The transcriptional and regulatory identity of erythropoietin producing cells.


Journal

Nature medicine
ISSN: 1546-170X
Titre abrégé: Nat Med
Pays: United States
ID NLM: 9502015

Informations de publication

Date de publication:
05 2023
Historique:
received: 23 01 2022
accepted: 17 03 2023
medline: 24 5 2023
pubmed: 28 4 2023
entrez: 27 4 2023
Statut: ppublish

Résumé

Erythropoietin (Epo) is the master regulator of erythropoiesis and oxygen homeostasis. Despite its physiological importance, the molecular and genomic contexts of the cells responsible for renal Epo production remain unclear, limiting more-effective therapies for anemia. Here, we performed single-cell RNA and transposase-accessible chromatin (ATAC) sequencing of an Epo reporter mouse to molecularly identify Epo-producing cells under hypoxic conditions. Our data indicate that a distinct population of kidney stroma, which we term Norn cells, is the major source of endocrine Epo production in mice. We use these datasets to identify the markers, signaling pathways and transcriptional circuits characteristic of Norn cells. Using single-cell RNA sequencing and RNA in situ hybridization in human kidney tissues, we further provide evidence that this cell population is conserved in humans. These preliminary findings open new avenues to functionally dissect EPO gene regulation in health and disease and may serve as groundwork to improve erythropoiesis-stimulating therapies.

Identifiants

pubmed: 37106166
doi: 10.1038/s41591-023-02314-7
pii: 10.1038/s41591-023-02314-7
doi:

Substances chimiques

Erythropoietin 11096-26-7
RNA 63231-63-0
EPO protein, human 0
Epo protein, mouse 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1191-1200

