Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye

Youkilis, J.C.; Bassnett, Steven

doi:10.1016/j.exer.2021.108811

Cited by 17 publications

(14 citation statements)

References 49 publications

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“…Table 5), indicating similar transcriptomic features of the ciliary epithelium bilayer. In agreement with a previous study [ 38 ] that compared the single-cell transcriptome between mouse PE and NPE, we also found that human NPE expressed higher levels of the ZIC family transcription factors ZIC1 and ZIC2 than PE (Fig. 2 E).…”

Section: Resultssupporting

confidence: 93%

A single-cell transcriptomic atlas of the human ciliary body

Lou

Zeng

Gao

et al. 2022

Cell. Mol. Life Sci.

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The ciliary body critically contributes to the ocular physiology with multiple responsibilities in the production of aqueous humor, vision accommodation and intraocular immunity. Comparatively little work, however, has revealed the single-cell molecular taxonomy of the human ciliary body required for studying these functionalities. In this study, we report a comprehensive atlas of the cellular and molecular components of human ciliary body as well as their interactions using single-cell RNA sequencing (scRNAseq). Cluster analysis of the transcriptome of 14,563 individual ciliary cells from the eyes of 3 human donors identified 14 distinct cell types, including the ciliary epithelium, smooth muscle, vascular endothelial cell, immune cell and other stromal cell populations. Cell-type discriminative gene markers were also revealed. Unique gene expression patterns essential for ciliary epithelium-mediated aqueous humor inflow and ciliary smooth muscle contractility were identified. Importantly, we discovered the transitional states that probably contribute to the transition of ciliary macrophage into retina microglia and verified no lymphatics in the ciliary body. Moreover, the utilization of CellPhoneDB allowed us to systemically infer cell–cell interactions among diverse ciliary cells including those that potentially participate in the pathogenesis of glaucoma and uveitis. Altogether, these new findings provide insights into the regulation of intraocular pressure, accommodation reflex and immune homeostasis under physiological and pathological conditions.

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Section: Resultssupporting

confidence: 93%

A single-cell transcriptomic atlas of the human ciliary body

Lou

Zeng

Gao

et al. 2022

Cell. Mol. Life Sci.

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“…Further subsetting and cluster analysis 30 was performed in the fibroblast group and 9 fibroblast subcluster (FBS) were identified based on the unique enriched markers (Figure 7E, Figures S10C, S10D, S11, Table S8). Specifically, FBS_1 and FBS_2 showed high expression of Pdgfa, a canonical fibroblast marker that was found in perivascular regions rarely overlapping with αSMA 34 ; FBS_3 and FBS_4 were enriched in lymphocyte markers; FBS_5 was an EC-like fibroblast cluster that highly expressed Cdh5 and Kdr , 35,36 suggesting potential endothelial-mesenchymal transition during fibrosis 37,38 ; FBS_6 highly expressed Col4a5 , a collagen marker that was found to be related to a matrix fibroblast signature with endoplasmic reticulum stress activation 39,40 ; FBS_7 highly expressed Mmps, also considered as matrix fibroblasts highly expressing Mmp3 40,41 ; FBS_8 highly expressed Col8a1, Col11a1, Angptl1, and Cthrc1 and was considered as a group of collagen-related pathological fibroblasts that are activated 42–45 ; and FBS_9 highly expressed Lyz2 and Ccl6 , considered as a group of inflammation-related activated fibroblasts 31 (Figure S11). A differential abundance analysis for the conditions in each fibroblast subcluster showed a decrease in FBS_2 (log2FC=−1.18, adj.…”

