Beruflich Dokumente
Kultur Dokumente
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Original Article
A BS T R AC T
BACKGROUND
Philadelphia chromosomelike acute lymphoblastic leukemia (Ph-like ALL) is characterized by a gene-expression profile similar to that of BCRABL1positive ALL,
alterations of lymphoid transcription factor genes, and a poor outcome. The frequency and spectrum of genetic alterations in Ph-like ALL and its responsiveness
to tyrosine kinase inhibition are undefined, especially in adolescents and adults.
METHODS
We performed genomic profiling of 1725 patients with precursor B-cell ALL and
detailed genomic analysis of 154 patients with Ph-like ALL. We examined the
functional effects of fusion proteins and the efficacy of tyrosine kinase inhibitors
in mouse pre-B cells and xenografts of human Ph-like ALL.
RESULTS
Ph-like ALL increased in frequency from 10% among children with standard-risk
ALL to 27% among young adults with ALL and was associated with a poor outcome.
Kinase-activating alterations were identified in 91% of patients with Ph-like ALL;
rearrangements involving ABL1, ABL2, CRLF2, CSF1R, EPOR, JAK2, NTRK3, PDGFRB,
PTK2B, TSLP, or TYK2 and sequence mutations involving FLT3, IL7R, or SH2B3 were
most common. Expression of ABL1, ABL2, CSF1R, JAK2, and PDGFRB fusions resulted in cytokine-independent proliferation and activation of phosphorylated STAT5.
Cell lines and human leukemic cells expressing ABL1, ABL2, CSF1R, and PDGFRB
fusions were sensitive in vitro to dasatinib, EPOR and JAK2 rearrangements were
sensitive to ruxolitinib, and the ETV6NTRK3 fusion was sensitive to crizotinib.
CONCLUSIONS
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Me thods
Study Design
A total of 154 patients with Ph-like ALL underwent detailed genomic analysis, 147 of whom
underwent one or more of the following types of
next-generation sequencing: transcriptome sequencing (136 patients), whole-genome sequencing (42), and whole-exome sequencing (12) of
The details of gene expression and single-nucleotide-polymorphism microarray profiling, fluorescence in situ hybridization, cell-line proliferation and tyrosine kinase inhibitor assays, protein
expression, and xenograft experiments are provided in Supplementary Appendix 2.
Statistical Analysis
R e sult s
Clinical Characteristics and Outcomes
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A Event-free Survival
100
90
80
70
60
50
40
Adolescents
30
Young adults
20
10
0
P<0.001
0
10
Years
No. at Risk
93
71
49
27
63
18
42
10
17
3
B Overall Survival
100
90
80
Children, high risk
70
60
Adolescents
50
40
30
Young adults
20
10
0
P<0.001
0
10
Years
No. at Risk
101
85
61
37
13
63
20
53
12
28
4
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1009
Other
JAKSTAT
ABL
Legend
Sample
Lesion
B-cell pathway
RNA-seq
WGS
WES
RT-PCR
Age
Sex
Outcome
ABL1
ABL2
CSF1R
PDGFRB
EPOR
JAK2
CRLF2
IL7R
FLT3
SH2B3
JAK1
JAK3
TYK2
TSLP
IL2RB
NTRK3
DGKH
PTK2B
DYRK1A
KRAS
NRAS
PTPN11
NF1
BRAF
Kinase
IKZF1
PAX5
EBF1
Fusion
Missense
Truncating
Age Group
Protein insertion/deletion
Deletion
Multiple mutations
CRLF2 rearranged
Outcome
Other JAKSTAT
No event
Event
Sex
Misc
Ras only
Female
Male
Unknown
SJBALL266_D
SJBALL021728_D1
SJBALL022244_D1
SJBALL021352_D1
SJBALL021494_D1
SJBALL020877_D1
SJBALL085_D
SJBALL020882_D1
SJBALL020012_D1
