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Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice

Abstract

Aging is characterized by an accumulation of myeloid-biased hematopoietic stem cells (HSCs) with reduced developmental potential. Genotoxic stress and epigenetic alterations have been proposed to mediate age-related HSC loss of regenerative and self-renewal potential. However, the mechanisms underlying these changes remain largely unknown. Genetic inactivation of the plant homeodomain 6 (Phf6) gene, a nucleolar and chromatin-associated factor, antagonizes age-associated HSC decline. Immunophenotyping, single-cell transcriptomic analyses and transplantation assays demonstrated markedly decreased accumulation of immunophenotypically defined HSCs, reduced myeloid bias and increased hematopoietic reconstitution capacity with preservation of lymphoid differentiation potential in Phf6-knockout HSCs from old mice. Moreover, deletion of Phf6 in aged mice rejuvenated immunophenotypic, transcriptional and functional hallmarks of aged HSCs. Long-term HSCs from old Phf6-knockout mice showed epigenetic rewiring and transcriptional programs consistent with decreased genotoxic stress-induced HSC aging. These results identify Phf6 as an important epigenetic regulator of HSC aging.

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Fig. 1: Abrogation of HSC accumulation and HSC aging-associated transcriptional programs in Phf6-knockout mice.
Fig. 2: Phf6 inactivation prevents age-associated accumulation of immunophenotypic HSCs with features of myeloid bias.
Fig. 3: Stem cell repopulation capacity and B cell differentiation potential, with simultaneous preclusion of myeloid differentiation bias, is preserved by Phf6 inactivation upon serial transplantation.
Fig. 4: Phf6 inactivation late in life reverses HSC age-associated markers and functionally reverses aging in old HSCs.
Fig. 5: RNA-seq analysis of Phf6 wild-type and knockout LT-HSCs shows reversal of age-associated transcriptional programs.
Fig. 6: ATAC-seq analysis of Phf6 wild-type and knockout LT-HSCs shows reversal of age-associated transcriptional programs.
Fig. 7: Decreased DNA damage in Phf6-knockout LT-HSCs from old mice compared with wild type.

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Data availability

Bulk and single-cell RNA-seq data that support the findings of this study have been deposited in the GEO under accession no. GSE165695. Public data analyzed in this study include expression data from HSPCs from homozygous Lig4 p.Arg278His43 mice and wild-type controls (GSE65195). We performed GSEA with gene sets available in the MSigDB (https://www.gsea-msigdb.org/gsea/msigdb/).

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Acknowledgements

This work was supported by NIH grants R35 CA210065 (to A.A.F.), R01 CA206501 (to A.A.F.) and P30 CA013696 (Confocal and Specialized Microscopy Shared Resource, Flow Cytometry Shared Resource, Genomics Shared Resource, Herbert Irving Comprehensive Cancer Center). J.A.B. was supported by funding from the National Cancer Institute of the National Institutes of Health (K99 CA267168). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. We are grateful to E. Passegué at the Columbia Stem Cell Initiative for critical reading of the manuscript.

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Authors and Affiliations

Authors

Contributions

A.A.W. and A.A.F. designed the study. A.A.W., S.A.Q., J.A.B., S.A., M.B. and T.G. performed research. S.A.Q. performed bioinformatics analyses. A.A.F. and T.P. supervised research. A.A.F. and wrote the manuscript with A.A.W., S.A. and S.A.Q.

Corresponding authors

Correspondence to Agnieszka A. Wendorff or Adolfo A. Ferrando.

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Competing interests

A.A.F., J.A.B. and S.A. are currently employed by Regeneron Pharmaceuticals. A.W. is currently employed by Calico. S.A.Q., M.B., T.G. and T.P. declare no competing interests.

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Nature Aging thanks Michael Milsom and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Cell cycle analysis of scRNA-sequencing data from Phf6 wild-type and knockout hematopoietic stem and progenitor cells (total LSK cells).

a, UMAP projection of scRNA-Seq data generated from LSK cells harvested from 16-week and 24-month-old Phf6 wild-type and knockout mice (n = 12, 3 samples per genotype, per age group). Cells are colored according to the cell cycle phase. b, UMAP projection of scRNA-Seq data as in a, indicating the cell cycle score for S phase. c. UMAP projection of scRNA-Seq data as in a, indicating the cell cycle score for and G2M. Data relates to Fig. 1.

Extended Data Fig. 2 Phf6 upregulation in old HSCs.

Relative gene expression levels of Phf6 based on RNA-Seq data from sorted LT-HSCs from young (12-week-old) and aged (24-month-old) wild-type C57/BL6 mice. Data relates to Fig. 5.

Extended Data Fig. 3 Enrichment of an aged LT-HSC-associated gene-set signature in the old scRNA-Seq wild-type HSC cluster compared with young HSC controls.