Commentaires et corrections

Type : CommentIn
Type : CommentIn

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

Orkin, S. H. Diversification of haematopoietic stem cells to specific lineages. Nat. Rev. Genet. 1, 57–64 (2000).
pubmed: 11262875
Jacobson, L. O., Goldwasser, E., Fried, W. & Plzak, L. Role of the kidney in erythropoiesis. Nature 179, 633–634 (1957).
pubmed: 13418752
Wenger, R. H. & Kurtz, A. Erythropoietin. Compr. Physiol. 1, 1759–1794 (2011).
pubmed: 23733688
Lacombe, C. et al. Peritubular cells are the site of erythropoietin synthesis in the murine hypoxic kidney. J. Clin. Invest. 81, 620–623 (1988).
pubmed: 3339134 pmcid: 329613
Wu, H., Liu, X., Jaenisch, R. & Lodish, H. F. Generation of committed erythroid BFU-E and CFU-E progenitors does not require erythropoietin or the erythropoietin receptor. Cell 83, 59–67 (1995).
pubmed: 7553874
Haemoglobin Concentrations for the Diagnosis of Anaemia and Assessment of Severity (World Health Organization, 2011); https://apps.who.int/iris/bitstream/handle/10665/85839/WHO_NMH_NHD_MNM_11.1_eng.pdf
Prchal, J. T. Polycythemia vera and other primary polycythemias. Curr. Opin. Hematol. 12, 112–116 (2005).
pubmed: 15725900
Haase, V. H. Hypoxia-inducible factor–prolyl hydroxylase inhibitors in the treatment of anemia of chronic kidney disease. Kidney Int. Suppl. 11, 8–25 (2021).
Gangaraju, R. et al. Upregulation of thrombo-inflammatory pathways may contribute to increased thrombotic risk in polycythemia vera and essential thrombocythemia. Blood 128, 3143 (2016).
Gordeuk, V. R. et al. Thrombotic risk in congenital erythrocytosis due to up-regulated hypoxia sensing is not associated with elevated hematocrit. Haematologica 105, e87–e90 (2020).
pubmed: 31289208 pmcid: 7049338
Rankin, E. B. et al. Hypoxia-inducible factor-2 (HIF-2) regulates hepatic erythropoietin in vivo. J. Clin. Invest. 117, 1068–1077 (2007).
pubmed: 17404621 pmcid: 1838939
Kapitsinou, P. P. et al. Hepatic HIF-2 regulates erythropoietic responses to hypoxia in renal anemia. Blood 116, 3039–3048 (2010).
pubmed: 20628150 pmcid: 2974609
Paliege, A. et al. Hypoxia-inducible factor-2alpha-expressing interstitial fibroblasts are the only renal cells that express erythropoietin under hypoxia-inducible factor stabilization. Kidney Int. 77, 312–318 (2010).
pubmed: 20016470
Semenza, G. L., Nejfelt, M. K., Chi, S. M. & Antonarakis, S. E. Hypoxia-inducible nuclear factors bind to an enhancer element located 3′ to the human erythropoietin gene. Proc. Natl Acad. Sci. USA 88, 5680–5684 (1991).
pubmed: 2062846 pmcid: 51941
Appelhoff, R. J. et al. Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor. J. Biol. Chem. 279, 38458–38465 (2004).
pubmed: 15247232
Simonson, T. S. et al. Genetic evidence for high-altitude adaptation in Tibet. Science 329, 72–75 (2010).
pubmed: 20466884
Yi, X. et al. Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329, 75–78 (2010).
pubmed: 20595611 pmcid: 3711608
Huerta-Sánchez, E. et al. Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA. Nature 512, 194–197 (2014).
pubmed: 25043035 pmcid: 4134395
Witt, K. E. & Huerta-Sánchez, E. Convergent evolution in human and domesticate adaptation to high-altitude environments. Philos. Trans. R. Soc. Lond. B Biol. Sci. 374, 20180235 (2019).
pubmed: 31154977 pmcid: 6560271
Moore, L. G., Young, D., McCullough, R. E., Droma, T. & Zamudio, S. Tibetan protection from intrauterine growth restriction (IUGR) and reproductive loss at high altitude. Am. J. Hum. Biol. 13, 635–644 (2001).
pubmed: 11505472
Beall, C. M. et al. Natural selection on EPAS1 (HIF2α) associated with low hemoglobin concentration in Tibetan highlanders. Proc. Natl Acad. Sci. USA 107, 11459–11464 (2010).
pubmed: 20534544 pmcid: 2895075
Lorenzo, F. R. et al. A genetic mechanism for Tibetan high-altitude adaptation. Nat. Genet. 46, 951–956 (2014).
pubmed: 25129147 pmcid: 4473257
Wiesener, M. S. et al. Widespread hypoxia-inducible expression of HIF-2alpha in distinct cell populations of different organs. FASEB J. 17, 271–273 (2003).
pubmed: 12490539
Imeri, F. et al. Generation of renal Epo-producing cell lines by conditional gene tagging reveals rapid HIF-2 driven Epo kinetics, cell autonomous feedback regulation, and a telocyte phenotype. Kidney Int. 95, 375–387 (2019).
pubmed: 30502050
Kobayashi, H. et al. Distinct subpopulations of FOXD1 stroma-derived cells regulate renal erythropoietin. J. Clin. Invest. 126, 1926–1938 (2016).
pubmed: 27088801 pmcid: 4855934
Obara, N. et al. Repression via the GATA box is essential for tissue-specific erythropoietin gene expression. Blood 111, 5223–5232 (2008).
pubmed: 18202227
Chang, Y.-T. et al. DNA methyltransferase inhibition restores erythropoietin production in fibrotic murine kidneys. J. Clin. Invest. 126, 721–731 (2016).
pubmed: 26731474 pmcid: 4731189
Loya, F., Yang, Y., Lin, H., Goldwasser, E. & Albitar, M. Transgenic mice carrying the erythropoietin gene promoter linked to lacZ express the reporter in proximal convoluted tubule cells after hypoxia. Blood 84, 1831–1836 (1994).
pubmed: 8080988
Bussolati, B. et al. Renal CD133(+)/CD73(+) progenitors produce erythropoietin under hypoxia and prolyl hydroxylase inhibition. J. Am. Soc. Nephrol. 24, 1234–1241 (2013).
pubmed: 23661806 pmcid: 3736703
Gerl, K. et al. Erythropoietin production by PDGFR-β(+) cells. Pflug. Arch. 468, 1479–1487 (2016).
Broeker, K. A. E. et al. Different subpopulations of kidney interstitial cells produce erythropoietin and factors supporting tissue oxygenation in response to hypoxia in vivo. Kidney Int. 98, 918–931 (2020).
pubmed: 32454122
Marchetti, P., Bugliani, M., De Tata, V., Suleiman, M. & Marselli, L. Pancreatic beta cell identity in humans and the role of type 2 diabetes. Front. Cell Dev. Biol. 5, 55 (2017).
pubmed: 28589121 pmcid: 5440564
Laha, D., Grant, R., Mishra, P. & Nilubol, N. The role of tumor necrosis factor in manipulating the immunological response of tumor microenvironment. Front. Immunol. 12, 656908 (2021).
pubmed: 33986746 pmcid: 8110933
Dahl, S.L. et al. Fate‐mapping of erythropoietin‐producing cells in mouse models of hypoxaemia and renal tissue remodelling reveals repeated recruitment and persistent functionality. Acta Physiol. (Oxf.) 234, e13768 (2022).
pubmed: 34982511