SJBALL020014_D1
SJBALL020825_D1
SJBALL010_D
SJBALL021521_D1
SJBALL269_D
SJBALL020994_D1
SJBALL020091_D1
SJBALL262_D
SJBALL022489_D1
SJBALL022245_D1
SJBALL020625_D1
SJBALL020980_D1
SJBALL020644_D1
SJBALL020812_D1
SJBALL204_D
SJBALL020832_D1
SJBALL153_D
SJBALL012_D
SJBALL021318_D1
SJBALL020475_D1
SJBALL020552_D1
SJBALL020529_D1
SJBALL020704_D1
SJBALL267_D
SJBALL022486_D1
SJBALL021748_D1
SJBALL020100_D1
SJBALL020649_D1
SJBALL020579_D1
SJBALL020824_D1
SJBALL020941_D1
SJBALL021409_D1
SJBALL020084_D1
SJBALL021411_D1
SJBALL020069_D1
SJBALL020138_D1
SJBALL020936_D1
SJBALL265_D
SJBALL021329_D1
SJBALL022246_D1
SJBALL020966_D1
SJBALL022488_D1
SJBALL021856_D1
SJBALL020081_D1
SJBALL020765_D1
SJBALL021780_D1
SJBALL021367_D1
SJBALL021866_D1
SJBALL020589_D1
SJBALL020681_D1
SJBALL021344
SJBALL020939_D1
SJBALL021814_D1
SJBALL021087_D1
SJBALL195_D
SJBALL020789_D1
SJBALL021100_D1
SJBALL021113_D1
SJBALL021118_D1
SJBALL020077_D1
SJBALL270_D
SJBALL020145_D1
SJBALL020963_D1
SJBALL021510_D1
SJBALL021313_D1
SJBALL021120_D1
SJBALL083_D
SJBALL191_D
SJBALL021083_D1
SJHYPER013_D
SJBALL020013_D1
SJBALL020087_D1
SJBALL021143_D1
SJBALL021053_D1
SJBALL020853_D1
SJDOWN013_D
SJHYPO110_D
SJBALL101_D
SJBALL020971_D1
SJBALL021076_D1
SJBALL020125_D1
SJBALL021813_D1
SJBALL020073_D1
SJBALL239_D
SJBALL020984_D1
SJBALL021373_D1
SJBALL020807_D1
SJBALL021415_D1
SJBALL231_D
SJHYPO109_D
SJBALL021486_D1
SJBALL063_D
SJBALL020836_D1
SJBALL015_D
SJBALL021507_D1
SJBALL021772_D1
SJBALL021413_D1
SJBALL263_D
SJBALL021058_D1
SJBALL021786_D1
SJBALL021305_D1
SJBALL021393_D1
SJHYPER120_D
SJBALL021784_D1
SJHYPER150_D
SJBALL021517_D1
SJBALL020015_D1
SJHYPO018_D1
SJBALL021720_D1
SJBALL021327_D1
SJBALL021738_D1
SJBALL020700_D1
SJBALL021794_D1
SJBALL020422_D1
SJBALL021018_D1
SJHYPER003_D
SJBALL247_D
SJBALL021398_D1
SJBALL021530_D1
SJERG021891_D1
SJHYPO147_D
SJBALL264_D
SJBALL268_D
SJHYPER146_D
SJBALL021109_D1
SJHYPO020_D
SJBALL021102_D1
SJHYPO123_D
SJHYPER025_D
SJHYPO146_D
SJBALL020811_D1
SJBALL020488_D1
SJBALL255_D
SJBALL021080_D1
SJBALL011_D
SJBALL021047_D1
SJBALL021644_D1
SJBALL020518_D1
SJHYPO151_D
SJBALL021722_D1
SJBALL020852_D1
SJBALL021549_D1
SJHYPER021_D
SJHYPER206_D
SJHYPER227_D
ABL-class fusions
No kinase
alteration
Ras
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Tyrosine Kinase
Inhibitor
Fusion
Partners
Patients
5 Genes
number
ABL1
Dasatinib
14
ABL2
Dasatinib
CSF1R
Dasatinib
SSBP2*
PDGFRB
Dasatinib
11
CRLF2
JAK2 inhibitor
30
JAK2
JAK2 inhibitor
10
19
EPOR
JAK2 inhibitor
IGH,11 IGK*
DGKH
Unknown
ZFAND3*
IL2RB
MYH9*
NTRK3
Crizotinib
ETV625-27
PTK2B
FAK inhibitor
KDM6A,* STAG2*
TSLP
JAK2 inhibitor
IQGAP2*
TYK2
TYK2 inhibitor
MYB*
IGH,21 P2RY822
ATF7IP,* BCR, EBF1,* ETV6,23 PAX5,11 PPFIBP1,* SSBP2,24
STRN3,11 TERF2,* TPR*
11
B
1010
120
Empty vector
RCSD1ABL1 + Ik6
RCSD1ABL2 + Ik6
SSBP2CSF1R + Ik6
109
PAX5JAK2 + Ik6
108
80
40
107
106
10
0
0.01
15
0.1
10
100
Dasatinib (nM)
Days
Control
Basal
Untreated
Ruxolitinib
RCSD1
ABL2
Dasatinib
Untreated
Ruxolitinib
SSBP2
CSF1R
Dasatinib
Untreated
103
104
105
pSTAT5
103
104
105
PAX5
JAK2
Dasatinib
Ruxolitinib
pCRKL
mutations in other lymphoid transcription factors (ETV6, EBF1, ERG, PAX5, and TCF3), 86% of
patients with Ph-like ALL (209 of 244) were
found to have alterations affecting lymphoid
development, as compared with 61% of patients
with nonPh-like ALL (762 of 1241, P<0.001).
