Table 6 Summary of key findings related to drug resistance mechanisms induced by clonal expansion of leukemia using single-cell sequencing

AML

scRNA-seq

RNA-based clonal evolution tracking was conducted on AML LSCs from matched pre- and post-treatment samples. Commonly evolved signaling networks mediating metabolism, apoptosis and chemokine signaling evolved and became the signature of relapsed samples.

Identified that co-targeting BCL2 and CXCR4 signaling may help improve therapeutic response.

[118]

CLL

Targeted scDNA-seq

After BTK and BCL2 targeting agent (TA) treatments, mutual exclusivity of clonal architecture was observed among multiple resistance mutations to the same targeting therapies. Also, the co-occurrence of multiple novel mutations conferred resistance to dual TA treatment.

Proposed that CLL progression after dual TA treatment is complex but consistently oligoclonal. Different clones have distinct identifiable resistance mechanisms.

[119]

CLL

scRNA-seq; scATAC-seq; mtscATAC-seq

MtDNA mutation was stable over the years and largely changed under strong selective pressure such as allo-HSCT or chemotherapy. The Chromatin state of CLL was also changed (SPIB, SPI1 depletion) and higher expression of CXCR4 was observed at relapse.

Marked that mtDNA mutations and chromosomal state as a clonal tracking method for leukemia progression.

[120]

CLL

scRNA-seq; ATAC-seq

Consistent regulatory program in BTKi treatment was observed starting with a sharp decrease of NF-κB binding, continued with decreased activation of lineage-defining transcription factors and the final acquisition of a quiescent signature.

Established the time-dependent expression and gene regulatory response after BTKi treatment, offering a new method for treatment monitoring.

[121]

CLL

Computational system combining scRNA-seq and DNA barcoding

An integrative lineage tracing system was developed (ClonMapper), which combines DNA barcoding scRNA-seq. ClonMapper identified CLL subpopulations with distinct molecular features and survivorship trajectories during chemotherapy.

Associating CXCR4, Wnt and Notch signaling with the higher survival rate of CLL after chemotherapy.

[123]

CLL

scRNA-seq; WES; Methylome sequencing

Pre-existing stem-cell-like subpopulations that conferred resistance after allo-HSCT treatment in early relapse samples. Early relapse featured a stable genome whereas late relapse featured strong genetic evolution, neoantigen depletion, and epigenomic instability.

Described clinical kinetics post-HSCT treatment in CLL.

[125]

ALL

scRNA-seq

Stem cell properties with the quiescent feature, and activation of glucocorticoid response were marked as relapse-initiating subpopulation in MLL-rearranged infant ALL (MLL-r iALL).

Provided insights for the risk stratification of MLL-r iALL

[127]

B-ALL

sc-CyTOF, RNA-seq

Coordination between the glucocorticoid receptor pathway and B-cell developmental pathway was identified. The BCR signaling pathway was enriched during GC treatment, marked by activation of PI3K/mTOR and CREB signaling and accounted for the GC resistance. Dasatinib targets these active signaling and eliminates the GC resistance.

Indicated that the combination of GCs and TKIs may improve therapeutic outcomes in B-ALL patients.

[128]

AML

scDNA-seq

AML Patients treated with VEN-based therapy with higher response rates were associated with NPM1 or IDH2 mutations, and poor responses or relapse were associated with TP53 loss or kinase activation, particularly FLT3 activation.

Provided insights for the risk stratification and prognostic prediction with older AML patients receiving venetoclax-based combination therapies.

[133]

AML

scDNA-seq

VEN + AraC treatment induced adaptive resistance in AML, characterizing changes in oxidative phosphorylation, electron transport chain complex I (ETCI) and the TP53 pathway. ETC inhibition, pyruvate dehydrogenase inhibitors and mitochondrial ClpP protease agonists improved therapeutic outcomes in VEN + AraC-resistant AML samples.

Noted that the mitochondrial and energy-related inhibitors may be clinically combined with VEN-based therapy to improve therapy outcomes.

[134]

AML

scDNA-seq; DNA methylation profilling

RAS/MAPK pathway, which leads to increased MCL-1 protein expression was the major mechanism for resistance to the VEN. MCL-1 protein maintained the respiration in VEN-resistant cells.

Identified the importance of combining VEN and the RAS/MAPK/MCL-1 pathway inhibitor for AML treatment. This strategy may overcome the VEN resistance and improve AML patient survival.

[135]

CLL

CITE-seq; single-cell short and long read RNA sequencing

Multilayered resistant mechanism was observed in VEN-resistant CLL, including mutations in BCL2 and MCL1 amplification. Universal upregulation of the MCL1 gene was observed, driven by NF-κB pathway activation, and this stopped after discontinuation of VEN therapy.

Proposed that the NF-κB pathway targeting may be a key for improving clinical outcomes in VEN-resistant CLL.

[136]