Integrated Transcriptome Analysis of Long Noncoding RNA and mRNA in Developing and Aging Mouse Retina.

Mice have emerged as a widely employed model for investigating various retinal diseases. However, the availability of comprehensive datasets capturing the entire developmental and aging stages of the mouse retina, particularly during the elderly period, encompassing integrated lncRNA and mRNA expression profiles, is limited. In this study, we assembled a total of 18 retina samples from mice across 6 distinct stages of development and aging (5 days, 3 weeks, 6 weeks, 10 weeks, 6 months, and 15 months) to conduct integrated lncRNA and mRNA sequencing analysis. This invaluable dataset offers a comprehensive transcriptomic resource of mRNA and lncRNA expression profiles during the natural progression of retinal development and aging. The discoveries stemming from this investigation will significantly contribute to the elucidation of the underlying molecular mechanisms associated with various retinal diseases, such as congenital retinal dysplasia and retinal degenerative diseases.

Integrative Single-Cell RNA-Seq and ATAC-Seq Analysis of Mouse Corneal Epithelial Cells.

Purpose: Corneal epithelial homeostasis is maintained by coordinated gene expression across distinct cell populations, but the gene regulatory programs underlying this cellular diversity remain to be characterized. Here we applied single-cell multi-omics analysis to delineate the gene regulatory profile of mouse corneal epithelial cells under normal homeostasis. Methods: Single cells isolated from the cornea epithelium (with marginal conjunctiva) of adult mice were subjected to scRNA-seq and scATAC-seq using the 10×Genomics platform. Cell types were clustered by the graph-based visualization method uniform manifold approximation and projection and unbiased computational informatics analysis. The scRNA-seq and scATAC-seq datasets were integrated following the integration pipeline described in ArchR and Seurat. Results: We characterized diverse corneal epithelial cell types based on gene expression signatures and chromatin accessibility. We found that cell type-specific accessibility regions were mainly located at distal regions, suggesting essential roles of distal regulatory elements in determining corneal epithelial cell diversity. Trajectory analyses revealed a continuum of cell state transition and higher coordination between transcription factor (TF) motif accessibility and gene expression during corneal epithelial cell differentiation. By integrating transcriptomic and chromatin accessibility analysis, we identified cell type-specific and shared gene regulation programs. We also uncovered critical TFs driving corneal epithelial cell differentiation, such as nuclear factor I (NFI) family members, Rarg, Elf3. We found that nuclear factor-κB (NF-κB) family members were positive TFs in limbal cells and some superficial cells, but they were involved in regulating distinct biological processes. Conclusions: Our study presents a comprehensive gene regulatory landscape of mouse cornea epithelial cells, and provides valuable foundations for future investigation of corneal epithelial homeostasis in the context of cornea pathologies and regenerative medicine.

Assessing the effects of aging on the liver endothelial cell landscape using single-cell RNA sequencing.

Endothelial cell (EC) function declines with age and contributes to the development of many vascular-related disease processes. Currently, the effects of aging on the molecular regulatory mechanisms of liver ECs have not been fully elucidated. Here, we employed single-cell RNA sequencing to map the transcriptome of ECs and analyzed their relationship with aging. We identified 8 different EC subtypes, interestingly, 2 of which were specially expressed in aged mice ECs namely aged capillary ECs (Aged ECs) and pro-inflammation capillary ECs (Proinfla.ECs). Double immunostaining for an EC marker (Cd31) and a marker of these specialized EC phenotypes confirmed the single-cell RNA sequencing data. Gene ontology analysis revealed that Aged ECs and Proinfla.ECs were associated with inflammatory response. Then we found that liver proliferating capillary ECs (Prolife.ECs) were most affected by senescence. Single-cell transcript analysis suggests that Prolife.ECs and angiogenic capillary ECs may form a poor microenvironment that promotes angiogenesis and tumorigenesis. Pseudo-temporal trajectories revealed that Prolife.ECs have different differentiation pathways in young and aged mice. In aged mice, Prolife.ECs could specifically differentiate into an unstable state, which was mainly composed of angiogenic capillary ECs. Intercellular communication revealed inflammatory activation in old group. Overall, this work compared the single-cell RNA profiles of liver ECs in young and aged mice. These findings provide a new insight into liver aging and its molecular mechanisms, and further exploration of Aged ECs and Proinfla.ECs may help to elucidate the molecular mechanisms associated with senescence.