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Discussion
In this study of 1725 children, adolescents, and
young adults with precursor B-cell ALL, we defined the frequency and poor outcome of Ph-like
ALL, characterized the genetic landscape of alterations activating kinase signaling, and found
that the majority of patients with Ph-like ALL
have genetic alterations responsive to Food and
Drug Administrationapproved tyrosine kinase
inhibitors. Building on the precedent established
for BCRABL1positive ALL,33 these findings
provide a strong rationale for testing new therapies to improve the outcome of Ph-like ALL. We
studied more than 500 adolescents and young
adults with ALL, for whom treatment outcomes
are substantially inferior to those of children
with ALL. The frequency of Ph-like ALL is higher than 25% among young adults with ALL. Because BCRABL1positive ALL represents more
than 20% of precursor B-cell ALL cases in this
age group, about half of young adults with precursor B-cell ALL are candidates for tyrosine
kinase inhibitor therapy. The frequency of Phlike ALL among older adults with ALL is unknown but merits investigation in view of the
poor treatment outcome in this age group.
We identified several subgroups of Ph-like
ALL distinguished by the type of cytokine receptor or kinase alteration that was present. The
frequencies of CRLF2 rearrangement (47%) and
concomitant JAK1 or JAK2 mutation (55% among
patients with CRFL2 rearrangement) in the entire
cohort are consistent with previous reports,11,35
with the highest frequency observed in adolescent ALL (60%). Previous reports have shown
that the JAK2 inhibitor ruxolitinib is active in
models of ALL with CRLF2 rearrangement, which
suggests that JAK inhibition may be used in the
treatment of these high-risk patients.36,37
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Appendix
The authors full names and academic degrees are as follows: KathrynG.Roberts,Ph.D., YongjinLi,Ph.D., DebbiePayneTurner,B.S.,
RichardC.Harvey,Ph.D., YungLiYang,M.D., DeqingPei,M.S., KellyMcCastlain,B.S., LiDing,Ph.D., CharlesLu,Ph.D., Guang
chunSong,M.S., JingMa,Ph.D., JaredBecksfort,M.S., MichaelRusch,B.A., ShannChingChen,Ph.D., JohnEaston,Ph.D., JinjunCheng,M.D., KristyBoggs,Ph.D., NataliaSantiagoMorales,B.S., IlariaIacobucci,Ph.D., RobertS.Fulton,Ph.D., JiWen,Ph.D.,
MarcusValentine,B.A., ChengCheng,Ph.D., StevenW.Paugh,Ph.D., MeenakshiDevidas,Ph.D., IMingChen,D.V.M., ShaliniReshmi,Ph.D., AmySmith,B.S., ErinHedlund,Ph.D., PankajGupta,M.S., PandukaNagahawatte,M.S., GangWu,Ph.D., XiangChen,Ph.D.,
DonaldYergeau,Ph.D., BhavinVadodaria,B.A., HeatherMulder,B.S., NaomiJ.Winick,M.D., EricC.Larsen,M.D., WilliamL.Carroll,M.D., NylaA.Heerema,Ph.D., AndrewJ.Carroll,Ph.D., GuyGrayson,M.D., SarahK.Tasian,M.D., AndrewS.Moore,M.D.,
FrankKeller,M.D., MelissaFreiJones,M.D., JamesA.Whitlock,M.D., ElizabethA.Raetz,M.D., DeborahL.White,Ph.D., TimothyP.Hughes,M.D., JaimeM.GuidryAuvil,Ph.D., MalcolmA.Smith,M.D., GuidoMarcucci,M.D., ClaraD.Bloomfield,M.D., KrzysztofMrzek,M.D., JessicaKohlschmidt,Ph.D., WendyStock,M.D., StevenM.Kornblau,M.D., MarinaKonopleva,M.D., ElisabethPaietta,Ph.D., ChingHonPui,M.D., SimaJeha,M.D., MaryV.Relling,Pharm.D., WilliamE.Evans,Pharm.D., DanielaS.Gerhard,Ph.D.,
JulieM.GastierFoster,Ph.D., ElaineMardis,Ph.D., RichardK.Wilson,Ph.D., MignonL.Loh,M.D., JamesR.Downing,M.D., StephenP.Hunger,M.D., CherylL.Willman,M.D., JinghuiZhang,Ph.D., and CharlesG.Mullighan,M.D.
