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Frontiers of Medicine

ISSN 2095-0217

ISSN 2095-0225(Online)

CN 11-5983/R

Postal Subscription Code 80-967

2018 Impact Factor: 1.847

Front. Med.    2021, Vol. 15 Issue (3) : 347-371    https://doi.org/10.1007/s11684-020-0821-6
REVIEW
Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia
Jianfeng Li1, Yuting Dai1, Liang Wu1, Ming Zhang1, Wen Ouyang1, Jinyan Huang1,2(), Saijuan Chen1,2()
1. Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
2. Pôle de Recherches Sino-Français en Science du Vivant et Génomique, Laboratory of Molecular Pathology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Abstract

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by genetic alterations with high heterogeneity. Precise subtypes with distinct genomic and/or gene expression patterns have been recently revealed using high-throughput sequencing technology. Most of these profiles are associated with recurrent non-overlapping rearrangements or hotspot point mutations that are analogous to the established subtypes, such as DUX4 rearrangements, MEF2D rearrangements, ZNF384/ZNF362 rearrangements, NUTM1 rearrangements, BCL2/MYC and/or BCL6 rearrangements, ETV6-RUNX1-like gene expression, PAX5alt (diverse PAX5 alterations, including rearrangements, intragenic amplifications, or mutations), and hotspot mutations PAX5 (p.Pro80Arg) with biallelic PAX5 alterations, IKZF1 (p.Asn159Tyr), and ZEB2 (p.His1038Arg). These molecular subtypes could be classified by gene expression patterns with RNA-seq technology. Refined molecular classification greatly improved the treatment strategy. Multiagent therapy regimens, including target inhibitors (e.g., imatinib), immunomodulators, monoclonal antibodies, and chimeric antigen receptor T-cell (CAR-T) therapy, are transforming the clinical practice from chemotherapy drugs to personalized medicine in the field of risk-directed disease management. We provide an update on our knowledge of emerging molecular subtypes and therapeutic targets in BCP-ALL.

Keywords BCP-ALL      subtypes      translocation      aneuploidy      sequence mutations     
Corresponding Author(s): Jinyan Huang,Saijuan Chen   
Just Accepted Date: 27 November 2020   Online First Date: 24 December 2020    Issue Date: 18 June 2021
 Cite this article:   
Jianfeng Li,Yuting Dai,Liang Wu, et al. Emerging molecular subtypes and therapeutic targets in B-cell precursor acute lymphoblastic leukemia[J]. Front. Med., 2021, 15(3): 347-371.
 URL:  
https://academic.hep.com.cn/fmd/EN/10.1007/s11684-020-0821-6
https://academic.hep.com.cn/fmd/EN/Y2021/V15/I3/347
Subtype Adult Childhood Key features Molecular targeting agents Outcomes
Ph 15%–25% 2%–5% Gene fusion of BCR-ABL1 (Ph), mutation of RUNX1, and common deletions of PAX5, IKZF1, and CDKN2A/2B TKI; JAK/STAT, BTK/BCR, PD-1/PD-L1, CDK8, Aurora kinase A/B/C inhibitors Poor outcome and improved with TKI.
