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Integrated single-cell transcriptome analysis of CD34 + enriched leukemic stem cells revealed intra- and inter-patient transcriptional heterogeneity in pediatric acute myeloid leukemia

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To gain insights into the idiosyncrasies of CD34 + enriched leukemic stem cells, we investigated the nature and extent of transcriptional heterogeneity by single-cell sequencing in pediatric AML. Whole transcriptome analysis of 28,029 AML single cells was performed using the nanowell cartridge–based barcoding technology. Integrated transcriptional analysis identified unique leukemic stem cell clusters of each patient and intra-patient heterogeneity was revealed by multiple LSC-enriched clusters differing in their cell cycle processes and BCL2 expression. All LSC-enriched clusters exhibited gene expression profile of dormancy and self-renewal. Upregulation of genes involved in non-coding RNA processing and ribonucleoprotein assembly were observed in LSC-enriched clusters relative to HSC. The genes involved in regulation of apoptotic processes, response to cytokine stimulus, and negative regulation of transcription were upregulated in LSC-enriched clusters as compared to the blasts. Validation of top altered genes in LSC-enriched clusters confirmed upregulation of TCF7L2, JUP, ARHGAP25, LPAR6, and PRDX1 genes, and serine/threonine kinases (STK24, STK26). Upregulation of LPAR6 showed trend towards MRD positive status (Odds ratio = 0.126; 95% CI = 0.0144–1.10; p = 0.067) and increased expression of STK26 significantly correlated with higher RFS (HR = 0.231; 95% CI = 0.0506–1.052; p = 0.04). Our findings addressed the inter- and intra-patient diversity within AML LSC and potential signaling and chemoresistance-associated targets that warrant investigation in larger cohort that may guide precision medicine in the near future.

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We are grateful to BD Biosciences for their support with single-cell experiments and reagents.


This work was supported by Indian Council of Medical Research under the center for advanced research in excellence in Acute myeloid leukemia to Prof. RG (No. 55/4/10/CARE-AML/2018-NCD-II).

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Authors and Affiliations



Conceptualization—R.G., D.T., and GK; Methodology—D.T., N.J., V.S., A.K.; Software—V.S.; Validation—D.T., A.K., and V.S.; Formal Analysis—V.S and D.T.; Investigation—D.T. and V.K.; Resources—R.G.; Data Curation—V.S. and D.T.; Writing—D.T. and V.S.; Writing—Review & Editing—RG.; Visualization—R.G.; Supervision—D.T. and R.G..; Project Administration—R.G. and N.J.; Funding Acquisition, R.G.

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Correspondence to Ritu Gupta.

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Approval for the conduct of the study was obtained from Institute Ethics Committee, All India Institute of Medical Sciences, New Delhi (Approval No. IC-SCR/92/19(o).

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Thakral, D., Singh, V.K., Gupta, R. et al. Integrated single-cell transcriptome analysis of CD34 + enriched leukemic stem cells revealed intra- and inter-patient transcriptional heterogeneity in pediatric acute myeloid leukemia. Ann Hematol 102, 73–87 (2023).

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