Abstract

We identify SMARCD2 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily D, member 2), also known as BAF60b (BRG1/Brahma-associated factor 60b), as a critical regulator of myeloid differentiation in humans, mice, and zebrafish. Studying patients from three unrelated pedigrees characterized by neutropenia, specific granule deficiency, myelodysplasia with excess of blast cells, and various developmental aberrations, we identified three homozygous loss-of-function mutations in SMARCD2. Using mice and zebrafish as model systems, we showed that SMARCD2 controls early steps in the differentiation of myeloid–erythroid progenitor cells. In vitro, SMARCD2 interacts with the transcription factor CEBPɛ and controls expression of neutrophil proteins stored in specific granules. Defective expression of SMARCD2 leads to transcriptional and chromatin changes in acute myeloid leukemia (AML) human promyelocytic cells. In summary, SMARCD2 is a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia.

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Acknowledgements

We thank all medical and laboratory staff members involved in taking care of patients and performing scientific experiments, in particular R. Conca (FACS sorting), J. Hinke (genomic facility), and P. Robinson and S. Mundlos for next-generation sequencing expertise. We thank S. Hollizeck, D. Kotlarz, M. Lyszkiewicz, and N. Zietara for critical scientific discussion. We thank B. Zeller, R. Abdennour, and H. Nordgarden for clinical care of patients and A. Tierens for initial FACS and histological workup. We thank J. Lessard (IRIC, Université de Montréal) for providing antibodies to SMARCD1, SMARCD2, and SMARCD3 and for critical discussion.

The study has been supported by the European Research Council (ERC Advanced Grant 'Explore'), the Else Kröner-Fresenius-Stiftung, the DZIF (German Center for Infection Research), the Deutsche Forschungsgemeinschaft (Gottfried Wilhelm Leibniz Program), the German PID-NET (BMBF), and the Care-for-Rare Foundation.

V.P. was supported by a Monash International Postgraduate Research Scholarship (MIPRS) and a Monash Graduate Scholarship (MGS). G.L. was supported by the NHMRC (1069284, 1044754). The Australian Regenerative Medicine Institute (ARMI) is supported by grants from the State Government of Victoria and the Australian Government. This research was supported in part by the Intramural Research Program of the US National Institutes of Health, NLM. W.E. and C.Z. were supported by the Deutsche Forschungsgemeinschaft (DFG) through LMUexcellent and SFB1243 (subproject A14). J.G. was supported by the Bundesministerium für Bildung und Forschung, Juniorverbund in der Sytemmedizin 'mitOmics' grant FKZ 01ZX1405A, and C.M. is supported by EU Horizon2020 Collaborative Research Project SOUND (633974).

Author information

Author notes

    • Jacek Puchałka

    Deceased.

Affiliations

  1. Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany.

    • Maximilian Witzel
    • , Daniel Petersheim
    • , Yanxin Fan
    • , Ehsan Bahrami
    • , Tomas Racek
    • , Meino Rohlfs
    • , Jacek Puchałka
    • , Heinrich Schmidt
    •  & Christoph Klein
  2. Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.

    • Maximilian Witzel
    • , Christian Mertes
    • , Julien Gagneur
    •  & Christoph Klein
  3. Department of Informatics, Technical University of Munich, Munich, Germany.

    • Julien Gagneur
  4. Anthropology and Human Genomics, Department of Biology II, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.

    • Christoph Ziegenhain
    •  & Wolfgang Enard
  5. Norwegian National Unit for Newborn Screening, Oslo University Hospital, Oslo, Norway.

    • Asbjørg Stray-Pedersen
  6. Department of Paediatric Allergy and Immunology, University of Manchester, Royal Manchester Children's Hospital, Manchester, UK.

    • Peter D Arkwright
  7. Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon.

    • Miguel R Abboud
  8. Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia.

    • Vahid Pazhakh
    •  & Graham J Lieschke
  9. Medical Genetics and Human Genetic, Charite University Hospital, Berlin, Germany.

    • Peter M Krawitz
  10. Molecular Animal Breeding and Biotechnology, Gene Center Ludwig-Maximilians-Universität München, Munich, Germany.

