Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single cell resolution

Abstract

Early hematopoiesis is a continuous process in which hematopoietic stem and progenitor cells (HSPCs) gradually differentiate toward specific lineages. Aging and myeloid malignant transformation are characterized by changes in the composition and regulation of HSPCs. In this study, we used single cell RNA sequencing (scRNAseq) to characterize an enriched population of human hematopoietic stem and progenitor cells (HSPCs) obtained from young and elderly healthy individuals. Based on their transcriptional profile, we identified changes in the proportions of progenitor compartments during aging, and differences in their functionality, as evidenced by gene set enrichment analysis. Trajectory inference revealed that altered gene expression dynamics accompanied cell differentiation, which could explain age-associated changes in hematopoiesis. Next, we focused on key regulators of transcription by constructing gene regulatory networks and detected regulons that were specifically active in elderly individuals. Using previous findings in healthy cells as a reference, we analyzed scRNA-seq data obtained from patients with myelodysplastic syndrome (MDS) and detected specific alterations of the expression dynamics of genes involved in erythroid differentiation in all patients with MDS such as TRIB2. In addition, the comparison between transcriptional programs and gene regulatory networks (GRN) regulating normal HSPCs and MDS HSPCs allowed identification of regulons that were specifically active in MDS cases such as SMAD1, HOXA6, POU2F2 and RUNX1 suggesting a role of these TF in the pathogenesis of the disease. In summary, we demonstrate that the combination of single cell technologies with computational analysis tools enable the study of a variety of cellular mechanisms involved in complex biological systems such as early hematopoiesis and can be used to dissect perturbed differentiation trajectories associated with perturbations such as aging and malignant transformation. Furthermore, the identification of abnormal regulatory mechanisms associated with myeloid malignancies could be exploited for personalized therapeutic approaches in individual patients.

Data availability

All the single cell RNA sequencing data is available at Gene Expression Omnibus under accession number GSE180298. The scripts needed to replicate the analysis are deposited on GitHub:https://github.com/mainciburu/scRNA-Hematopoiesis

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Marina Ainciburu

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    For correspondence
    mainciburu@alumni.unav.es
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6483-1901
  2. Teresa Ezponda

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  3. Nerea Berastegui

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  4. Ana Alfonso-Pierola

    Clinica Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  5. Amaia Vilas-Zornoza

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  6. Patxi San Martin-Uriz

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  7. Diego Alignani

    Flow Cytometry Core, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  8. Jose Lamo de Espinosa

    Clinica Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  9. Mikel San Julian

    Clinica Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  10. Tamara Jiménez Solas

    Hospital Universitario de Salamanca, Salamanca, Spain
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5894-2023
  11. Felix Lopez

    Hospital Universitario de Salamanca, Salamanca, Spain
    Competing interests
    No competing interests declared.
  12. Sandra Muntion

    Hospital Universitario de Salamanca, Salamanca, Spain
    Competing interests
    No competing interests declared.
  13. Fermin Sanchez-Guijo

    Hospital Universitario de Salamanca, Salamanca, Spain
    Competing interests
    No competing interests declared.
  14. Antonieta Molero

    Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
    Competing interests
    No competing interests declared.
  15. Julia Montoro

    Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
    Competing interests
    No competing interests declared.
  16. Guillermo Serrano

    Computational Biology Program, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  17. Aintzane Diaz-Mazkiaran

    Computational Biology Program, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  18. Miren Lasaga

    Translational Bioinformatics Unit, NavarraBiomed, Pamplona, Spain
    Competing interests
    No competing interests declared.
  19. David Gomez-Cabrero

    Translational Bioinformatics Unit, NavarraBiomed, Pamplona, Spain
    Competing interests
    No competing interests declared.
  20. Maria Diez-Campelo

    Hospital Universitario de Salamanca, Salamanca, Spain
    Competing interests
    No competing interests declared.
  21. David Valcarcel

    Department of Hematology, Vall d'Hebron Hospital Universitari, Barcelona, Spain
    Competing interests
    No competing interests declared.
  22. Mikel Hernaez

