Key Leukemia Targets Beyond CAR-T: FLT3, Menin, BCL-2, BTK, and Cell-Surface Antigens

CAR-T is an immune-cell therapy platform, whereas molecules such as CD19, CD22, CD33, and CD123 are the actual recognition targets. Beyond CAR-T, targeted leukemia research also covers aberrant kinases, oncogenic metabolites, apoptotic dependencies, transcriptional regulatory complexes, and cell-surface antigens. FLT3, IDH1/2, BCR::ABL1, BTK, and BCL-2 have relatively well-defined molecular stratification bases, whereas Menin, CD123, MCL-1, and myeloid immune targets remain active areas of development.

Keywords: leukemia targets; FLT3; Menin; BCL-2; BTK; BCR::ABL1; CD123; targeted therapy

1 Classification Boundaries of Emerging Leukemia Targets

1.1 CAR-T and Leukemia Targets

CAR-T uses genetic engineering to enable T cells to express chimeric antigen receptors and is therefore an immune-cell therapy modality rather than a single molecular target. Cell-surface molecules such as CD19, CD22, CD33, CD123, and CD7 can serve not only as CAR-T targets but also as targets for bispecific antibodies, antibody-drug conjugates, monoclonal antibodies, and NK-cell engagers. Therefore, when discussing treatment strategies beyond CAR-T, these surface antigens with non-CAR-T development value should still be included.

1.2 Major Types of Leukemia Targets

(1) Driver Mutations and Kinases

Targets such as FLT3, BCR::ABL1, BTK, and members of the JAK family maintain leukemic clones through persistent activation of proliferation, survival, and migration signaling. These targets are generally addressed using ATP-competitive inhibitors, allosteric inhibitors, covalent inhibitors, or protein-degradation strategies. Drug efficacy is closely related to kinase conformation, mutation sites, target expression, and bypass signaling.

(2) Abnormal Metabolism and Apoptotic Dependence

Mutant IDH1/2 can generate D-2-hydroxyglutarate and block myeloid differentiation, whereas BCL-2, MCL-1, and BCL-XL regulate the apoptotic threshold of leukemia cells by controlling mitochondrial outer-membrane permeabilization. These targets do not necessarily directly determine proliferation rate but can substantially affect cellular differentiation, metabolic adaptation, and drug tolerance.

(3) Transcriptional Regulatory Complexes

Menin participates in the abnormal HOX/MEIS transcriptional program in KMT2A-rearranged and NPM1-mutated leukemia. BET proteins, DOT1L, and other chromatin regulators can also maintain transcriptional dependencies in specific leukemia subtypes. Targeting transcriptional regulation often manifests as induction of differentiation, clonal-state transition, or reduced long-term proliferative capacity rather than immediate large-scale cell death.

(4) Cell-Surface Antigens

CD19, CD22, CD20, CD33, and CD123 can serve as entry points for effector-cell recruitment, antibody binding, or delivery of cytotoxic payloads. Their targeting value depends not only on the proportion of antigen-positive cells but also on single-cell antigen density, internalization capacity, expression on normal hematopoietic cells, and antigen drift after treatment.

1.3 Target Distribution Across Leukemia Subtypes

(1) Acute Myeloid Leukemia

Major targets in acute myeloid leukemia (AML) include FLT3, IDH1, IDH2, BCL-2, Menin, CD33, and CD123. TP53, the RAS pathway, MCL-1, TIM-3, and bone-marrow-microenvironment-associated pathways also have research value, although their maturity, applicable clones, and therapeutic windows differ substantially.

(2) Acute Lymphoblastic Leukemia

Major targets in B-cell acute lymphoblastic leukemia (B-ALL) include CD19, CD22, CD20, and BCR::ABL1. Certain cases also involve ABL-class fusions, CRLF2, and JAK-STAT abnormalities. Potential targets in T-cell acute lymphoblastic leukemia (T-ALL) include NOTCH1, JAK-STAT, PI3K-AKT-mTOR, BCL-2, BCL-XL, and CD7.

(3) Chronic Leukemias

The central driver target in chronic myeloid leukemia (CML) is BCR::ABL1, with research focused on kinase-domain mutations, compound resistance mutations, and residual leukemia stem cells. Chronic lymphocytic leukemia (CLL) mainly depends on B-cell receptor signaling, BTK, BCL-2, and CD20, while microenvironment-mediated migration and survival signaling also affect drug sensitivity.