    • Maik Dahlhoff
    • , Marlon R Schneider
    •  & Eckhard Wolf
  11. Pathology Institute, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany.

    • Hans-Peter Horny
  12. National Center for Biotechnology Information, US National Institutes of Health, US Department of Health and Human Services, Bethesda, Maryland, USA.

    • Alejandro A Schäffer

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Contributions

M.W. designed, performed, and interpreted experiments and wrote and edited the manuscript. D.P. performed ATAC–seq and RNA–seq, Y.F., E.B., T.R., and M.R. were involved in genomic and biochemical analyses, J.P. led the computational biology efforts, C.M. and J.G. analyzed ATAC–seq and RNA–seq data, and C.Z. and W.E. performed mouse RNA–seq and digital gene expression analysis. A.S.-P., P.D.A., and M.R.A. provided clinical care for patients, V.P. and G.J.L. generated and analyzed zebrafish models, and P.M.K. analyzed whole-exome sequencing in initial patients. M.D., M.R.S., and E.W. generated mice. H.-P.H. performed immunohistochemistry analysis of bone marrow biopsies, H.S. provided expert clinical genetic consulting, and A.A.S. guided bioinformatics studies and helped write and edit the manuscript. C.K. designed and guided the study, supervised M.W., provided laboratory resources, and wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Christoph Klein.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–14, Supplementary Note and Supplementary Tables 1, 2 and 18

  2. 2.

    Supplementary Data 1–5

    Supplementary Data 1–5

Excel files

  1. 1.

    Supplementary Table 3

    Primers for human, mouse, and zebrafish studies; morpholinos and sgRNAs for zebrafish studies.

  2. 2.

    Supplementary Table 4

    Differentially expressed genes in Smarcd2+/+ vs. Smarcd2−/− LSK cells.

  3. 3.

    Supplementary Table 5

    Up- and downregulated clusters of genes in Smarcd2+/+ vs. Smarcd2−/− LSK cells.

  4. 4.

    Supplementary Table 6

    CEBPɛ target genes, Venn intersections, and pathways.

  5. 5.

    Supplementary Table 7

    Differentially expressed genes in Smarcd2+/+ vs. Smarcd2−/− LSK cells.

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    Supplementary Table 8

    Differentially expressed genes in Smarcd2+/+ vs. Smarcd2−/− CMP cells.

  7. 7.

    Supplementary Table 9

    Differentially expressed genes in Smarcd2+/+ vs. Smarcd2−/− GMP cells.

  8. 8.

    Supplementary Table 10

    Differentially expressed genes in Smarcd2+/+ vs. Smarcd2−/− MEP cells.

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    Supplementary Table 11

    Up- and downregulated GO terms in Smarcd2+/+ vs. Smarcd2−/− CMP cells.

  10. 10.

    Supplementary Table 12

    Up- and downregulated GO terms in Smarcd2+/+ vs. Smarcd2−/− GMP cells

  11. 11.

    Supplementary Table 13

    Up- and downregulated GO terms in Smarcd2+/+ vs. Smarcd2−/− LSK cells.

  12. 12.

    Supplementary Table 14

    Up- and downregulated GO terms in Smarcd2+/+ vs. Smarcd2−/− MEP cells.

  13. 13.

    Supplementary Table 15

    Differentially expressed genes in ATAC–seq and RNA–seq, CTRL vs. shRNA1-, shRNA2-treated NB4 cells, vehicle DMSO treated.

  14. 14.

    Supplementary Table 16

    Differentially expressed genes in ATAC–seq and RNA–seq, CTRL vs. shRNA1-, shRNA2-treated NB4 cells, ATRA treated.

  15. 15.

    Supplementary Table 17

    Available blood counts of patients A, B, and C, chronologically arranged.

  16. 16.

    Supplementary Table 19

    Definition and number of replicates performed per experiment.

  17. 17.

    Supplementary Table 20

    Numbers used for dot-bot diagrams and statistical analysis, statistical test results.

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https://doi.org/10.1038/ng.3833

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