Ph-like 20%–25% 6%–15% Gene fusions of CRLF2, ABL1/ABL2, JAK2, EPOR, PDGFRB, and CSF1R and mutations of NRAS, KRAS, JAK2, and PTPN11 TKI; JAK/STAT, BCL2 inhibitors Poor outcome and amenable to TKI therapy
KMT2A 4%–10% 3%–4% Gene fusions of KMT2A fused to AFF1, MLLT1, MLLT3, MLLT10, and EPS15 and mutations of NRAS, KRAS, and FLT3; De-regulated gene expression of HOXA gene family, particularly HOAX9 DOT1L, HDAC, CDK4/6, BCL2, MEN1 inhibitors; Poor outcome
KMT2A-like <1% <1% Gene fusions of MED12-HOXA9 and AFF1-TMEM156 / Poor outcome
ETV6-RUNX1 <1% 15%–25% Gene fusion of ETV-RUNX1 and mutations of WHSC1, KRAS, and NRAS / Favorable outcome
ETV6-RUNX1-like <1% 2%–3% Co-existing ETV6 and IKZF1 aberrations; CD27 positive, CD44 low to negative / Intermediate outcome
TCF3-PBX1 2%–5% 4%–7% Gene fusion of TCF3-PBX1 and mutations of TP53 CDK4/6 inhibitors Intermediate outcome with intensive therapy, and association with CNS relapse
HLF <1% <1% Gene fusions of TCF3-HLF and TCF4-HLF CDK4/6, TKI, BCL2, BCR/BCL6 inhibitors Poor outcome
DUX4 4%–7% 4%–7% Gene fusions of IGH-DUX4 and ERG-DUX4; De-regulated gene expression of ERGalt; CD2 and CD371 positive / Favorable outcome with ERG deletions; Intermediate outcome without ERG deletions
MEF2D 2%–7% 2%–4% Gene fusions of MEF2D fused to BCL9, SS18, FOXJ2, CSF1R, DAZAP1, STAT6, HNRNPUL1, HNRNPH1, and HNRNPM; De-regulated gene expression of HDAC9; CD10 negative and CD38 positive HDAC inhibitors Poor outcome
ZNF384 3%–8% 3%–5% Gene fusions of ZNF384 fused to EP300, TCF3, TAF15, CREBBP, EWSR1, ARID1B, SMARCA2, SMARCA4, SYNRG, and NIPBL and mutations of NRAS, KRAS, FLT3, PTPN11, SETD1B, ZEB2, EZH2, KMT2D, and CREBBP; Mixed-phenotype FLT3 inhibitors Intermediate outcome
ZNF384-like <1% <1% Gene fusions of ZNF362 fused to SMARCA2 and TAF15 / /
PAX5alt 4%–8% 8%–10% Gene fusions of PAX5 fused to ETV6, NOL4L, FOXP1, AUTS2, CBFA2T2/3, P2RY8-CRLF2, deletions of PAX5, and mutations of PAX5, NRAS, KRAS, FLT3, and JAK1 TKI Intermediate outcome
BCL/MYC 1%–2% <1% Gene fusions of IGH-BCL2, IGH-MYC, and IGH-BCL6 CDK7 inhibitors; BCL2 inhibitors Poor outcome
NUTM1 <1% 1%–2% Gene fusions of NUTM1 fused to ACIN1, CUX1, AFF1, BRD9, ZNF618, SLC12A6, and IKZF1 Bromodomain inhibitors Favorable outcome
High hyperdiploidy <1% 15%–25% >50 chromosomes, mutations of NRAS, KRAS, FLT3, PTPN1, KMT2D, and CREBBP / Favorable outcome
Near-haploid <1% 2%–3% 25–29 chromosomes, mutations of NRAS, FLT3, and PAX5, and inactivation of IKZF3 and PAG1 BCL2 inhibitors Poor outcome
Low hypodiploid 1%–2% 10%–15% 32–39 chromosomes, mutations of TP53, deletions of CDKN2A/2B and RB2, and inactivation of IKZF2 BCL2 inhibitors Poor outcome
High hypodiploid <1% <1% 40–43 chromosomes / Poor outcome
iAMP21 <1% 2%–3% Complex structural alterations of chromosome 21 / Intermediate outcome
PAX5 P80R 3%–4% <1% Hotspot mutations of PAX5 p.Pro80Arg (P80R) and activating-mutations of NRAS, KRAS, FLT3, and PTPN11 TKI Intermediate outcome
IKZF1 N159Y <1% <1% Hotspot mutations of IKZF1 p.Asn159Tyr (N159Y) / /
ZEB2 H1038R/IGH-CEBPE <1% <1% Gene fusion of IGH-CEBPE and mutations of ZEB2 p.His1038Arg (H1038R), NRAS, KMT2D, KRAS, KMT2A, and CDKN2A / /
Tab.1  Overview of biological subtypes of adult and childhood BCP-ALL
Fig.1  Estimated percentage of major molecular subtypes and the genomic landscape of genetic mutations. (A) Pie plot represents the percentage of molecular subtypes in adult and children patients with BCP-ALL. (B) Cycle plot indicates the genomic landscape of major genetic alterations, including gene fusions, sequence mutations, and DNA CNVs. Chromosomes are separately arranged from chromosome 1 to X. Gene fusions are linked by ribbons, and the fusions involving ETV6-RUNX1, BCR-ABL1, TCF3-PBX1, TCF3/4-HLF, IGH, KMT2A, MEF2D, ZNF384, NUTM1, and PAX5 are highlighted. Genes affected by sequence mutations and DNA CNVs are listed at the external lines according to chromosome location. * Genes affected by different types of variations, i.e., fusion genes, CNVs, and sequence mutations.