2 Driver Mutations and Kinase Targets

2.1 FLT3

(1) FLT3-ITD

FLT3 internal tandem duplication mutations can constitutively activate the receptor in the absence of ligand, enhancing STAT5, RAS-MAPK, and PI3K-AKT signaling, promoting blast proliferation, and maintaining an anti-apoptotic state. After FLT3 inhibition, reduced p-FLT3 and p-STAT5, cell-cycle arrest, and enhanced mitochondrial apoptosis may be observed.

(2) FLT3-TKD

FLT3 tyrosine-kinase-domain mutations can alter the conformation of the kinase activation loop and the drug-binding state. Different FLT3 inhibitors do not cover ITD and TKD mutations to the same extent. Studies should therefore define the mutation type, allelic burden, and presence of multiclonal mutations.

(3) Resistance Mechanisms

Resistance to FLT3-targeted therapy can result from secondary kinase-domain mutations, activation of the RAS-MAPK bypass pathway, increased FLT3 ligand, bone-marrow stromal protection, and shifts toward BCL-2 or MCL-1 dependence. Continued target expression does not indicate persistent drug efficacy. Resistance analysis should simultaneously cover the binding site, downstream signaling, and clonal composition.

2.2 IDH1 and IDH2

Mutant IDH1 or IDH2 converts α-ketoglutarate into D-2-hydroxyglutarate, inhibits α-ketoglutarate-dependent dioxygenases, causes abnormal DNA and histone methylation, and blocks myeloid differentiation. The major effect of IDH inhibition is reduction of the abnormal metabolite and restoration of differentiation programs. Drug-efficacy evaluation should combine D-2-hydroxyglutarate measurement, differentiation markers such as CD11b and CD14, cellular morphology, and blast proportion.

2.3 BCR::ABL1

(1) ATP-Binding Site

The BCR::ABL1 fusion protein constitutively activates RAS-MAPK, JAK-STAT, and PI3K-AKT pathways and is a central driver of CML and Philadelphia chromosome-positive ALL. Most tyrosine kinase inhibitors act on the ATP-binding region of ABL1. Sensitivity is affected by T315I and other kinase-domain mutations, gene amplification, and bypass signaling.

(2) Allosteric Regulatory Site

The ABL1 myristoyl pocket provides an allosteric intervention site distinct from the ATP-binding region. Allosteric inhibition can stabilize the inactive conformation of ABL1 and can be combined with ATP-competitive inhibition to achieve dual-site blockade, providing an alternative strategy for studying certain binding-site resistance and compound mutations.

(3) Molecular Residual Disease

Persistent BCR::ABL1 transcripts may reflect incomplete elimination of leukemia stem cells. Even when short-term cell proliferation has been suppressed, a basis for relapse may remain. Evaluation of BCR::ABL1-targeted therapy should combine transcript quantification, p-CRKL, kinase-domain sequencing, and colony-forming capacity.

 

Figure 1. Constitutive BCR-ABL kinase activation and imatinib-mediated targeted inhibition mechanism

2.4 BTK

BTK occupies a key position in the B-cell receptor signaling network and regulates PLCγ2, NF-κB, ERK, and AKT signaling, thereby affecting CLL-cell survival, migration, and interactions with the lymphoid-tissue microenvironment. Covalent BTK inhibitors generally depend on binding to the C481 residue, and alterations in C481 or PLCγ2 can cause resistance. Noncovalent BTK inhibitors do not depend on this covalent site and can be used in certain models resistant to covalent inhibitors.

3 Apoptotic Dependencies and Transcriptional Regulatory Targets

3.1 BCL-2

(1) Regulation of Mitochondrial Apoptosis

BCL-2 binds pro-apoptotic BH3 proteins such as BIM and restricts BAX- and BAK-mediated mitochondrial outer-membrane permeabilization. Certain AML blasts and CLL cells show marked survival dependence on BCL-2. Inhibition of BCL-2 releases pro-apoptotic proteins, leading to loss of mitochondrial membrane potential, Cytochrome c release, and activation of the Caspase cascade.

