BWDFY3LPAR6DO CK6CNN3NXNC6or f 25M M P17RASD1FAM 69BCALN1SI PA1L2SM AD1NPR1WFS1EG FL7ERGSHANK3I TG A6CD34DAPK1TDRD9PTPRDFRM D4ATTC28SPP1RG S18VNN1ATP9ASALL4G ATA3TFPIPCDH10ESAMM AST4VASH2CASC15DEF8H1F0FSCN1AG AP3NPDC1CDH11M ACRO D2PPM 1HPVRL1CSM D1ARHG AP24BTNL9KLF11LO C729737TNS1CYBBPADI 2M POCEACAM 6TUBB6SYTL2I G LL5SEL1L3M CO LN2M ARCKSKI AA0125ANXA5M S4A1TTNLTBTESSH2D1AAHNAKG PRI N3FCRL1M TSS1S100A10FCG R3AG NLYPRF1G ZM BTCF7CD6RO RAI TKVCANI TG A2BPPBPLG ALS1LM NACRI P1SELLM PEG 1THBS1I FI TM 1JCHAI NBM P3PTCH1F13A1ARHG EF12M YH10SPATS2LALDH1A1FLT1DCHS1AASSLO C284581G NG 11KLF4FAT1UNC79VLDLRSERI NC2LI NC01226DDI T4LHS3ST4SO X7G LDCLO C613266LO C728989HDG FRP3PCDH9STAP1CHST2PTPRMAG AP1CLEC12ALHFPL2M PPED2RG M BSDK1PCDH17SHRO O M 3SDC2M LLT4FM NL2APBB2M TCL1SNX25NETO 1FSTL4M DG A1PO U4F1KI AA0226LAKAP12LI NC01163LG R5PTG DRANKRD30BTM PRSS15CO L24A1CDH4NPR3SPO N1PLCB4TI NAG L1PREX2SETBP1TBC1D9SLI TRK4CYB5R2O VCH2G O LG A8AG O LG A8BM YEF2M CTP2I KZF2CRM P1SULF2LAM A3I G F2BP2SO X11ZNF711NRN1LI NC00689M YT1LDO CK1SCN3ACDC42BPBCECR2PLEKHG 4BRG S9M CAMM TSS1LCPXM 1KCNQ 5NFATC4ATP1A3DTX1RASAL1PTPN14NEG R1USP53SYNMCD96EVPLNAV2M EG F10KI R3DX1PDG FRBKCNA5ABCA9PTPRKSYT1APBA1NPYFG FR1CO L27A1ARHG AP32PHG DHPARD3ADG RA3SLI T2I G F2BP3THSD7AI FNLR1VAT1LLAM P5CAM K2DI RF4EFEM P1TENM 4G PR176RPS17M AP1BPAX8- AS1USP6PRO M 1M YO 10G REM 1YES1CD109KCNK17LCN10LCN6FZD6PLCH1TI AM 2KLF8BAALCNEI L1STAB1SH3BP5DPEP1PLEKHG 1PFKFB2CDC42EP3I RX2RCAN1I D3EPHA7NT5EPO N2SO CS2PCLOCTG FLI NC01013CHST15BLACEP2RY14CYTL1PLVAPFAM 69CECM 1TSPAN7SLC2A5ELFN2LI NC00114M YO 1BTM EM 236VWA2NRXN3M UC4ADG RF1ADG RG 1DENND3PRXEPAS1ARHG EF17PALD1NRP1BM P2SEM A6ATP53I NP1M M ERI M S3ARPP21LRI G 1PEG 10RAPG EF5ARHG AP29KHDRBS3ATP10AAHRKCTD12KLF9SCM L1NKAI N4NPTX1M YO 7BCPNE7M YO 18BSDK2SCN4AFAM 150BAO X2PTCL6TCL1BLO C101927697RAG 1BAHCC1VPREB1TCL1ADNTTI G LL1VPREB3
Genetic alteration
PAX5 P80R
Other PAX5 mutations
PAX5 deletion
DDDD- - D- DD- DDD- - D- - DD- ZZ- ZZZZZ- ZZZ- ZZZZZZZZZ- ZZ- Z- - - - - - - - - - - - - - - - - KKKKKB- - - - - - - - HHBBBBBBBBBBBBBBBB- B- B- - - - - - - - - B- - - - - L - - P- - - L - PM- - - - - L - - - B- - - - - - - - - - - - - - P- Z- - MB- - - - - - - B- - B
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ++++++++++++++- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - + - - + - - - - - - - - - - - - - - - - - - - - - - - +++- - - - - - - - ++ - - - . - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + - - - - +++- - . - - - - - - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + - - - - - - - - - - - - -
. . . . - ++ - . + . . + - . - . + - - . . . . + . - . - . . . - + . . - - . - + . . - . . . - - - - - - - ++++++++- - . . . . . . - . . . . . + . . . - + - + . . . - . - - - . . - . + - - - - . - . - - - - + - - . . . ++++ . - . . . - - - - - - . . . . . - . . . . . . - + - - + . - . ++ . + . . . - . . . . . + . . . . . . .