Therapy targets Classification Agents Pubmed ID ClinicalTrials.gov identifier Associated subtype
CD19 Immunotherapy Blinatumomab; Denintuzumab; SGN19a (denintuzumab mafodotin); SAR3419 (coltuximab ravtansine); AFM11; ADCT-42; KTE-C19 (autologous CD19 CAR T); CART-19 (autologous); UCART19 (allogeneic); C-CAR-011; iC9-CAR19 (autologous); CD19CAR-4-1BB-CD3zeta-EGFR-texpressing T lymphocytes (autologous); CART-19 (autologous); 4SCAR19 (autologous); CTL019 T-cells; CTL019 autologous T-cells (with tocilizumab); CD19CAT-41BBZ CAR T-cells (autologous); huCART19 (autologous); iC9/CAR.19/IL15-transduced CB-NK cells (umbilical and cord-blood derived); PCAR-019 (autologous); CD19 CAR-NK cells (allogeneic) 16352804, 20424114, 21849486, 22592608, 23307031, 24731302, 26041741, 26516065, 26907630, 27460500, 27846391, 27887660, 27571406, 28249141, 28202953, 28490811, 28698205, 28827408, 29385376, 30728140 NCT00450944, NCT01860937, NCT01864889, NCT01865617, NCT01974479, NCT01974479, NCT02003222, NCT02028455, NCT02030847, NCT02101853, NCT02143414, NCT02185781, NCT02228096, NCT02374333, NCT02412306, NCT02443831, NCT02454270, NCT02456350, NCT02458014, NCT02614066, NCT02669264, NCT02746952, NCT02772198, NCT02799550, NCT02807883, NCT02810223, NCT02819583, NCT02848911, NCT02851589, NCT02877303, NCT02879695, NCT02892695, NCT02906371, NCT02924753, NCT02935257, NCT02935543, NCT02968472, NCT02975687, NCT02997761, NCT03016377, NCT03018093, NCT03027739, NCT03056339, NCT03064269, NCT03076437, NCT03103971, NCT03109093, NCT03110640, NCT03114865, NCT03937544, NCT04012879 /
CD20 Immunotherapy Rituximab; Ofatumumab; REGN1979; CD20-CAR transduced T-cells (autologous) 18381448, 18780832, 18971949, 20628151, 21298738 NCT01363128, NCT02419469, NCT02651662, NCT01735604 /
CD22 Immunotherapy Epratuzumab; Inotuzumab; BL22 and moxetumomab pasudotox; CART22 cells (autologous) 21869836, 22128838, 23243285, 24579885, 25484043, 25552705, 25728039, 28152223, 28449314, 29155426, 31110217, NCT01371630, NCT01925131, NCT02311998, NCT02650414, NCT03094611, NCT03104491 /
CD19/CD20 Immunotherapy CD19/20-CAR transduced T-cells (autologous or allogeneic) 28515942 NCT03097770 /
CD19/CD22 Immunotherapy Combotox; Deglycosylated ricin A chain conjugated CD19/CD22 immunotoxins; DT2219ARL 10803517, 12592332, 17706771, 19327829, 21732928, 29155426, 30581986, 31182121 NCT01408160, NCT03330691, NCT04094766 /
CD19/CD28 Immunotherapy CAR T (autologous; CD19, CD28) 10048973, 20424114, 23515080, 28039295 NCT02146924 /
CD19/CD28/CD137 Immunotherapy CD19.CAR/28 and CD19.CAR/28.137 T-cells (autologous) 27887866 NCT01853631, NCT02685670 /
CD19/CD133 Immunotherapy Tandem CAR (TanCAR) of CD19 and CD133 30046161 / /
CD19/CD137 Immunotherapy Second generation CAR-T (CD19, CD137) 27887866 NCT02965092 /
CD20/CD22 Immunotherapy Hexavalent antibodies (HexAbs); Bs20x22 18025153, 20628151, 21347809 / /
CD28/CD137 Immunotherapy 3rd generation CAR T (CD28, CD137) 14961035, 27887866 NCT02186860 /
CD25 Immunotherapy ADCT-301 25337274 NCT02588092 /