(2) Determination of Functional Dependence

Increased BCL-2 protein expression does not necessarily indicate absolute dependence on BCL-2. BH3 profiling, the BIM-BCL-2 binding state, mitochondrial membrane potential, and BAX/BAK function are more informative for drug sensitivity than BCL-2 expression alone.

(3) Compensatory Resistance

Resistance after BCL-2 inhibition is often associated with upregulation of MCL-1 or BCL-XL, monocytic-like differentiation, mitochondrial metabolic reprogramming, and abnormalities in the BAX/BAK pathway. Resistant clones may shift toward dependence on other anti-apoptotic proteins without a marked reduction in BCL-2 expression.

3.2 Menin-KMT2A/NPM1 Axis

(1) KMT2A Rearrangements

KMT2A fusion proteins maintain abnormal transcriptional programs involving HOXA9, MEIS1, and related genes through Menin and associated transcriptional complexes, keeping leukemia cells in an undifferentiated state. Menin inhibition disrupts key protein interactions, downregulates HOX/MEIS expression, and promotes myeloid maturation.

(2) NPM1 Mutations

Although NPM1-mutated AML generally lacks KMT2A fusions, it can depend on Menin to maintain a similar HOX/MEIS transcriptional network. Common readouts after Menin inhibition include decreased HOXA9 and MEIS1, increased CD11b and CD14, morphological maturation, and reduced blast proportion.

(3) Menin Resistance

Resistance to Menin inhibition may involve MEN1 binding-interface mutations, RAS-pathway co-mutations, transcriptional-network remodeling, and changes in cellular differentiation state. Experiments should simultaneously evaluate target engagement, transcriptional changes, differentiation phenotypes, and clonal evolution.

3.3 MCL-1 and BCL-XL

MCL-1 and BCL-XL can serve as compensatory survival targets after BCL-2 inhibition and may have greater functional importance in certain monocytic-like AML, T-ALL, and residual resistant clones. Because MCL-1 participates in cardiomyocyte survival and BCL-XL contributes to platelet homeostasis, direct inhibition may be limited by the therapeutic window. Studies should combine short-term pharmacological treatment, inducible genetic intervention, and normal hematopoietic-cell controls to confirm selectivity.

3.4 TP53 and MDM2

Wild-type TP53 can be negatively regulated by MDM2. Therefore, certain leukemias retaining wild-type TP53 but showing high MDM2 activity may be sensitive to MDM2 intervention. TP53-mutated or TP53-deleted leukemia is generally associated with defective DNA-damage responses, complex karyotypes, and treatment resistance. Normal p53 function cannot be restored simply by blocking MDM2, so experimental design should first define TP53 genotype, protein status, and transcriptional activity.

4 Cell-Surface Antigens and Non-CAR-T Immune Targeting

4.1 CD19, CD22, and CD20

(1) CD19

CD19 is widely expressed in B-cell precursor leukemia and can be used by CD19×CD3 bispecific molecules to recruit endogenous T cells. After treatment, reduced antigen expression, splice variants, or lineage switching may occur. CD19-positive-cell proportion, single-cell antigen density, and leukemia-lineage markers should therefore be monitored longitudinally.

(2) CD22

CD22 has strong internalization capacity and is suitable for delivering cytotoxic payloads through antibody-drug conjugates. Studies should simultaneously analyze antigen density, antibody internalization, lysosomal trafficking, payload release, and DNA damage rather than using CD22 positivity alone to predict activity.

(3) CD20

CD20 is mainly targeted in certain mature B-cell leukemias and CD20-positive B-ALL and can exert effects through complement-dependent cytotoxicity, antibody-dependent cellular cytotoxicity, and direct signaling regulation. Its expression is affected by cellular maturation stage, prior treatment, and clonal evolution.

4.2 CD33 and CD123

(1) CD33

CD33 is expressed in most AML blasts and has a certain degree of internalization capacity, making it suitable for antibody-drug conjugates and bispecific molecules. Targeting efficacy is affected by antigen density, splice isoforms, drug efflux, and DNA-damage-repair capacity. Expression on normal myeloid cells also limits the therapeutic window.

