Integrated multi-omics single cell atlas of the human retina

Li, Jin; Wang, Jun; Ibarra, Ignacio L; Cheng, Xuesen; Luecken, Malte D; Lu, Jiaxiong; Monavarfeshani, Aboozar; Yan, Wenjun; Zheng, Yiqiao; Zuo, Zhen; Zayas Colborn, Samantha Lynn; Cortez, Berenice Sarahi; Owen, Leah A; Tran, Nicholas M; Shekhar, Karthik; Sanes, Joshua R; Stout, J Timothy; Chen, Shiming; Li, Yumei; DeAngelis, Margaret M; Theis, Fabian J; Chen, Rui

doi:10.1101/2023.11.07.566105

Cited by 3 publications

(1 citation statement)

References 120 publications

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“…Raw sequencing reads were processed using the CellRanger v6.1.2 (10X Genomics) pipeline, against the hg38 reference genome (https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz). Then, quality control was performed separately for each sample through a quality control pipeline (https://github.com/lijinbio/cellqc) 25,26 . Real cells were filtered by dropkick v1.2.8 27 and ambient RNA was removed using SoupX v1.6.2 28 .…”

Section: Methodsmentioning

confidence: 99%

To be or not to be - Decoding the Trabecular Meshwork Cell Identity

Tian,

Baidouri,

Kim

et al. 2024

Preprint

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The trabecular meshwork within the conventional outflow apparatus is critical in maintaining intraocular pressure homeostasis.In vitrostudies employing primary cell cultures of the human trabecular meshwork (hTM) have conventionally served as surrogates for investigating the pathobiology of TM dysfunction. Despite its abundant use, translation of outcomes fromin vitrostudies toex vivoand/orin vivostudies remains a challenge. Given the cell heterogeneity, performing single-cell RNA sequencing comparing primary hTM cell cultures to hTM tissue may provide important insights on cellular identity and translatability, as such an approach has not been reported before. In this study, we assembled a total of 14 primary hTMin vitrosamples across passages 1-4, including 4 samples from individuals diagnosed with glaucoma. This dataset offers a comprehensive transcriptomic resource of primary hTMin vitroscRNA-seq data to study global changes in gene expression in comparison to cells in tissuein situ. We have performed extensive preprocessing and quality control, allowing the research community to access and utilize this public resource.

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Section: Methodsmentioning

confidence: 99%

To be or not to be - Decoding the Trabecular Meshwork Cell Identity

Tian,

Baidouri,

Kim

et al. 2024

Preprint

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Sphingosine-1-phosphate signaling regulates the ability of Müller glia to become neurogenic, proliferating progenitor-like cells

Taylor,

DeGroff,

El-Hodiri

et al. 2024

Preprint

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The purpose of these studies is to investigate how Sphingosine-1-phosphate (S1P) signaling regulates glial phenotype, dedifferentiation of Müller glia (MG), reprogramming into proliferating MG-derived progenitor cells (MGPCs), and neuronal differentiation of the progeny of MGPCs. We found that S1P-related genes are highly expressed by retinal neurons and glia, and levels of expression were dynamically regulated following retinal damage.S1PR1is highly expressed by resting MG and is rapidly downregulated following acute retinal damage. Drug treatments that activate S1PR1 or increase levels of S1P suppressed the formation of MGPCs, whereas treatments that inhibit S1PR1 or decreased levels of S1P stimulated the formation of MGPCs. Inhibition of S1PR1 or SPHK1 significantly enhanced the neuronal differentiation of the progeny of MGPCs. Further, ablation of microglia from the retina, wherein the formation of MGPCs in damaged retinas is impaired, has a significant impact upon expression patterns of S1P-related genes in MG. Inhibition of S1PR1 and SPHK1 partially rescued the formation of MGPCs in damaged retinas missing microglia. Finally, we show that TGFβ/Smad3 signaling in the resting retina maintains S1PR1 expression in MG. We conclude that the S1P signaling is dynamically regulated in MG and MGPCs and activation of S1P signaling depends, in part, on signals produced by reactive microglia.

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Iso-Seq enables discovery of novel isoform variants in human retina at single cell resolution

Wang,

Urrutia-Cabrera,

Hung

et al. 2024

Preprint

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Recent single cell transcriptomic profiling of the human retina provided important insights into the genetic signals in heterogeneous retinal cell populations that enable vision. However, conventional single cell RNAseq with 3’ short-read sequencing is not suitable to identify isoform variants. Here we utilized Iso-Seq with full-length sequencing to profile the human retina at single cell resolution for isoform discovery. We generated a retina transcriptome dataset consisting of 25,302 nuclei from three donor retina, and detected 49,710 known transcripts and 241,949 novel transcripts across major retinal cell types. We surveyed the use of alternative promoters to drive transcript variant expression, and showed that 1-8% of genes utilized multiple promoters across major retinal cell types. Also, our results enabled gene expression profiling of novel transcript variants for inherited retinal disease (IRD) genes, and identified differential usage of exon splicing in major retinal cell types. Altogether, we generated a human retina transcriptome dataset at single cell resolution with full-length sequencing. Our study highlighted the potential of Iso-Seq to map the isoform diversity in the human retina, providing an expanded view of the complex transcriptomic landscape in the retina.

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Integrated multi-omics single cell atlas of the human retina

Cited by 3 publications

References 120 publications

To be or not to be - Decoding the Trabecular Meshwork Cell Identity

To be or not to be - Decoding the Trabecular Meshwork Cell Identity

Sphingosine-1-phosphate signaling regulates the ability of Müller glia to become neurogenic, proliferating progenitor-like cells

Iso-Seq enables discovery of novel isoform variants in human retina at single cell resolution

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