Table 1 Summary of key findings related to clonal evolution in leukemia by single-cell sequencing

MDS, AML

Single-cell targeted DNA sequencing

Pre-MDS stem cells and MDS stem cells contributed to MDS transformation to AML in a nonlinear and parallel clonal evolutionary pattern

Identified that crucial role of small and diverse aberrant stem cell subpopulations may confer leukemic transformation

CH, MPN, AML

scDNA-seq; Simultaneous single-cell mutational profiling and immunophenotyping.

Increased clonal complexity was observed from CH to MPN to AML. Mutations in signaling genes often occur in distinct subclones more than once. Noted that epigenetic modifiers such as DTAI (DNMT3A, TET2, ASXL1, and/or IDH1 or IDH2) are the most prevalent AML-initiating mutation and the combination of them may confer clonal dominance.

Identified multiple important characteristics in the clonal architecture along the progression of AML.

AML

scDNA-seq; Simultaneous single-cell mutational profiling and immunophenotyping.

Driver mutations of AML are often in a co-occurring and mutually exclusive pattern. Linear and branching pattern of AML phylogeny was observed, and some of the branching patterns showed convergence.

Summarized the mutational and phylogenetic features in AML that may underly risk stratification and prognosis determination.

CLL

scRNA-seq; single-cell targeted mutation analysis in DNA and RNA

LCP1 and WNK1 were identified as novel CLL drivers. Convergent expression profile was detected in CLL despite genetic differences.

Identified novel driver mutation for therapeutic targeting CLL. Highlighted that the targeted scRNA mutation analysis may sensitively determine the mutation profile with transcriptomics.

ALL

Targeted scDNA-seq of SNVs, deletions and lgH

Structural variants mostly occur before SNVs in ALL. KRAS occurs in late ALL development and is not enough to confer clonal dominance.

Ordered genetic events of ALL, which is prognostically informative. Characterized the function of KRAS mutation in ALL.

T-ALL

Targeted scDNA-seq; scRNA-seq

Mutation gain was ordered in T-ALL. Inactivation of CDKN2A/B and T-cell receptor deletions and fusion genes are intermediate events and NOTCH1 mutation is the late event.

Emphasized the importance of targeting NOTCH signaling in T-ALL.

T-ALL

Targeted scDNA-seq

NOTCH1 mutation can also be detected at diagnosis of the T-ALL although typically occurs later. The presence of small clones at diagnosis can evolve into major clones in later stages.

Revealed the heterogeneity of NOTCH1 mutation in different subpopulations and provided evidence for differentially targeting the NOTCH pathway.

ALL

scDNA-seq;

Simultaneous targeted single-cell DNA sequencing and cell-surface protein expression analysis

Lineage related mutations (ETV6, IKZF1, and PAX5) occurs earlier than kinase activating mutations (JAK1, JAK2, KRAS, NRAS, FLT3)

Highlighted and summarized the sequential gain of the genetic event in ALL, which may be prognostically informative.

MPN, AML

scRNA-seq

Increased expression of DUSP6 underlies JAKi resistance disease transformation from MPN to sAML. DUSP6 functions through the DUSP6-RSK1-S6 axis. Pharmacological inhibition of DUSP6 eliminated the resistance to JAKi.

Highlighted DUSP6-RSK1 is a vulnerable, therapeutically targetable pathway in myeloid malignancies.

MPN, AML

TARGET-seq

The effect of chronic inflammation in TP53-mutation-driven clonal evolution in AML was characterized. Chronic inflammation suppressed TP53 WT HSCs while enhancing the fitness advantage of TP53-mutant cells and promoting genetic evolution.

First noted the importance of chronic inflammation in TP53-mutant AML progression. Facilitated the risk-stratification, early detection and treatment strategies for TP53-mutant leukemia.

CLL

scRNA-seq

Putative driver SF3B1 mutation was found to dysregulate multiple cellular pathways including DNA damage response, telomere maintenance, and Notch signaling (mediated by KLF8 upregulation, increased TERC and TERT expression, or altered splicing of DVL2 transcript, respectively).

Characterized how SF3B1 mutation functions in CLL progression and offers selective advantages. These pathways can be therapeutically targeted in SF3B1 mutated CLL patients.

AML

scRNA-seq

Myc targets are upregulated along the progression of AML, among which are splicing factors. The tipping point of HSC transformation into leukemia cells was characterized by dramatically increased splicing factors and unusual RNA velocity. Exon 4 skipping of Tmem134 in high-risk subset resulted in the production of cell-cycle-promoting Tmem134β.

Characterized that Myc-driven CLL progression was related to the RNA splicing events, promoting that the splicing factor may underly important therapeutic targets.

AML

CITE-seq; ATAC-seq

Flt3-ITD mutation, when cooperates with NUP98 and Runx1 mutations, activates distinct transcriptional programs. Flt3-ITD/Runx1del caused aberrant expansion of myeloid progenitors, while Flt3ITD/NHD13 selectively controlled IFN-I signaling to drive the clonal expansion of the pre-AML population.

Provided insight into how to context-specifically treat pediatric and adult AML, since Flt3-ITD/NHD13 and Flt3-ITD/RUNX1del respectively represent the most prevailing mutation in pediatric and adult AML.