From the Departments of Pathology (K.G.R., D.P.-T., Y.-L.Y., K. McCastlain, G.S., J.M., S.-C.C., J.C., N.S.-M., I.I., J.W., J.R.D.,
C.G.M.), Computational Biology and Bioinformatics (Y.L., J.B., M.R., E.H., P.G., P.N., G.W., X.C., J.Z.), Biostatistics (D.P., C.C.),
Pharmaceutical Sciences (S.W.P., M.V.R., W.E.E.), and Oncology (C.-H.P., S.J.), the Pediatric Cancer Genome Project (Y.L., L.D., C.L.,
M.R., J.E., J.C., K.B., R.S.F., E.H., P.G., P.N., G.W., X.C., D.Y., B.V., H.M., M.V.R., W.E.E., E.M., R.K.W., J.R.D., J.Z., C.G.M.), and
Cytogenetics Shared Resource (M.V.), St. Jude Childrens Research Hospital, Memphis, TN; the University of New Mexico Cancer Center and School of Medicine, Albuquerque (R.C.H., I-M.C., C.L.W.); the Genome Institute at Washington University (L.D., C.L., R.S.F.,
E.M., R.K.W.), the Department of Genetics, Washington University School of Medicine (L.D., C.L., R.S.F., E.M., R.K.W.), and Siteman
Cancer Center, Washington University (E.M., R.K.W.) all in St. Louis; Epidemiology and Health Policy Research, College of Medicine,
University of Florida, Gainesville (M.D.); the Research Institute at Nationwide Childrens Hospital (S.R., A.S., J.M.G.-F.), the Department of Pathology, College of Medicine, Ohio State University (N.A.H.), and Ohio State University Comprehensive Cancer Center (G.M.,
C.D.B., K. Mrzek, J.K.) all in Columbus, OH; the Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas (N.J.W.), Scott and White Hospitals and Clinics and Texas A&M Health Science Center, Temple (G.G.), the University of Texas
Health Science Center San Antonio, San Antonio (M.F.-J.), and the Departments of Leukemia and Stem Cell Transplantation, Division
of Cancer Medicine, University of Texas M.D. Anderson Cancer Center, Houston (S.M.K., M.K.) all in Texas; Maine Childrens Cancer Program, Scarborough (E.C.L.); New York University Cancer Institute, New York (W.L.C.), and the Department of Medicine (Oncology), Albert Einstein College of Medicine, Bronx (E.P.) both in New York; the Department of Genetics, University of Alabama at
Birmingham, Birmingham (A.J.C.); the Division of Oncology, Childrens Hospital of Philadelphia, Philadelphia (S.K.T.); Queensland
Childrens Medical Research Institute, University of Queensland and Royal Childrens Hospital Brisbane, Herston (A.S.M.), and Cancer
Theme, South Australian Health and Medical Research Institute, Adelaide (D.L.W., T.P.H.) both in Australia; Childrens Healthcare
of Atlanta and Emory University School of Medicine both in Atlanta (F.K.); the Division of HaematologyOncology, Hospital for Sick
Children, and University of Toronto both in Toronto (J.A.W.); Hunstman Cancer Institute, University of Utah, Salt Lake City (E.A.R.);
the Office of Cancer Genomics (J.M.G.A., D.S.G.) and Cancer Therapy Evaluation Program (M.A.S.), National Cancer Institute, and the
Childrens Oncology Group TARGET ALL project (M.D., I-M.C., S.R., W.L.C., J.M.G.A., M.A.S., M.V.R., D.S.G., J.M.G.-F., M.L.L.,
J.R.D., S.P.H., C.L.W., J.Z., C.G.M.), National Institutes of Health, Bethesda, MD; Alliance for Clinical Trials in Oncology Statistics and
Data Center, Mayo Clinic, Rochester, MN (J.K.); the University of Chicago Medicine, Chicago (W.S.); the Department of Pediatrics,
Benioff Childrens Hospital, and the Helen Diller Family Cancer Center, University of California, San Francisco, San Francisco (M.L.L.);
and the University of Colorado School of Medicine and Childrens Hospital Colorado both in Aurora (S.P.H.).
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