Single-cell RNA sequencing and binary hierarchical clustering define lung interstitial macrophage heterogeneity in response to hypoxia.

التفاصيل البيبلوغرافية
العنوان:	Single-cell RNA sequencing and binary hierarchical clustering define lung interstitial macrophage heterogeneity in response to hypoxia.
المؤلفون:	Campbell NV; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Mickael C; Department of Medicine-Pulmonary Sciences & Critical Care, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Kumar S; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Zhang H; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Campbell IL; School of Humanities and Science, Stanford University, Stanford, California., Gillen AE; Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado., Trentin CO; Department of Medicine-Pulmonary Sciences & Critical Care, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Diener K; Department of Medicine-Pulmonary Sciences & Critical Care, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Gao B; Department of Medicine-Pulmonary Sciences & Critical Care, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Kheyfets VO; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Gu S; Department of Medicine-Pulmonary Sciences & Critical Care, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Kumar R; Division of Hematology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado., Phang T; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine-Bioinformatics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Brown RD; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado., Graham BB; Department of Medicine, University of California, San Francisco, California., Stenmark KR; Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.; Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado.
المصدر:	American journal of physiology. Lung cellular and molecular physiology [Am J Physiol Lung Cell Mol Physiol] 2022 Jul 01; Vol. 323 (1), pp. L58-L68. Date of Electronic Publication: 2022 May 24.
نوع المنشور:	Journal Article; Research Support, Non-U.S. Gov't; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.
اللغة:	English
بيانات الدورية:	Publisher: American Physiological Society Country of Publication: United States NLM ID: 100901229 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1522-1504 (Electronic) Linking ISSN: 10400605 NLM ISO Abbreviation: Am J Physiol Lung Cell Mol Physiol Subsets: MEDLINE
أسماء مطبوعة:	Original Publication: Bethesda, MD : American Physiological Society, c1989-
مواضيع طبية MeSH:	Hypertension, Pulmonary/metabolism , Hypoxia/metabolism, Animals ; Cluster Analysis ; Lung/pathology ; Macrophages/metabolism ; Mice ; Sequence Analysis, RNA
مستخلص:	Few studies have examined lung interstitial macrophage (IM) molecular phenotypes after being exposed to hypoxia in vivo at the single-cell level, even though macrophages contribute to hypoxic pulmonary hypertension (PH). We aimed to determine IM diversity and its association with hypoxia-induced PH. We hypothesized that integrating single-cell RNA sequencing (scRNAseq) and binary hierarchal clustering (BHC) could resolve IM heterogeneity under normal homeostatic conditions and changes induced by hypoxia exposure. Cx3cr1 ^GFP/+ reporter mice were exposed to normoxic conditions (∼21% [Formula: see text]) or exposed to 1 day ( D1 ) or 7 days ( D7 ) of hypoxia (∼10% [Formula: see text]). We used flow cytometry to isolate Cx3cr1 ⁺ IMs and the 10X Genomics platform for scRNAseq, Cell Ranger, Seurat, ClusterMap, monocle, ingenuity pathway analysis, and Fisher's exact test ( q value < 0.05) for functional investigations. n = 374 (normoxia), n = 2,526 ( D1 ), and n = 1,211 ( D7 ) IMs were included in the analyses. We identified three normoxia-related cell types, five hypoxia-associated cell types that emerged at D1 , and three that appeared at D7 . We describe the existence of a putative resident trained innate IM, which is present in normoxia, transiently depleted at D1 , and recovered after 7 days of sustained hypoxia. We also define a rare putative pathogenic population associated with transcripts implicated in PH development that emerges at D7 . In closing, we describe the successful integration of BHC with scRNAseq to determine IM heterogeneity and its association with PH. These results shed light on how resident-trained innate IMs become more heterogeneous but ultimately accustomed to hypoxia.
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معلومات مُعتمدة:	T32 HL007171 United States HL NHLBI NIH HHS; R56 HL152250 United States HL NHLBI NIH HHS; R01 HL152250 United States HL NHLBI NIH HHS; K25 HL133481 United States HL NHLBI NIH HHS; P01 HL152961 United States HL NHLBI NIH HHS; R01 HL135872 United States HL NHLBI NIH HHS
فهرسة مساهمة:	Keywords: PH; hypoxia; macrophages; single-cell RNAseq
تواريخ الأحداث:	Date Created: 20220524 Date Completed: 20220712 Latest Revision: 20230912
رمز التحديث:	20240628
مُعرف محوري في PubMed:	PMC9273277
DOI:	10.1152/ajplung.00104.2022
PMID:	35608266
قاعدة البيانات:	MEDLINE

الوصف
تدمد:	1522-1504
DOI:	10.1152/ajplung.00104.2022