(2) CD123

CD123 is the IL-3 receptor α chain and is highly expressed in certain AML blasts and leukemic stem/progenitor cells. It can be targeted using bispecific antibodies, antibody-drug conjugates, toxin-fusion proteins, and NK-cell engagers. CD123 is also expressed on normal hematopoietic progenitors, so studies need to evaluate leukemia clearance, myelosuppression, and hematopoietic recovery simultaneously.

4.3 TIM-3 and CD47

TIM-3 may be expressed on subsets of leukemia stem cells, T cells, NK cells, and myeloid immune cells. Intervention can therefore produce both direct effects on leukemia cells and remodeling of the immune microenvironment. CD47 contributes to immune escape by suppressing macrophage phagocytosis, but its expression on red blood cells and normal tissues limits the therapeutic window. Both are better regarded as exploratory targets requiring precise patient stratification and combination-mechanism validation.

Table 1 Major Emerging Leukemia Targets and Research Positioning

Target	Major Associated Subtypes	Core Function	Non-CAR-T Intervention Approaches	Major Research Limitations
FLT3	FLT3-mutated AML	Activates STAT5, RAS-MAPK, and PI3K-AKT	Small-molecule kinase inhibitors	Secondary mutations and bypass activation
IDH1/2	IDH-mutated AML	Generates D-2-hydroxyglutarate and blocks differentiation	Mutant-selective inhibitors	Differentiation recovery with persistent clones
Menin	KMT2A-rearranged and NPM1-mutated AML	Maintains HOX/MEIS transcriptional programs	Protein-interaction inhibitors	MEN1 mutations and transcriptional-network remodeling
BCL-2	AML, CLL, and certain ALL	Suppresses mitochondrial apoptosis	BH3 mimetics	MCL-1 and BCL-XL compensation
BCR::ABL1	CML and Ph-positive ALL	Constitutively activates proliferation and survival signaling	ATP-site and allosteric inhibitors	Kinase-domain and compound mutations
BTK	CLL	Transduces B-cell receptor signaling	Covalent and noncovalent BTK inhibitors	C481- and PLCγ2-associated resistance
CD19	B-ALL and certain CLL	B-cell lineage antigen	Bispecific antibodies	Antigen loss and lineage switching
CD22	B-ALL	Internalizable B-cell antigen	Antibody-drug conjugates	Antigen downregulation and payload-related toxicity
CD33	AML	Myeloid cell-surface antigen	Antibody-drug conjugates and bispecific molecules	Expression on normal myeloid cells
CD123	AML and certain myeloid malignancies	Leukemic stem/progenitor-cell-associated antigen	Bispecific antibodies and toxin-fusion proteins	Expression on normal progenitors and myelosuppression

5 Experimental Applications of Leukemia Targets

5.1 AML Target Stratification

(1) Genomic Stratification

AML studies should prioritize detection of FLT3, NPM1, IDH1, IDH2, KMT2A, TP53, and RAS-pathway abnormalities, determine whether mutations are located in the dominant clone, and analyze allelic burden. Detection of a mutation alone does not establish stable drug dependence and should be combined with signaling-activity and cellular-function validation.

(2) Protein and Metabolic Detection

FLT3 studies can measure p-FLT3 and p-STAT5. IDH studies can measure D-2-hydroxyglutarate and myeloid differentiation. Menin studies can assess HOXA9, MEIS1, and CD11b. BCL-2 studies should examine mitochondrial membrane potential, Cytochrome c release, and Caspase activation.

(3) Distinguishing Types of Drug Effects

Inhibition of different targets may primarily result in cell death, slower proliferation, restored differentiation, or reduced colony-forming capacity. A single short-term cell-viability readout cannot distinguish these effect types. Experimental endpoints should therefore be selected according to the target mechanism.

5.2 Target Analysis in ALL, CLL, and CML

(1) B-ALL

B-ALL should be stratified according to expression density of CD19, CD22, and CD20, together with abnormalities involving BCR::ABL1, ABL-class fusions, CRLF2, and the JAK pathway. Surface-antigen analysis should account for expression drift before and after treatment, whereas fusion-kinase research should combine fusion-transcript detection with downstream phosphorylation signaling.

