Single-cell RNA sequencing identifies TGF-β as a key regenerative cue following LPS-induced lung injury

Riemondy, Kent; Jansing, Nicole L.; Jiang, Peng; Redente, Elizabeth F.; Gillen, Austin E.; Fu, Rui; Miller, Alyssa J.; Spence, Jason R.; Gerber, Anthony N.; Hesselberth, Jay R.; Zemans, Rachel L.

doi:10.1172/jci.insight.123637

Cited by 130 publications

(230 citation statements)

References 75 publications

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“…4a-c and Extended Data Fig. 5), similar to a previously reported population of transdifferentiating AT2 cells observed after lipopolysaccharide-induced lung injury 51 . These data effectively identified a subpopulation of AT2 cells whose transcriptomic profile is most consistent with transdifferentiating alveolar epithelium.…”

Section: Atac-seqsupporting

confidence: 89%

STAT3–BDNF–TrkB signalling promotes alveolar epithelial regeneration after lung injury

et al. 2020

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Alveolar epithelial regeneration is essential for recovery from devastating lung diseases. This process occurs when type II alveolar pneumocytes (AT2 cells) proliferate and transdifferentiate into type I alveolar pneumocytes (AT1 cells). We used genome-wide analysis of chromatin accessibility and gene expression following acute lung injury to elucidate repair mechanisms. AT2 chromatin accessibility changed substantially following injury to reveal STAT3 binding motifs adjacent to genes that regulate essential regenerative pathways. Single-cell transcriptome analysis identified brain-derived neurotrophic factor (Bdnf) as a STAT3 target gene with newly accessible chromatin in a unique population of regenerating AT2 cells. Furthermore, the BDNF receptor tropomyosin receptor kinase B (TrkB) was enriched on mesenchymal alveolar niche cells (MANCs). Loss or blockade of AT2-specific Stat3, Bdnf or mesenchyme-specific TrkB compromised repair and reduced Fgf7 expression by niche cells. A TrkB agonist improved outcomes in vivo following lung injury. These data highlight the biological and therapeutic importance of the STAT3-BDNF-TrkB axis in orchestrating alveolar epithelial regeneration.

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Section: Atac-seqsupporting

confidence: 89%

STAT3–BDNF–TrkB signalling promotes alveolar epithelial regeneration after lung injury

et al. 2020

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“…1D). Our finding that among lung cells, basal expression of Rα2 is restricted to Fibs is consistent with single-cell transcriptomic studies reported in human 44 and mouse 45 lung tissues. Delta Ct values for human Rα1 and Rα2 (normalized to GAPDH) are provided in Supplementary Table 1.…”

supporting

confidence: 92%

Transcriptional regulation of the IL-13Rα2 gene in human lung fibroblasts

Penke

Ouchi

Speth

et al. 2020

Sci Rep

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peters-Golden 1,2* interleukin (iL)−13 is a type 2 cytokine with important roles in allergic diseases, asthma, and tissue fibrosis. Its receptor (R) α1 is primarily responsible for the biological actions of this cytokine, while Rα2 possesses a decoy function which can block IL-13 signaling. Although the expression of Rα2 is known to be subject to modulation, information about its transcriptional regulation is limited. In this study, we sought to expand the understanding of transcriptional control of Rα2 in lung fibroblasts. We confirmed previous reports that IL-13 elicited modest induction of Rα2 in normal adult human lung fibroblasts, but found that prostaglandin E 2 (pGe 2) and fibroblast growth factor 2 (FGF-2)-mediators known to influence fibroblast activation in tissue fibrosis but not previously investigated in this regard-led to a much greater magnitude of Rα2 induction. Although both PGE 2 (via protein kinase A) and FGF-2 (via protein kinase B, also known as AKT) depended on activation of cAMP-responsive element-binding protein (cReB) for induction of Rα2 expression, they nevertheless demonstrated synergy in doing so, likely attributable to their differential utilization of distinct transcriptional start sites on the Rα2 promoter. Our data identify CREB activation via PGE 2 and FGF-2 as a previously unrecognized molecular controller of Rα2 gene induction and provide potential new insights into strategies for therapeutic manipulation of this endogenous brake on IL-13 signaling. Interleukin (IL)−13 is an important type 2 cytokine best known for its roles in allergic diseases and asthma 1 , but which also contributes to other inflammatory diseases such as Crohn's disease and ulcerative colitis 2 , tissue fibrosis 3,4 , and various forms of cancer 5-7. IL-13 recognition is complex, involving heterodimers comprised of three distinct receptor subunits. IL-13 receptor α1 (IL-13Rα1 or Rα1) has low affinity for IL-13, but when associated with the IL-4 receptor (IL-4Rα) subunit, ligand binding results in productive signaling via JAK/STAT6 8,9. IL-13 receptor α2 (IL-13Rα2 or Rα2) has greater affinity for IL-13, but its impact on signaling upon ligand binding depends on cell type and context 10,11. Rα2 lacks a cytoplasmic domain, and accordingly, many studies have reported that Rα2 fails to initiate signal transduction 10 and in fact, can act as a decoy receptor capable of binding ligand and thus preventing productive signaling through Rα1 12-15. On the other hand, more recent reports have identified cytoplasmic interactors for Rα2 16 and described Rα2-mediated activation of various intracellular signaling pathways 17-19. In keeping with such divergent signaling responses, Rα2 has been reported to both mediate and attenuate mouse models of allergic asthma 20-22 as well as pulmonary fibrosis 18,23,24. Although Rα1 is exclusively a membrane-bound receptor, mouse Rα2 has been shown to exist in membrane-bound as well as soluble forms, which reflect distinct splice variants 25,26. Although the soluble form does not exist ...