Dahl, S. L., Bapst, A. M., Khodo, S. N., Scholz, C. C. & Wenger, R. H. Fount, fate, features, and function of renal erythropoietin-producing cells. Pflug. Arch. 474, 783–797 (2022).
Shanks, J. H., Hill, C. M., Lappin, T. R. & Maxwell, A. P. Localization of erythropoietin gene expression in proximal renal tubular cells detected by digoxigenin-labelled oligonucleotide probes. J. Pathol. 179, 283–287 (1996).
pubmed: 8774484
Yamazaki, S. et al. A mouse model of adult-onset anaemia due to erythropoietin deficiency. Nat. Commun. 4, 1950 (2013).
pubmed: 23727690
Franke, K. et al. HIF-1α is a protective factor in conditional PHD2-deficient mice suffering from severe HIF-2α-induced excessive erythropoiesis. Blood 121, 1436–1445 (2013).
pubmed: 23264599 pmcid: 3628111
Kobayashi, H., Davidoff, O., Pujari-Palmer, S., Drevin, M. & Haase, V. H. EPO synthesis induced by HIF-PHD inhibition is dependent on myofibroblast transdifferentiation and colocalizes with non-injured nephron segments in murine kidney fibrosis. Acta Physiol. 235, e13826 (2022).
Bek-Pedersen, K. Norns in Old Norse Mythology (Dunedin Academic Press, 2013).
Suresh, S., Rajvanshi, P. K. & Noguchi, C. T. The many facets of erythropoietin physiologic and metabolic response. Front. Physiol. 10, 1534 (2019).
pubmed: 32038269
Young, M. D. et al. Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science 361, 594–599 (2018).
pubmed: 30093597 pmcid: 6104812
Park, J. et al. Single-cell transcriptomics of the mouse kidney reveals potential cellular targets of kidney disease. Science 360, 758–763 (2018).
pubmed: 29622724 pmcid: 6188645
Ransick, A. et al. Single-cell profiling reveals sex, lineage, and regional diversity in the mouse kidney. Dev. Cell 51, 399–413 (2019).
pubmed: 31689386 pmcid: 6948019
Combes, A. N. et al. Single cell analysis of the developing mouse kidney provides deeper insight into marker gene expression and ligand-receptor crosstalk. Development 146, dev178673 (2019).
pubmed: 31118232
England, A. R. et al. Identification and characterization of cellular heterogeneity within the developing renal interstitium. Development 147, dev190108 (2020).
pubmed: 32586976 pmcid: 7438011
Hochane, M. et al. Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development. PLoS Biol. 17, e3000152 (2019).
pubmed: 30789893 pmcid: 6400406
Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–779 (2014).
pubmed: 24531970 pmcid: 4412462
Keren-Shaul, H. et al. MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing. Nat. Protoc. 14, 1841–1862 (2019).
pubmed: 31101904
Baran, Y. et al. MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions. Genome Biol. 20, 206 (2019).
pubmed: 31604482 pmcid: 6790056
Nishiyama, A. & Kim-Mitsuyama, S. New approaches to blockade of the renin–angiotensin–aldosterone system: overview of regulation of the renin–angiotensin–aldosterone system. J. Pharmacol. Sci. 113, 289–291 (2010).
pubmed: 20675960
Pan, X. et al. Isolation and characterization of renal erythropoietin-producing cells from genetically produced anemia mice. PLoS ONE 6, e25839 (2011).
pubmed: 22022454 pmcid: 3191152
Gimm, T. et al. Hypoxia-inducible protein 2 is a novel lipid droplet protein and a specific target gene of hypoxia-inducible factor-1. FASEB J. 24, 4443–4458 (2010).
pubmed: 20624928
Mondéjar-Parreño, G. et al. Uncovered contribution of Kv7 channels to pulmonary vascular tone in pulmonary arterial hypertension. Hypertension 76, 1134–1146 (2020).
pubmed: 32829658
Schödel, J. et al. High-resolution genome-wide mapping of HIF-binding sites by ChIP-seq. Blood 117, e207–e217 (2011).
pubmed: 21447827 pmcid: 3374576
Orlando, I. M. C. et al. Distal and proximal hypoxia response elements cooperate to regulate organ-specific erythropoietin gene expression. Haematologica 105, 2774–2784 (2020).
pubmed: 33256376
Semenza, G. L., Koury, S. T., Nejfelt, M. K., Gearhart, J. D. & Antonarakis, S. E. Cell-type-specific and hypoxia-inducible expression of the human erythropoietin gene in transgenic mice. Proc. Natl Acad. Sci. USA 88, 8725–8729 (1991).
pubmed: 1924331 pmcid: 52582
Hirano, I. et al. Renal anemia model mouse established by transgenic rescue with an erythropoietin gene lacking kidney-specific regulatory elements. Mol. Cell. Biol. 37, e00451-16 (2017).
pubmed: 27920250 pmcid: 5288576
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432 pmcid: 2898526
Bruse, N. & van Heeringen, S. J. GimmeMotifs: an analysis framework for transcription factor motif analysis. Preprint at bioRxiv https://doi.org/10.1101/474403 (2018).
Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nat. Methods 14, 1083–1086 (2017).
pubmed: 28991892 pmcid: 5937676
Bornstein, C. et al. Single-cell mapping of the thymic stroma identifies IL-25-producing tuft epithelial cells. Nature 559, 622–626 (2018).
pubmed: 30022162
Plasschaert, L. W. et al. A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte. Nature 560, 377–381 (2018).
pubmed: 30069046 pmcid: 6108322
Quaggin, S. E. et al. The basic-helix-loop-helix protein pod1 is critically important for kidney and lung organogenesis. Development 126, 5771–5783 (1999).
pubmed: 10572052
Ide, S. et al. Transcription factor 21 is required for branching morphogenesis and regulates the Gdnf-axis in kidney development. J. Am. Soc. Nephrol. 29, 2795–2808 (2018).
pubmed: 30377232 pmcid: 6287866
Helman, A. & Melton, D. A. A stem cell approach to cure type 1 diabetes. Cold Spring Harb. Perspect. Biol. 13, a035741 (2021).
pubmed: 32122884 pmcid: 7778150
Bapst, A. M., Dahl, S. L., Knöpfel, T. & Wenger, R. H. Cre-mediated, loxP independent sequential recombination of a tripartite transcriptional stop cassette allows for partial read-through transcription. Biochim. Biophys. Acta Gene Regul. Mech. 1863, 194568 (2020).
pubmed: 32344203
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
pubmed: 25751142 pmcid: 4655817
Giladi, A. et al. Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis. Nat. Cell Biol. 20, 836–846 (2018).
pubmed: 29915358
Geirsdottir, L. et al. Cross-species single-cell analysis reveals divergence of the primate microglia program. Cell 179, 1609–1622 (2019).
pubmed: 31835035
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587 (2021).
pubmed: 34062119 pmcid: 8238499