(2) T-ALL

T-ALL research can focus on NOTCH1, JAK-STAT, PI3K-AKT-mTOR, and BCL-2-family dependencies. T-ALL cells at different maturation stages may differ in their dependence on BCL-2 and BCL-XL. Drug selection should therefore combine immunophenotyping with functional apoptosis assays.

(3) CLL

CLL drug-efficacy systems can be established around BTK, PLCγ2, BCL-2, and CD20. BTK inhibition may alter leukemia-cell tissue homing and peripheral-blood distribution. Evaluation should therefore jointly analyze cell migration, chemotactic signaling, lymphoid-tissue burden, and apoptosis.

(4) CML

CML research centers on BCR::ABL1 transcript quantification and kinase-domain sequencing and can additionally measure p-CRKL and downstream signaling. Comparisons between ATP-site and allosteric inhibitors should consider compound mutations, colony-forming capacity, and residual leukemia stem cells.

5.3 Resistance and Combination Targeting

(1) Clonal Evolution

Relapsed and resistant samples should be paired with pretreatment samples to analyze secondary mutations, subclonal expansion, and changes in the clone carrying the target. Continued target-protein expression does not indicate that the original drug remains effective. Resistance may arise at the levels of drug binding, downstream signaling, or cellular state.

(2) Shifts in Apoptotic Dependence

FLT3, Menin, or BTK inhibition can alter dependence on BCL-2, MCL-1, and BCL-XL, creating new combination-intervention windows. Combination studies should use concentration matrices, treatment sequencing, and BH3 profiling to determine the source of synergy rather than relying on a single fixed-concentration combination.

(3) Bone-Marrow Microenvironment Protection

Stromal cells, cytokines, hypoxia, and adhesion signaling can reduce leukemia-cell sensitivity to targeted drugs. Coculture systems, three-dimensional bone-marrow models, and patient-derived xenograft models can be used to evaluate microenvironmental dependence and protection of resistant clones.

6 Frequently Asked Questions

6.1 Is CAR-T Itself a Leukemia Target?

No. CAR-T is a cell-therapy platform, whereas CD19, CD22, CD33, CD123, CD7, and related molecules are recognition targets. The same antigen can also be used for bispecific antibodies, antibody-drug conjugates, and other immune-intervention strategies.

6.2 Which Emerging Targets Should Be Prioritized in AML?

FLT3, IDH1/2, BCL-2, and Menin have relatively well-defined molecular stratification bases, whereas CD33 and CD123 are suitable for surface-targeting research. Applications of TP53, MCL-1, TIM-3, and microenvironmental pathways should be determined according to the specific clone and functional dependence.

6.3 Is NPM1 a Direct Binding Target of Menin Inhibitors?

No. Menin inhibitors directly act on Menin-associated protein interactions. NPM1-mutated AML depends on Menin to maintain an abnormal HOX/MEIS transcriptional program and can therefore respond to Menin inhibition.

6.4 Does Increased BCL-2 Expression Necessarily Indicate Sensitivity to BCL-2 Inhibitors?

No. Drug sensitivity also depends on BIM loading, compensation by MCL-1 and BCL-XL, BAX/BAK function, and mitochondrial state. Functional BH3 profiling generally reflects apoptotic dependence more accurately than BCL-2 expression alone.

6.5 Does High CD123 Expression Make All CD123-Targeting Approaches Suitable?

Not necessarily. Bispecific antibodies, antibody-drug conjugates, and toxin-fusion proteins differ in their requirements for antigen density, internalization rate, and effector-cell status. Expression on normal hematopoietic progenitors and the risk of myelosuppression should also be evaluated.