GSEA enrichment plots of a gene-set comprised of top 250 genes upregulated and downregulated in old LT-HSCs in the scRNA-Seq HSC cluster of 16-week vs. 24-month-old Phf6 wild-type mice. Normalized enrichment score (NES) and the FEWER p-value are shown. Data relates to Fig. 1.

Extended Data Fig. 4 Differential gene expression and pathway analysis comparison between scRNA-Seq sub-clusters identified in the HSC sub-population of total LSK cells in bone marrow of Phf6 wild-type and knockout aged mice.

Network representation of gene sets enriched in the old HSC subcluster i (enriched in Phf6 knockout HSCs from old mice) and HSC subcluster ii (enriched in Phf6 wild-type HSCs from old mice). Node size indicates the number of genes in each represented gene-set. The width of the edges indicates fraction of shared genes between gene-set pairs. Data relates to Fig. 1.

Extended Data Fig. 5 Evaluation of hematopoietic stem and progenitor-cell population representation from young and aged Phf6 wild-type and knockout mice.

a, Representative FACS plots of the total stem and progenitor subset (LSK) and committed myeloid progenitor population (MyP) frequency in the bone marrow of 8-week-old Phf6 wild-type (Phf6+/Y) and hematopoietic-specific knockout mice (Phf6−/Y). b, Quantification of absolute cell numbers of LSK and MyP populations, as in a. Total cell numbers are shown for n = 5 animals per group, per genotype. c, Representative FACS plots of LSK and MyP population frequency in the bone marrow of 24-month-old Phf6 wild-type (Phf6+/Y) and knockout mice (Phf6 −/Y). d, Quantification of absolute cell numbers of LSK and MyP populations, as in c. Total cell numbers are shown for n = 8 and n = 9 animals per genotype, respectively. e. Quantification of absolute cell number/animal of LT-HSC, ST-HSC, MPP2, MPP3 and MPP4 populations in the bone marrow of 24-month-old Phf6 wild-type (Phf6+/Y) and knockout mice (Phf6−/Y). Total cell numbers are shown for n = 8 and n = 9 animals per genotype, respectively. f, Gating strategy for phenotypic identification and quantitation of LT-HSC, ST-HSC, MPP2, MPP3 and MPP4 populations by FACS. g, Gating strategy for phenotypic identification and quantitation of CLP progenitor cells by FACS. h-j, Complete blood count analysis of white blood cells (WBCs), neutrophils (NE) and lymphocytes (LY). k-n, Complete blood count analysis of hematocrit (HCT), red blood cells (RBC), hemoglobin (Hb) and mean corpuscular volume (MCV). o, Complete blood count analysis of platelets (PLT). Peripheral blood counts were scored in 4-month-old wild-type (Phf6+/Y), 4-month-old knockout (Phf6−/Y), 21-month-old wild-type (Phf6+/Y) and 21-month-old knockout (Phf6−/Y) animals (n = 4 mice per group). Graphs represent mean ± SD and p-values were assessed using two-tailed unpaired Student’s t-test.

Source data

Extended Data Fig. 6 Surface expression analysis of age-associated markers in LT-HSCs.

a, Representative histograms depicting surface CD150 expression and quantitation intervals in LT- and ST-HSCs (total CD48neg LSK cells) from aged Phf6 wild-type (Phf6+/Y) and knockout mice (Phf6-/Y). b, Representative histograms depicting surface CD49b expression in LT-HSCs from aged Phf6 wild-type and knockout mice. c, Representative histograms depicting surface CD41 expression in LT-HSCs from aged Phf6 wild type and knockout mice. d, Representative contour plots depicting surface CD117 expression in LT-HSCs from aged Phf6 wild-type and knockout mice. Representative data relates to Fig. 2.

Extended Data Fig. 7 LT-HSC differentiation potential and surface expression analysis of age-associated markers in HSCs recovered after secondary transplantation of LT-HSCs from old Phf6 wild-type and knockout donor mice.

a, Representative contour plots of CD150 and CD48 surface expression and quantitation gates for LT-HSC, ST-HSC, MPP2 and MPP3 stem and progenitor cell subsets within the bone-marrow LSK fraction of recipient mice of serially transplanted aged Phf6 wild-type and knockout LT-HSCs. b, Representative pseudo-color density plots depicting the frequency of donor-derived (CD45.2+) and residual host-derived (CD45.1+) cells in peripheral blood of mice serially transplanted with aged Phf6 wild-type and knockout LT-HSCs. c, Representative histograms indicating CD150, CD49b and CD41 expression on donor-derived LT-HSCs recovered from mice transplanted with aged Phf6 wild-type and knockout LT-HSCs. Representative data relates to Fig. 3.

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Wendorff, A.A., Aidan Quinn, S., Alvarez, S. et al. Epigenetic reversal of hematopoietic stem cell aging in Phf6-knockout mice. Nat Aging 2, 1008–1023 (2022). https://doi.org/10.1038/s43587-022-00304-x

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