-3.0 -2.9 -2.8 -2.7 -2.6 -2.5 -2.4 -2.3 -2.2 -2.1 -2.0 -1.9 -1.8 -1.7 -1.6 -1.4 -1.3 -1.2 -1.1 -1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0
ZNF384DUX4/ERG PAX5P80R
Classifying alterations
ZNF384 fusion BCR-ABL1-like rearrangement Low hypodiploidy PAX5 fusionDUX4 rearrangement MLL/KMT2A rearrangement Hyperdiploidy MEF2D fusion
PAX5 alterationsPositive Negative Not available
BK
-
LH
.
PM
Pro80Arg
Gene expression profilingGene mutation analysis
RNA-seq analysis for « B-other » ALL cases
Passet et al., Blood 2019
0.00
0.20
0.40
0.60
0.80
1.00
Ove
rall
Su
rviv
al
14 10 10 10 9 9 5 1 1 0PAX5P80R
298 140 107 87 64 43 25 8 4 0No PAX5P80R
Number at risk
0 1 2 3 4 5 6 7 8 9Time(years)
P=0.036
Biological and clinical features associated with PAX5 P80R
0.00
0.20
0.40
0.60
0.80
1.00
Overa
ll S
urv
ival
0 1 2 3 4 5 6 7 8 9
Time(years)
PAX5P80R
No PAX5P80R
B_
SL12
0B
_SL
152
B_
SL01
602
9-00
5602
1-03
54B
_SL
099
1304
4B
_SL
121
B_
SL13
715
112
B_
SL04
402
1-00
2701
5-02
26B
_SL
143
008-
0382
1650
40B
_SL
134
1500
113
054
B_
SL04
7B
_SL
142
B_
SL03
600
5-01
12B
_SL
087
B_
SL05
112
044
1146
1112
045
1508
712
078
RNA-seqCGH-array
Targeted NGSSanger PAX5
PAX5 P80R
PAX5 2nd allele
CDKN2A loss
IKZF1 deletion
Signaling
NRAS
KRAS
IL7R
PTPN11
P2RY8-CRLF2
FLT3
NF1
JAK2
PTPRC
SH2B3
PAX5 P80R PAX5 2nd allele CDKN2A loss IKZF1 deletion
Homozygous
Heterozygous
Deleted
Mutated
Monoallelic
Biallelic
Whole
Intragenic
Negative
Not available
Passet et al., Blood 2019
✓ Inactivation of PAX5 2nd allele, CDKN2A loss, RAS signalling
✓ Good response to treatment, favorable outcome
Hyperdiploidy
Hypo/neartriploidy
MLLr
Other
PAX5P80R
TCF3-PBX1
Genomic classification at RNA-seq era: update GRAALL-2014-B on 310 patients
BCR-ABL1-like18%
MLL/KMT2A16%
Low hypodiploidy10%
High hyperdiploidy7%
DUX4/ERG6%
ZNF384 fusion6%
PAX5 P80R6%TCF3-PBX1
4%MYC+/-BCL2
3%
IGH-CEBP3%ETV6-RUNX1
2%
PAX5 fusion2%
New2%
iAMP211%
TCF3-HLF1%
MEF2D-BCL91%
Other12%
ZD
+
321
0-1-2-3
Classifying alterations
BCR-ABL1-likeKMT2A
B_
SL
06
7B
_S
L0
61
B_
SL
05
0B
_S
L0
52
B_
SL
13
8B
_S
L1
69
B_
SL
03
2B
_S
L0
60
B_
SL
09
3B
_S
L0
23
B_
SL
06
3B
_S
L0
76
B_
SL
01
1B
_S
L0
06
B_
SL
03
1B
_S
L0
37
B_
SL
11
1B
_S
L0
13
B_
SL
15
5B
_S
L0
42
B_
SL
10
7B
_S
L1
28
B_
SL
07
4B
_S
L1
08
B_
SL
16
5B
_S
L0
46
B_
SL
00
2B
_S
L1
27
B_
SL
02
2B
_S
L1
09
B_
SL
06
9B
_S
L0
71
B_
SL
11
8B
_S
L1
40
B_
SL
12
3B
_S
L0
98
B_
SL
14
5B
_S
L1
46
B_
SL
10
3B
_S
L0
21
B_
SL
01
4B
_S
L0
30
B_
SL