7 Products for Leukemia Target Research

7.1 AML-Related Target Inhibitors

Product Name	CAS No.	Target and Mechanistic Characteristics	Application Positioning
Midostaurin	120685-11-2	Multitarget kinase inhibitor that inhibits FLT3, KIT, and related kinases	Used for research on FLT3 signaling, AML drug sensitivity, and combination interventions
Gilteritinib	1254053-43-4	FLT3/AXL inhibitor active against FLT3-ITD and certain FLT3-TKD mutations	Used for research on FLT3-mutated models, STAT5 signaling, and resistance mechanisms
Quizartinib	950769-58-1	Type II FLT3 inhibitor with pronounced activity in FLT3-ITD-dependent models	Used for research on FLT3 kinase conformation, mutation sensitivity, and combination therapy
Ivosidenib	1448347-49-6	Mutant IDH1 inhibitor that reduces abnormal D-2-hydroxyglutarate production	Used for research on IDH1 mutations, metabolic reprogramming, and myeloid differentiation
Enasidenib	1446502-11-9	Mutant IDH2 inhibitor	Used for research on IDH2 mutations, D-2-hydroxyglutarate, and restoration of differentiation
Venetoclax	1257044-40-8	Selective BCL-2 inhibitor that releases mitochondrial apoptotic blockade	Used for research on apoptotic dependence in AML and CLL, BH3 function, and combination strategies
Revumenib	2169919-21-3	Inhibitor of Menin-associated protein interactions	Used for research on KMT2A rearrangements, NPM1 mutations, and HOX/MEIS transcription
Ziftomenib	2134675-36-6	Menin inhibitor	Used for research on NPM1-mutated AML, myeloid differentiation, and Menin resistance

7.2 CLL-Related Target Inhibitors

Product Name	CAS No.	Target and Mechanistic Characteristics	Application Positioning
Ibrutinib	936563-96-1	Covalent BTK inhibitor that primarily binds the BTK C481 residue	Used for research on B-cell receptor signaling, CLL-cell migration, and BTK resistance
Acalabrutinib	1420477-60-6	Selective covalent BTK inhibitor	Used for research on BTK signaling, CLL drug sensitivity, and BTK/BCL-2 combination strategies
Pirtobrutinib	2101700-15-4	Noncovalent BTK inhibitor that does not depend on covalent C481 binding	Used for research on C481 mutations and resistance to covalent BTK inhibitors
Idelalisib	870281-82-6	PI3Kδ inhibitor that suppresses B-cell-receptor-associated survival signaling	Used for research on CLL-cell survival, microenvironmental dependence, and PI3K-AKT signaling
Venetoclax	1257044-40-8	Selective BCL-2 inhibitor	Used for research on mitochondrial apoptosis in CLL, BTK/BCL-2 combination strategies, and resistance

7.3 BCR::ABL1-Related Target Inhibitors

Product Name	CAS No.	Target and Mechanistic Characteristics	Application Positioning
Imatinib	152459-95-5	ATP-competitive BCR::ABL1 inhibitor	Used for basic CML models and research on BCR::ABL1 signaling and acquired resistance
Dasatinib	302962-49-8	BCR::ABL1 and SRC-family kinase inhibitor	Used for research on CML, Ph-positive ALL, and SRC bypass signaling
Nilotinib	641571-10-0	Type II BCR::ABL1 inhibitor	Used for research on BCR::ABL1 conformation, mutation sensitivity, and drug comparison
Bosutinib	380843-75-4	BCR::ABL1/SRC inhibitor	Used for research on CML signaling, kinase selectivity, and resistant clones
Ponatinib	943319-70-8	BCR::ABL1 inhibitor active against certain resistant mutations including T315I	Used for research on CML, Ph-positive ALL, and kinase-domain resistance
Asciminib	1492952-76-7	Allosteric inhibitor targeting the ABL1 myristoyl pocket	Used for research on BCR::ABL1 allosteric regulation, dual-site blockade, and compound mutations

Leukemia-target research has expanded from individual surface antigens to driver mutations, abnormal metabolism, apoptotic dependencies, and transcriptional regulation. Target value should be determined according to disease subtype, clonal attribution, functional dependence, and resistance mechanisms rather than relying solely on gene mutations, protein expression, or short-term cell-viability measurements.

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[4] Iacobucci I, Mullighan CG. Genetic Basis of Acute Lymphoblastic Leukemia. J Clin Oncol. 2017;35(9):975-983.

[5] Rai KR, Jain P. Chronic lymphocytic leukemia (CLL)-Then and now. Am J Hematol. 2016;91(3):330-340.

[6] Carroll M, Ohno-Jones S, Tamura S, Buchdunger E, Zimmermann J, et al. CGP 57148, a tyrosine kinase inhibitor, inhibits the growth of cells expressing BCR-ABL, TEL-ABL, and TEL-PDGFR fusion proteins. Blood. 1997;90(12):4947-4952.

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