Auteurs

Bjørt K Kragesteen (BK)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel. bjort.kragesteen@weizmann.ac.il.

Amir Giladi (A)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, Utrecht, the Netherlands.
Oncode Institute, Utrecht, the Netherlands.

Eyal David (E)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Shahar Halevi (S)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Laufey Geirsdóttir (L)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Olga M Lempke (OM)

Institute of Physiology, University of Zurich, Zurich, Switzerland.

Baoguo Li (B)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Andreas M Bapst (AM)

Institute of Physiology, University of Zurich, Zurich, Switzerland.

Ken Xie (K)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Yonatan Katzenelenbogen (Y)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Sophie L Dahl (SL)

Institute of Physiology, University of Zurich, Zurich, Switzerland.

Fadi Sheban (F)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Anna Gurevich-Shapiro (A)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
Division of Haematology, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.
Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.

Mor Zada (M)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.

Truong San Phan (TS)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Roberto Avellino (R)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Shuang-Yin Wang (SY)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Oren Barboy (O)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Shir Shlomi-Loubaton (S)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.

Sandra Winning (S)

Institute of Physiology, University of Duisburg-Essen, Essen, Germany.

Philipp P Markwerth (PP)

Institute for Forensic Medicine, University Hospital Essen, Essen, Germany.

Snir Dekalo (S)

Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Urology Department, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.

Hadas Keren-Shaul (H)

Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel.

Merav Kedmi (M)

Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel.

Martin Sikora (M)

GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

Joachim Fandrey (J)

Institute of Physiology, University of Duisburg-Essen, Essen, Germany.

Thorfinn S Korneliussen (TS)

GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

Josef T Prchal (JT)

Department of Medicine, University of Utah, Salt Lake City, UT, USA.

Barak Rosenzweig (B)

Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
Department of Urology, Sheba Medical Center, Ramat Gan, Israel.

Vladimir Yutkin (V)

Department of Urology, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.

Fernando Racimo (F)

GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

Eske Willerslev (E)

GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.

Chamutal Gur (C)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
Department of Medicine, Hadassah Medical Center, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.

Roland H Wenger (RH)

Institute of Physiology, University of Zurich, Zurich, Switzerland.
National Centre of Competence in Research 'Kidney.CH', University of Zurich, Zurich, Switzerland.

Ido Amit (I)

Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel. ido.amit@weizmann.ac.il.

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