05
3B
_S
L1
35
B_
SL
08
6B
_S
L1
14
B_
SL
05
5B
_S
L1
61
B_
SL
05
8B
_S
L0
09
B_
SL
01
5B
_S
L1
53
B_
SL
03
6B
_S
L1
42
B_
SL
04
4B
_S
L1
34
B_
SL
12
1B
_S
L0
16
B_
SL
04
7B
_S
L1
20
B_
SL
15
2B
_S
L0
99
B_
SL
13
7B
_S
L1
43
B_
SL
08
7B
_S
L0
51
B_
SL
06
2B
_S
L0
88
B_
SL
13
0B
_S
L0
27
B_
SL
07
0B
_S
L0
96
B_
SL
09
4B
_S
L1
10
B_
SL
09
7B
_S
L1
06
B_
SL
01
0B
_S
L1
67
B_
SL
06
4B
_S
L1
31
B_
SL
03
8B
_S
L0
80
B_
SL
11
7B
_S
L0
25
B_
SL
08
5B
_S
L0
54
B_
SL
06
6B
_S
L1
16
B_
SL
02
8B
_S
L0
03
B_
SL
04
5B
_S
L0
04
B_
SL
13
3B
_S
L0
84
B_
SL
02
0B
_S
L1
12
B_
SL
01
8B
_S
L0
17
B_
SL
02
4B
_S
L0
34
B_
SL
00
5B
_S
L0
68
B_
SL
07
7B
_S
L0
75
B_
SL
11
9B
_S
L0
08
B_
SL
05
7B
_S
L1
36
B_
SL
16
6B
_S
L1
49
B_
SL
07
8B
_S
L1
25
B_
SL
10
5B
_S
L0
29
B_
SL
15
4B
_S
L0
33
B_
SL
14
7B
_S
L1
70
B_
SL
08
9B
_S
L1
64
B_
SL
04
0B
_S
L0
95
B_
SL
05
6B
_S
L1
48
B_
SL
03
5B
_S
L1
59
B_
SL
17
2B
_S
L1
56
B_
SL
01
2B
_S
L0
91
B_
SL
12
6B
_S
L1
29
B_
SL
05
9B
_S
L1
32
B_
SL
00
1B
_S
L0
90
B_
SL
06
5B
_S
L0
26
B_
SL
04
8B
_S
L1
68
B_
SL
08
2B
_S
L0
19
B_
SL
14
1B
_S
L1
57
B_
SL
16
0B
_S
L1
39
B_
SL
10
0B
_S
L0
79
B_
SL
04
9B
_S
L0
07
B_
SL
03
9B
_S
L0
73
B_
SL
12
2B
_S
L1
63
B_
SL
10
1B
_S
L1
51
B_
SL
14
4B
_S
L1
50
B_
SL
17
4B
_S
L0
43
B_
SL
09
2B
_S
L1
02
B_
SL
12
4B
_S
L1
71
B_
SL
17
3B
_S
L1
04
B_
SL
08
3B
_S
L1
13
B_
SL
11
5B
_S
L0
72
USP32P1G PM 6BCO L6A3CXCL12HLA- DRB6HLA- DQ A2ZNF516FAM 171A1B3G NT5CREB5DI RAS1PLK2RG S16SPRY1SO CS3G PR183RG S1RG S2HSPA1BI TG A9SERPI NE1SNAI 1EFNB1XI RP1PER1EG R1EG R2EG R3BHLHE40FO SBDLL1HBEG FSI K1ATF3G RASPM AFFNR4A1BRE- AS1FO SL2NR4A2NR4A3PVRL2RTP5ELL2SG K1I FI T2SNX9DUSP8SYTL3PELI 1ERM NTNFPTG S2CXCL8ADMI ER3PLI N2UNC13BCEBPAADG RE2M YRI PFLT3ABHD17CEM P1SPRY2ADM 2N4BP3ETV5PDG FAI RX1LAM B2CACNA2D4CSF1RCCNA1M M P14NI NLCLEC11AAI F1LCO L5A1DDR1STAG 3CLEC14ANO S2BCL6BFLT4CD9S100A16HSPG 2PALMHTRA3UG T3A2LO C101928841LG R6LO C728175ZNF185CYG BM N1LCN8I FI 44LCPAM D8CO BLTM CC3ANKRD33BKI AA1462FAM 101BWDFY3LPAR6DO CK6CNN3NXNC6or f 25M M P17RASD1FAM 69BCALN1SI PA1L2SM AD1NPR1WFS1EG FL7ERGSHANK3I TG A6CD34DAPK1TDRD9PTPRDFRM D4ATTC28SPP1RG S18VNN1ATP9ASALL4G ATA3TFPIPCDH10ESAMM AST4VASH2CASC15DEF8H1F0FSCN1AG AP3NPDC1CDH11M ACRO D2PPM 1HPVRL1CSM D1ARHG AP24BTNL9KLF11LO C729737TNS1CYBBPADI 2M POCEACAM 6TUBB6SYTL2I G LL5SEL1L3M CO LN2M ARCKSKI AA0125ANXA5M S4A1TTNLTBTESSH2D1AAHNAKG PRI N3FCRL1M TSS1S100A10FCG R3AG NLYPRF1G ZM BTCF7CD6RO RAI TKVCANI TG A2BPPBPLG ALS1LM NACRI P1SELLM PEG 1THBS1I