CD38 Immunotherapy Isatuximab 26631114, 28483761, 30858549, 30862646 NCT03860844 /
CD52 Immunotherapy Alemtuzumab 28123068, 29264111 NCT00773149
CD123 Immunotherapy XmAb14045 19454491, 27571406 NCT02730312 /
Integrin alpha4 Immunotherapy Chemotherapy combined with Natalizumab 23319569 / /
ROR1 Immunotherapy ROR1 CAR-specific T lymphocytes (autologous) 21813176, 29476010, 29849118, 30631148 NCT02706392 /
EPHA3 Immunotherapy IIIA4 27922598 /
PD-1/PD-L1 Inhibitors Nivolumab; Pembrolizumab; REG2810 / NCT02651662, NCT02767934, NCT02819804 Ph
CTLA-4 Inhibitors Ipilimumab / NCT00060372, NCT02879695 /
CDK4/6 Inhibitors Palbociclib; Ribociclib; PD0332991 17537993, 24736461, 25744718, 25813205, 26637365, 27099147, 29408328 NCT02310243, NCT03472573, NCT03515200, NCT03132454, NCT03792256 KMT2A, TCF3-PBX1, TCF3/4-HLF
CDK7 Inhibitors THZ1 31085176 / BCL/MYC
CDK8 Inhibitors YKL-06-101 31628323 / BCR-ABL1
Tyrosine kinase Inhibitors Dasatinib, PLX3397, Nilotinib, Sunitinib, Sorafenib, Ponatinib; ABL001 (Asciminib) 17068151, 17077147, 19322212, 20807819, 22297722, 22897847, 23861246, 23974192, 24711557, 24464015, 24828076, 25049327, 25207766, 25759025, 26872634, 26773044, 27919910, 28329763, 28461505, 28408464, 28555080, 28819281, 29348129, 29681510, 29997224, NCT01620216, NCT02081378, NCT02390752, NCT02883049 Ph, Ph-like, HLF, PAX5alt, PAX5 P80R
BTK/BCR Inhibitors Ibrutinib 28031181 NCT02815059, NCT02997761, NCT02997761, NCT03267186, NCT03267186 Ph
FLT3, PI3K/mTOR pathway Inhibitors PKC412; Idelalisib; Sirolimus; Quizartinib; Crenolanib; Dactolisib; Rapamycin; CCI-779; TGR-1202 16195324, 17942929, 18704194, 22705992, 22955920, 27461063, 27784673, 28424165 NCT00651261, NCT00866281, NCT01162551, NCT01756118, NCT02779283, NCT03742323 ZNF384
JAK/STAT Inhibitors Ruxolitinib; AZD1480, CHZ868 20018760, 22955920, 25049327, 26175414, 26500062, 27860260, 28331226, 28369050, 28461505, 29907650 NCT01914484, NCT02420717, NCT02494882, NCT02723994 Ph
MEK1/2, RAS, B-Raf Inhibitors MEK162, Trametinib, Selumetinib; Trametinib/Sorafenib 27054332, 32220889 NCT02089230 /
SYK Inhibitors Entospletinib; PRT318; PRT260607 24948121, 26847027 NCT02404220 /
SRC Inhibitors / 24625531, 28804122 /
Aurora kinase A/B/C Inhibitors Danusertib EudraCT number 2007-004070- 18 Ph
PYST1 (Erk activation) Inhibitors BCI 26073130, 28804122 / /
JNK Inhibitors SP600125; JNK-IN-8 26310606, 26310606, 32552902 / /
Casein Kinase II (CK2) Inhibitors CX-4945 32396934 / /
VEGFR Inhibitors Axitinib 25686603 NCT02551718 /
LEPR Inhibitors 1-day fasting 27941793 /
HSP90 Inhibitors PU-H71 22271575, 26443624, 28619753 / /
DRD2 Inhibitors ONC201 29533922, 31127149 NCT02392572 /
MDM2 Inhibitors DS302-b; RG7112; Nutlin-3 19421231, 19710698, 21986948, 29653964, 21986948 NCT02319369 /
MEN1 Inhibitors VTP50469 31821784 / KMT2A
HER2 Inhibitors Trastuzumab 15531467, 18971949, 22267607 NCT00724360 /
PARP Inhibitors Talazoparib 24856976, 28634224 NCT02116777 /
Hedgehog Inhibitors PF-04449913 30487223, 31030089 NCT01841333 /