Section: Resultsmentioning

confidence: 99%

Perivascular Fibrosis Is Mediated by a KLF10-IL-9 Signaling Axis in CD4+ T Cells

Zhuang

Chen

Cheng

et al. 2022

Circulation Research

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BACKGROUND: Perivascular fibrosis, characterized by increased amount of connective tissue around vessels, is a hallmark for vascular disease. Ang II (angiotensin II) contributes to vascular disease and end-organ damage via promoting T-cell activation. Despite recent data suggesting the role of T cells in the progression of perivascular fibrosis, the underlying mechanisms are poorly understood. METHODS: TF (transcription factor) profiling was performed in peripheral blood mononuclear cells of hypertensive patients. CD4-targeted KLF10 (Kruppel like factor 10)-deficient ( Klf10 fl/fl CD4 Cre+ ; [TKO]) and CD4-Cre ( Klf10 +/+ CD4 Cre+ ; (Cre)) control mice were subjected to Ang II infusion. End point characterization included cardiac echocardiography, aortic imaging, multiorgan histology, flow cytometry, cytokine analysis, aorta and fibroblast transcriptomic analysis, and aortic single-cell RNA-sequencing. RESULTS: TF profiling identified increased KLF10 expression in hypertensive human subjects and in CD4+ T cells in Ang II-treated mice. TKO mice showed enhanced perivascular fibrosis, but not interstitial fibrosis, in aorta, heart, and kidney in response to Ang II, accompanied by alterations in global longitudinal strain, arterial stiffness, and kidney function compared with Cre control mice. However, blood pressure was unchanged between the 2 groups. Mechanistically, KLF10 bound to the IL (interleukin)-9 promoter and interacted with HDAC1 (histone deacetylase 1) inhibit IL-9 transcription. Increased IL-9 in TKO mice induced fibroblast intracellular calcium mobilization, fibroblast activation, and differentiation and increased production of collagen and extracellular matrix, thereby promoting the progression of perivascular fibrosis and impairing target organ function. Remarkably, injection of anti-IL9 antibodies reversed perivascular fibrosis in Ang II-infused TKO mice and C57BL/6 mice. Single-cell RNA-sequencing revealed fibroblast heterogeneity with activated signatures associated with robust ECM (extracellular matrix) and perivascular fibrosis in Ang II-treated TKO mice. CONCLUSIONS: CD4+ T cell deficiency of Klf10 exacerbated perivascular fibrosis and multi-organ dysfunction in response to Ang II via upregulation of IL-9. Klf10 or IL-9 in T cells might represent novel therapeutic targets for treatment of vascular or fibrotic diseases.

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“…Overall, tallying the existing data demonstrated that apart from the 2013 OTDB resource, until about 2021 it was mostly single GEO datasets that dominated the ocular transcriptomics landscape, and these data were rarely utilized. More recently, however, several comprehensive resources popped up, including eyeIntegration ( Swamy and McGaughey, 2019 ) and eye-transcriptome.com ( Wolf et al, 2022 ) along with more specialized single-cell datasets ( Patel et al, 2020 ; van Zyl et al, 2020 ; Thomson et al, 2021 ; Wieghofer et al, 2021 ; Youkilis and Bassnett, 2021 ). For the future, several groups are working on more comprehensive single-cell datasets of the eye, and on other omics modalities, so that a surge of future data generation and utilization can be expected, and as long as data are deposited under FAIR criteria whenever possible, a bright future is in sight.…”

Section: Discussionmentioning

confidence: 99%

“…Single-cell data may carry the most detailed information, and some newer GEO datasets and corresponding papers report single-cell data of interest. Three of these, that is, GSE168200 ( Thomson et al, 2021 ) for mouse, GSE146188 ( van Zyl et al, 2020 ) for human/monkey/mouse/pig, and PRJNA616025 (no GSE identifier) ( Patel et al, 2020 ) for human consider aqueous humor outflow pathways (focusing on the trabecular meshwork and Schlemm’s canal), while others consider ciliary epithelium including fibroblasts (GSE178667; Youkilis and Bassnett, 2021 , for mouse), and myeloid cells of, among other eye tissues, the conjunctiva (GSE160797; Wieghofer et al, 2021 , also for mouse). While single-cell data can give a much more detailed description of a tissue, their coverage of eye tissues is still limited, use of such data is still in its infancy, and their long-term translational value still needs to be demonstrated.…”

Section: Gene Expression Data Of the Eye With A Focus On The Anterior...mentioning

confidence: 99%

Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions

Fuellen

Jünemann

2022

Front. Neurosci.

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Glaucoma treatment options as well as its etiology are far from understood. Gene expression (transcriptomics) data of the anterior segment of the eye can help by elucidating the molecular-mechanistic underpinnings, and we present an up-to-date description and discussion of what gene expression data are publicly available, and for which purposes these can be used. We feature the few resources covering all segments of the eye, and we then specifically focus on the anterior segment, and provide an extensive list of the Gene Expression Omnibus data that may be useful. We also feature single-cell data of relevance, particularly three datasets from tissues of relevance to aqueous humor outflow. We describe how the data have been used by researchers, by following up resource citations and data re-analyses. We discuss datasets and analyses pertaining to fibrosis following glaucoma surgery, and to glaucoma resulting from the use of steroids. We conclude by pointing out the current lack and underutilization of ocular gene expression data, and how the state of the art is expected to improve in the future.

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Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye

Cited by 17 publications

References 49 publications

A single-cell transcriptomic atlas of the human ciliary body

A single-cell transcriptomic atlas of the human ciliary body

Perivascular Fibrosis Is Mediated by a KLF10-IL-9 Signaling Axis in CD4+ T Cells

Gene Expression Data for Investigating Glaucoma Treatment Options and Pharmacology in the Anterior Segment, State-of-the-Art and Future Directions

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