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ACUTE LYMPHOBLASTIC LEUKEMIA

miR-126 identifies a quiescent and chemo-resistant human B-ALL cell subset that correlates with minimal residual disease

Leukemia volume 37, pages 1994–2005 (2023)Cite this article

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Abstract

Complete elimination of B-cell acute lymphoblastic leukemia (B-ALL) by a risk-adapted primary treatment approach remains a clinical key objective, which fails in up to a third of patients. Recent evidence has implicated subpopulations of B-ALL cells with stem-like features in disease persistence. We hypothesized that microRNA-126, a core regulator of hematopoietic and leukemic stem cells, may resolve intratumor heterogeneity in B-ALL and uncover therapy-resistant subpopulations. We exploited patient-derived xenograft (PDX) models with B-ALL cells transduced with a miR-126 reporter allowing the prospective isolation of miR-126(high) cells for their functional and transcriptional characterization. Discrete miR-126(high) populations, often characterized by MIR126 locus demethylation, were identified in 8/9 PDX models and showed increased repopulation potential, in vivo chemotherapy resistance and hallmarks of quiescence, inflammation and stress-response pathway activation. Cells with a miR-126(high) transcriptional profile were identified as distinct disease subpopulations by single-cell RNA sequencing in diagnosis samples from adult and pediatric B-ALL. Expression of miR-126 and locus methylation were tested in several pediatric and adult B-ALL cohorts, which received standardized treatment. High microRNA-126 levels and locus demethylation at diagnosis associate with suboptimal response to induction chemotherapy (MRD > 0.05% at day +33 or MRD+ at day +78).

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Fig. 1: miR-126 is associated with intra-tumoral heterogeneity in B-ALL.
Fig. 2: The miR-126 locus is heterogeneously methylated in hu-B-ALL and PDX-derived miR-126 -high and -low fractions.
Fig. 3: miR-126high B-ALL subpopulations exhibit higher repopulating capacity and chemotherapy resistance in patient-derived xenograft models.
Fig. 4: miR-126-high and -low blasts are functionally different entities with alterations in cell cycle and inflammation pathways.
Fig. 5: miR-126 expression and locus methylation correlate with MRD status in B-ALL patients.

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Data availability

ENA code for Bisulphite targeted sequencing is PRJEB63552. ENA code for Whole exome sequencing is PRJEB63520. Bulk RNA sequencing data can be found under the GEO superseries code GSE236142.

Code availability

All codes are available at the following git repository http://www.bioinfotiget.it/gitlab/custom/casertanucera_leukemia2023.

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Acknowledgements

We thank all members from the Gentner lab for help with experiments, discussion and useful insight; all Fractal and Alembic facility personnel for cell sorting and imaging; the center for Omics sciences (COSR) for advice and assistance with genomic sequencing; the OSR biobank for sample collection and storage; the Hematology department for fruitful discussions. We acknowledge Cristina Bugarin for sorting of pediatric patient samples. We thank Matteo Massidda from CRS, Cagliari, Italy, for help with bioinformatic analysis.

Funding

This research was supported by grants to B.G. from the Italian Association for Cancer Research (AIRC-IG 2018 Id.22143), a John Goldman Clinical Research Fellowship from the European Hematology Association (EHA 2014) and from the Telethon Foundation (TIGET 2016 core grant no. C1). Research was also supported by a grant to A.B. from the Italian Association for Cancer Research (AIRC-IG 2017 Id.20564).

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Author notes

  1. These authors contributed equally: Carolina Caserta, Silvia Nucera, Giovanni Cazzaniga, Bernhard Gentner.

Authors and Affiliations

  1. San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy

    Carolina Caserta, Matteo Barcella, Matteo Maria Naldini, Riccardo Pagani, Giacomo Desantis, Erika Zonari, Paola Capasso, Angelo Lombardo & Bernhard Gentner

  2. Vita-Salute San Raffaele University, Milan, Italy

    Carolina Caserta, Matteo Maria Naldini, Riccardo Pagani, Angelo Lombardo & Fabio Ciceri

  3. Tettamanti Center, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy

    Silvia Nucera, Grazia Fazio, Mariella D’Angiò, Daniela Silvestri, Andrea Biondi & Giovanni Cazzaniga

  4. School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy

    Silvia Nucera & Andrea Biondi

  5. National Research Council, Institute for Biomedical Technologies, Segrate, Italy

    Matteo Barcella & Ivan Merelli

  6. Hematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Hospital, Milan, Italy

    Francesca Pavesi, Fabio Ciceri & Bernhard Gentner

  7. Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy

    Orietta Spinelli & Alessandro Rambaldi

  8. Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy

    Maria Grazia Valsecchi

  9. Pediatrics, Fondazione IRCCS San Gerardo dei Tintori, Monza, Italia

    Andrea Biondi

  10. Genetics, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy

    Giovanni Cazzaniga

  11. Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland

    Bernhard Gentner

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  1. Carolina Caserta
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Contributions

C.C. planned and performed experiments, analyzed and interpreted data and prepared the manuscript; S.N. planned and performed experiments, analyzed and interpreted data and collected clinical data. M.Ba. developed and performed the bioinformatics analyses; G.F. and M.D.A. performed sequencing and analyzed data; M.M.N. performed experiments and helped in setting up scRNAseq; F.P. assisted with patient sample identification and collection; G.D. E.Z. and P.C. provided technical assistance and experimental expertise; A.L., I.M. provided supervision; D.S. and M.G.V. provided statistical analysis; F.C., O.S., A.R., A.B. provided supervision and access to patient cells. G.C. provided intellectual input, funding and research infrastructure; B.G. provided funding, designed and coordinated the research, interpreted the data, supervised research and wrote the manuscript.

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Correspondence to Bernhard Gentner.

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Caserta, C., Nucera, S., Barcella, M. et al. miR-126 identifies a quiescent and chemo-resistant human B-ALL cell subset that correlates with minimal residual disease. Leukemia 37, 1994–2005 (2023). https://doi.org/10.1038/s41375-023-02009-5

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