CXCR-4 Inhibitors BL-8040; Plerixafor (BKT140); AMD3100; LY2510924 12835717, 24502926, 26031918, 26398122, 27071778, 27307990, 28409853, 28280274, 30254339 NCT01352650, NCT02605460, NCT02763384 /
DNA methyltransferases (DNMT1/ DNMT3A/DNMT3B) Inhibitors Decitabine; Azacitidine; Pinometostat 19179467, 28171800, 29728108, 30841886 NCT00075010, NCT00349596, NCT01861002, NCT02141828, NCT02458235 /
Histone deacetylases (HDACs) Inhibitors Vorinostat; Panobinostat; Romidepsin; Entinostat; Chidamide; Givinostat (ITF2357) 27428428, 27824051, 28331226, 30171027, 31439580, 31969338 NCT00217412, NCT00462605, NCT01132573, NCT01321346, NCT01422499, NCT02551718, NCT02553460, NCT03117751, NCT03564470, NCT03564704 MEF2D, KMT2A
DOT1L Inhibitors EPZ-5676 23801631, 24993360, 28428443, 29724899 NCT01684150, NCT02141828, NCT03724084, NCT03701295 KMT2A
c-Myc Inhibitors Shikonins, TGR-1202, JQ1 21949397, 21986948, 22904298, 27784673 /
BCL2/BCL-XL - Inhibitors Venetoclax (ABT-199); ABT-737; Navitoclax (ABT-263) 23788110, 26214592, 27054332, 28122742, 28974549, 30631148, 30862722 NCT03181126, NCT03236857, NCT03319901, NCT03504644, NCT03576547, NCT03808610, NCT03181126, NCT03826992, NCT04029688 KMT2A, Ph-like, HLF, BCL/MYC, near-haploid, low hypodiploid
BCL-6 Inhibitors PRT062607; RI-BPI 23107779, 26214592, 25759025, 25780007, / /
Proteasome Inhibitors Ixazomib; Bortezomib; Carfilzomib; CX-4945 23357978, 26593250 NCT02228772, NCT02293109, NCT02535806, NCT02578511 /
BIRC5 (Survivin) Inhibitors YM155 25895498, 30991025 / /
Retinoid X receptor Inhibitors Bexarotene, Carbacyclin, ATRA, 9- and 13-cis RA 26321221 / /
Reactive oxygen species Inhibitors Verteporfin 26774450, 30563887, 31109083 / /
Bromodomain Inhibitors BMS-986158 30723300 NCT03936465 NUTM1
TP53 Agonist SB225002 19710698, 23334668, 28600336, 28557976, 29300620, 30657737 / /
IL-15 Agonist ALT-803 23644531, 25896649, 29365313, 29463563, 26980764 NCT01885897, NCT02890758 /
Fas Agonist Rimiducid (AP1903) 25977584, 28697888, 30514753 NCT03016377, NCT03056339 /
Tab.2  Summary of known and potential therapy targets in BCP-ALL
Fig.2  Schematic of the candidate therapy pathways and targets from the cell surface to the nucleus of leukemic blast cells of patients with BCP-ALL. Signaling pathways (e.g., Ras signaling and JAK-STAT signaling) are mutant or/and activated in most subtypes of BCP-ALL. Other cytokine receptors and signaling pathways (e.g., Hedgehog signaling and Notch signaling in NUTM1 fusions; CRLF2, IL-7, and EPOR in Ph-like subtype; and PAG1 in near-haploid) are enriched in specific subtypes. Cell surface antigens, including CD19, CD20, and CD22, are the most promising CAR-T therapy targets. De-regulated tumor suppressors or cell cycle regulators (e.g., TP53 and CDKN2A/2B), transcription factors (e.g., PAX5, IKZF1, and ERG), epigenetic modification (DNA methylation, histone acetylation, methylation, and deubiquitylation), and chromatin remodeling (e.g., CTCF and ARID1A/B) are the hallmarks of BCP-ALL in the nucleus.
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