    Computational Biology Program, Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
  23. Juan Pablo Romero

    Area de Hemato-Oncología, Universidad de Navarra, Pamplona, Spain
    Competing interests
    Juan Pablo Romero, Employed by 10x Genomics since February 2021; this employment had no bearing on this work.
  24. Felipe Prosper

    Clinica Universidad de Navarra, Pamplona, Spain
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6115-8790

Funding

Instituto de Salud Carlos III

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Ministerio de Ciencia e Innovación (PhD fellowship FPU18/05488)

  • Marina Ainciburu

Fundación Científica Asociación Española Contra el Cáncer (Investigador AECC award)

  • Teresa Ezponda

H2020 Marie Skłodowska-Curie Actions (Grant Agreement No. 898356)

  • Mikel Hernaez

Federación Española de Enfermedades Raras (PI17/00701,PI19/00726 and PI20/01308)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Centro de Investigación Biomédica en Red de Cáncer (CB16/12/00489 and CB16/12/00225)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Gobierno de Navarra (ERAPerMed MEET-AML 0011-2750-2019-000001; AGATA 0011-1411-2020-000010/0011-1411-2020-000011 and DIAN)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

la Caixa" Foundation " (GR-NET NORMAL-HIT HR20-00871)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Cancer Research UK (C355/A26819)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Fundación Científica Asociación Española Contra el Cáncer (Accelerator Award Program)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Associazione Italiana per la Ricerca sul Cancro (Accelerator Award Program)

  • Marina Ainciburu
  • Teresa Ezponda
  • Nerea Berastegui
  • Ana Alfonso-Pierola
  • Amaia Vilas-Zornoza
  • Patxi San Martin-Uriz
  • Diego Alignani
  • Jose Lamo de Espinosa
  • Mikel San Julian
  • Tamara Jiménez Solas
  • Felix Lopez
  • Sandra Muntion
  • Fermin Sanchez-Guijo
  • Antonieta Molero
  • Julia Montoro
  • Guillermo Serrano
  • Aintzane Diaz-Mazkiaran
  • Miren Lasaga
  • David Gomez-Cabrero
  • Maria Diez-Campelo
  • David Valcarcel
  • Mikel Hernaez
  • Juan Pablo Romero
  • Felipe Prosper

Gobierno de Navarra (PhD fellowship 0011-0537-2019-000001)

  • Nerea Berastegui

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Human subjects: The samples and data from the patients included in the study were provided by the Biobank of the University of Navarra and were processed according to standard operating procedures. Patients and healthy donors provided informed consent, together with consent for publication. The study was approved by the Clinical Research Ethics Committee of the Clinica Universidad de Navarra, following protocol # 2017.218.

Reviewing Editor

  1. Jiwon Shim, Hanyang University, Republic of Korea

Publication history

  1. Received: April 8, 2022
  2. Accepted: January 10, 2023
  3. Accepted Manuscript published: January 11, 2023 (version 1)

Copyright

© 2023, Ainciburu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Marina Ainciburu
  2. Teresa Ezponda
  3. Nerea Berastegui
  4. Ana Alfonso-Pierola
  5. Amaia Vilas-Zornoza
  6. Patxi San Martin-Uriz
  7. Diego Alignani
  8. Jose Lamo de Espinosa
  9. Mikel San Julian
  10. Tamara Jiménez Solas
  11. Felix Lopez
  12. Sandra Muntion
  13. Fermin Sanchez-Guijo
  14. Antonieta Molero
  15. Julia Montoro
  16. Guillermo Serrano
  17. Aintzane Diaz-Mazkiaran
  18. Miren Lasaga
  19. David Gomez-Cabrero
  20. Maria Diez-Campelo
  21. David Valcarcel
  22. Mikel Hernaez
  23. Juan Pablo Romero
  24. Felipe Prosper
(2023)
Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single cell resolution
eLife 12:e79363.
https://doi.org/10.7554/eLife.79363

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