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“…Interestingly, we found many TGF-beta target genes, including Sox4, integrin beta-6 (Itgb6), and connective tissue growth factor (Ctgf) peaking in the pre-AT1 phase ( Fig. 6g), suggesting that availability of TGF-beta is important for alveolar regeneration 18 . The non-muscle myosin heavy chain IIa (Myh9) also peaked in pre-AT1 cells, suggesting important additional cytoskeletal rearrangements and increased cell contractility in the already squamous Krt8+ alveolar progenitor cells in the final steps of maturation towards AT1 cells (Fig.…”

Section: Krt8+ Cells Are Alveolar Progenitors That Reconstitute the Amentioning

confidence: 97%

“…However, the negative regulation of the NFkappaB pathway mediated by Yap/Taz in AT2 cells was also shown to be key for successful alveolar regeneration 17 . Moreover, the TGF-beta pathway has been proposed to mediate cell cycle arrest in AT2 cells followed by transdifferentiation into AT1 cells 18 . The molecular details and spatiotemporal organization of such decisive signals and pathways during recovery of the AT1 cell layer have not been resolved.…”

mentioning

confidence: 99%

Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

Strunz

Ansari

et al. 2019

Preprint

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Lung disease is a major health burden accounting for one in six deaths globally 1 . The lung's large surface area is exposed to a great variety of environmental and microbial insults causing injuries to its epithelium that require a regenerative response mediated by tissue-resident stem and progenitor Lung injury activates quiescent stem and progenitor cells to regenerate alveolar structures. The sequence and coordination of transcriptional programs during this process has largely remained elusive. Using single cell RNA-seq, we first generated a whole-organ bird's-eye view on cellular dynamics and cell-cell communication networks during mouse lung regeneration from ~30,000 cells at six timepoints. We discovered an injury-specific progenitor cell state characterized by Krt8 in flat epithelial cells covering alveolar surfaces. The number of these cells peaked during fibrogenesis in independent mouse models, as well as in human acute lung injury and fibrosis. Krt8+ progenitors featured a highly distinct connectome of receptor-ligand pairs with endothelial cells, fibroblasts, and macrophages. To 'sky dive' into epithelial differentiation dynamics, we sequenced >30,000 sorted epithelial cells at 18 timepoints and computationally derived cell state trajectories that were validated by lineage tracing genetic reporter mice. Airway stem cells within the club cell lineage and alveolar type-2 cells underwent transcriptional convergence onto the same Krt8+ progenitor cell state, which later resolved by terminal differentiation into alveolar type-1 cells. We derived distinct transcriptional regulators as key switch points in this process and show that induction of TNF-alpha/NFkappaB, p53, and hypoxia driven gene expression programs precede a Sox4, Ctnnb1, and Wwtr1 driven switch towards alveolar type-1 cell fate. We show that epithelial cell plasticity can induce non-gradual transdifferentiation, involving intermediate progenitor cell states that may persist and promote disease if checkpoint signals for terminal differentiation are perturbed.

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Single-cell RNA sequencing identifies TGF-β as a key regenerative cue following LPS-induced lung injury

Cited by 130 publications

References 75 publications

STAT3–BDNF–TrkB signalling promotes alveolar epithelial regeneration after lung injury

STAT3–BDNF–TrkB signalling promotes alveolar epithelial regeneration after lung injury

Transcriptional regulation of the IL-13Rα2 gene in human lung fibroblasts

Longitudinal single cell transcriptomics reveals Krt8+ alveolar epithelial progenitors in lung regeneration

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