FI TM 1JCHAI NBM P3PTCH1F13A1ARHG EF12M YH10SPATS2LALDH1A1FLT1DCHS1AASSLO C284581G NG 11KLF4FAT1UNC79VLDLRSERI NC2LI NC01226DDI T4LHS3ST4SO X7G LDCLO C613266LO C728989HDG FRP3PCDH9STAP1CHST2PTPRMAG AP1CLEC12ALHFPL2M PPED2RG M BSDK1PCDH17SHRO O M 3SDC2M LLT4FM NL2APBB2M TCL1SNX25NETO 1FSTL4M DG A1PO U4F1KI AA0226LAKAP12LI NC01163LG R5PTG DRANKRD30BTM PRSS15CO L24A1CDH4NPR3SPO N1PLCB4TI NAG L1PREX2SETBP1TBC1D9SLI TRK4CYB5R2O VCH2G O LG A8AG O LG A8BM YEF2M CTP2I KZF2CRM P1SULF2LAM A3I G F2BP2SO X11ZNF711NRN1LI NC00689M YT1LDO CK1SCN3ACDC42BPBCECR2PLEKHG 4BRG S9M CAMM TSS1LCPXM 1KCNQ 5NFATC4ATP1A3DTX1RASAL1PTPN14NEG R1USP53SYNMCD96EVPLNAV2M EG F10KI R3DX1PDG FRBKCNA5ABCA9PTPRKSYT1APBA1NPYFG FR1CO L27A1ARHG AP32PHG DHPARD3ADG RA3SLI T2I G F2BP3THSD7AI FNLR1VAT1LLAM P5CAM K2DI RF4EFEM P1TENM 4G PR176RPS17M AP1BPAX8- AS1USP6PRO M 1M YO 10G REM 1YES1CD109KCNK17LCN10LCN6FZD6PLCH1TI AM 2KLF8BAALCNEI L1STAB1SH3BP5DPEP1PLEKHG 1PFKFB2CDC42EP3I RX2RCAN1I D3EPHA7NT5EPO N2SO CS2PCLOCTG FLI NC01013CHST15BLACEP2RY14CYTL1PLVAPFAM 69CECM 1TSPAN7SLC2A5ELFN2LI NC00114M YO 1BTM EM 236VWA2NRXN3M UC4ADG RF1ADG RG 1DENND3PRXEPAS1ARHG EF17PALD1NRP1BM P2SEM A6ATP53I NP1M M ERI M S3ARPP21LRI G 1PEG 10RAPG EF5ARHG AP29KHDRBS3ATP10AAHRKCTD12KLF9SCM L1NKAI N4NPTX1M YO 7BCPNE7M YO 18BSDK2SCN4AFAM 150BAO X2PTCL6TCL1BLO C101927697RAG 1BAHCC1VPREB1TCL1ADNTTI G LL1VPREB3
Genetic alteration
PAX5 P80R
Other PAX5 mutations
PAX5 deletion
DDDD- - D- DD- DDD- - D- - DD- ZZ- ZZZZZ- ZZZ- ZZZZZZZZZ- ZZ- Z- - - - - - - - - - - - - - - - - KKKKKB- - - - - - - - HHBBBBBBBBBBBBBBBB- B- B- - - - - - - - - B- - - - - L - - P- - - L - PM- - - - - L - - - B- - - - - - - - - - - - - - P- Z- - MB- - - - - - - B- - B
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ++++++++++++++- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - - - - - - - - - - - - - - - - - - - + - - + - - - - - - - - - - - - - - - - - - - - - - - +++- - - - - - - - ++ - - - . - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - - - - - - - - - + - - - - +++- - . - - - - - - + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - - + - - - - - - - - - - - - -
. . . . - ++ - . + . . + - . - . + - - . . . . + . - . - . . . - + . . - - . - + . . - . . . - - - - - - - ++++++++- - . . . . . . - . . . . . + . . . - + - + . . . - . - - - . . - . + - - - - . - . - - - - + - - . . . ++++ . - . . . - - - - - - . . . . . - . . . . . . - + - - + . - . ++ . + . . . - . . . . . + . . . . . . .
