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
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.
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
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14
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17
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18
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19
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20
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21
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22
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24
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