-3.0 -2.9 -2.8 -2.7 -2.6 -2.5 -2.4 -2.3 -2.2 -2.1 -2.0 -1.9 -1.8 -1.7 -1.6 -1.4 -1.3 -1.2 -1.1 -1.0 -0.9 -0.8 -0.7 -0.6 -0.5 -0.4 -0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.6 1.7 1.8 1.9 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 3.0
ZNF384DUX4/ERG
Classifying alterations
ZNF384 fusion BCR-ABL1-like rearrangement Low hypodiploidy PAX5 fusionDUX4 rearrangement MLL/KMT2A rearrangement Hyperdiploidy MEF2D fusion
BK
-
LH
.
PM
???
Gene expression profiling
RNA-seq analysis for « B-other » ALL cases
-> New genetic subtype to be explored
LAL-B Ph+
Ph. Rousselot, unpublished data
M o n th s
BC
R-A
BL
IS
%
-6 6 1 2 1 8 2 4 3 0 3 6 4 2 4 8 5 4 6 0
0 .0 0 1
0 .0 1
1
1 0
1 0 0
U n d e te c ta b le
M M R
0
AutoHSCT
IM Nilotinib
MRD1
IgH0.01
IgH neg IgH neg
BLINATUMOMAB
MRD positivity after auto-SCT 36y female, Ph+ ALL, e1a2
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
Neg
100%
10%
1%
0,01%
0,001%
0,1%
10010-110-210-410-5 10-3
PnqNeg
Ig/TCR
High number of discordant results between BCR-ABL1 and Ig/TCR
n=101 n=12
n = 433 samples
rp = 0.47
77 patients
BCR-ABL1/ABL1 transcripts
(Positive
not quantifiable)
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
BCR-ABL1/ABL1 transcripts
Neg
100%
10%
1%
0,01%
0,001%
0,1%
BM PB
10-110-210-410-5 10-3
PnqNeg
Ig/TCR100
n=181 samples
rp=0.60
n=252 samples
rp=0.38
More discordant results in peripheral blood than in bone marrow
n=36 n=61
-> In agreement with lower levels of B-cell ALL MRD in PB than in BM (van der Velden, Leukemia 2002)
MRD1
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
n=116
MRD2
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
MRD3
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
MRD4
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
n=126 n=96 n=95
BCR-ABL1/ABL1 transcripts
Ig/TCR
Dissociation persists at late timepoints
-> In agreement with persistance of BCR-ABL1 clonal hematopoiesis after
lymphoblasts clearance
Nagel, Blood 2017
BCR-ABL1–positive cells outside the B-lineage compartment
are found in 40% of adult patients with Ph-ALL
-6
-4
-2
0
-6 -4 -2 0
IgTcr
BC
R.A
BL
Neg
100%
10%
1%
0,01%
0,001%
0,1%
10010-110-210-410-5 10-3
PnqNeg
Ig/TCR
36/77 (47%) patients have dissociated kinetics:
≥ 1 log difference at ≥ 2 timepoints
n=101 n=12
n = 433 samples
rp = 0.47
77 patients
BCR-ABL1/ABL1 transcripts
1 log
36 patients
(Positive
not quantifiable)
Patients with dissociated kinetics exhibit
distinct clinico-biological features
Dissociated
N=36
Parallel
N=41P-value
Median age, years 45 48 0.66
Male/female ratio 2,6 1,05 0.067
Organ infiltration 11/34 [32] 10/35 [29] 0.80
WBC, G/L [quartiles] 27.1 [9.2;69.9] 12.3 [6.4;27.0] 0.056
Neutrophils, G/L [quartiles] 4.5 [2.0;9.5] 1.8 [0.8;2.8] 0.0009
Lymphocytes, G/L [quartiles] 3.1 [2.1;5.8] 2.8 [1.8;3.9] 0.20
Monocytes, G/L [quartiles] 0.4 [0.1;1.1] 0.1 [0;0.2] 0.019
Blast, G/L [quartiles] 8.4 [1.6;33.1] 6.9 [1.3;24.4] 0.5
Blast % in BM [quartiles] 84 [76;92] 92 [85;95] 0.028
Major BCR [%] 17/36 [47] 5/41 [12] 0.0009
IKZF1 intragenic deletion [%] 16/36 [44] 31/41 [76] 0.0094
Patients with dissociated kinetics exhibit
distinct clinico-biological features
Dissociated
N=36
Parallel
N=41P-value
Median age, years 45 48 0.66
Male/female ratio 2,6 1,05 0.067
Organ infiltration 11/34 [32] 10/35 [29] 0.80
WBC, G/L [quartiles] 27.1 [9.2;69.9] 12.3 [6.4;27.0] 0.056
Neutrophils, G/L [quartiles] 4.5 [2.0;9.5] 1.8 [0.8;2.8] 0.0009
Lymphocytes, G/L [quartiles] 3.1 [2.1;5.8] 2.8 [1.8;3.9] 0.20
Monocytes, G/L [quartiles] 0.4 [0.1;1.1] 0.1 [0;0.2] 0.019
Blast, G/L [quartiles] 8.4 [1.6;33.1] 6.9 [1.3;24.4] 0.5
Blast % in BM [quartiles] 84 [76;92] 92 [85;95] 0.028
Major BCR [%] 17/36 [47] 5/41 [12] 0.0009
IKZF1 intragenic deletion [%] 16/36 [44] 31/41 [76] 0.0094
Patients with dissociated kinetics exhibit
distinct clinico-biological features
Dissociated
N=36
Parallel
N=41P-value
Median age, years 45 48 0.66
Male/female ratio 2,6 1,05 0.067
Organ infiltration 11/34 [32] 10/35 [29] 0.80
WBC, G/L [quartiles] 27.1 [9.2;69.9] 12.3 [6.4;27.0] 0.056
Neutrophils, G/L [quartiles] 4.5 [2.0;9.5] 1.8 [0.8;2.8] 0.0009
Lymphocytes, G/L [quartiles] 3.1 [2.1;5.8] 2.8 [1.8;3.9] 0.20
Monocytes, G/L [quartiles] 0.4 [0.1;1.1] 0.1 [0;0.2] 0.019
Blast, G/L [quartiles] 8.4 [1.6;33.1] 6.9 [1.3;24.4] 0.5
Blast % in BM [quartiles] 84 [76;92] 92 [85;95] 0.028
Major BCR [%] 17/36 [47] 5/41 [12] 0.0009
IKZF1 intragenic deletion [%] 16/36 [44] 31/41 [76] 0.0094
Non leukemic
Chronic or pre-leukemic
Acute leukemic
Differenciation
Transformation
HSC Pro-B Pre-B Immature B
V(D)J rearrangements
IKZF1del
CML-like disease in relation with occurrence of BCR-ABL1 in
an early/non B-committed hematopoietic progenitor
CML-like Ph+ALL
BCR-ABL1
Consistant data at diagnosis in Nagel, Blood 2017
Clinical relevance of a BCR-ABL1 clonal hematopoiesis
after blast clearance ?
✓ Prognostic relevance of BCR-ABL1 clonal hematopoiesis ?
✓ Therapeutic management ?
✓ Different MRD marker for different therapeutic decision
Remerciements
Laboratoire d’HématologieUnité Hématologie moléculaire et
bioinformatiqueHôpital Saint-Louis, IUH
Marie PassetRathana KimIbrahima Ba
Samuel Quentin
François SigauxJean Soulier
All GRAALL investigators and biologists
Colombe Saillard, Mario Bargetzi, Xavier Thomas, Carlos Graux, Yves Chalandon, Thibaut Leguay, Etienne Lengliné, Johanna Konopacki Mathilde Hunault, Eric Delabesse, Marina Lafage, Cédric
Pastoret, Nathalie Grardel, Vahid Asnafi
Nicolas BoisselVéronique Lhéritier
Hervé Dombret