Single-Cell RNA Sequencing: Opportunities and Challenges for Studies on Corneal Biology in Health and Disease

Dry eye disease in mice activates adaptive corneal epithelial regeneration distinct from constitutive renewal in homeostasis

(2023) Joseph B. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PAX6 Expression Patterns in the Adult Human Limbal Stem Cell Niche

(2023) Naresh Polisetti et al.   Cells

Applications of single-cell RNA sequencing in drug discovery and development

(2023) Bram Van de Sande et al.   NATURE REVIEWS DRUG DISCOVERY

Restoration of functional PAX6 in aniridia patient iPSC-derived ocular tissue models using repurposed nonsense suppression drugs

(2023) Dulce Lima Cunha et al.   Molecular Therapy-Nucleic Acids

Time-resolved single-cell sequencing identifies multiple waves of mRNA decay during the mitosis-to-G1 phase transition

(2022) Lenno Krenning et al.   eLife

Heterogeneity of human corneal endothelium implicates lncRNA NEAT1 in Fuchs endothelial corneal dystrophy

(2022) Qun Wang et al.   Molecular Therapy-Nucleic Acids

Spatial multi-omic map of human myocardial infarction

(2022) Christoph Kuppe et al.   NATURE

Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types

(2022) Tavé van Zyl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hyaluronan supports the limbal stem cell phenotype during ex vivo culture

(2022) Sudan Puri et al.   Stem Cell Research & Therapy

Cellular and molecular profiles of larval and adult Xenopus corneal epithelia resolved at the single-cell level

(2022) Surabhi Sonam et al.   DEVELOPMENTAL BIOLOGY

Corneal Epithelial Regeneration: Old and New Perspectives

(2022) Alessia Nuzzi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Cyclin‐dependent kinase subunit2 (CKS2) promotes malignant phenotypes and epithelial‐mesenchymal transition‐like process in glioma by activating TGFβ/SMAD signaling

(2022) Fan Feng et al.   Cancer Medicine

Tissue dissociation for single-cell and single-nuclei RNA sequencing for low amounts of input material

(2022) Gordon Wiegleb et al.   Frontiers in Zoology

Core transcription regulatory circuitry orchestrates corneal epithelial homeostasis

(2021) Mingsen Li et al.   Nature Communications

Selecting single cell clustering parameter values using subsampling-based robustness metrics

(2021) Ryan B. Patterson-Cross et al.   BMC BIOINFORMATICS

Two-photon live imaging of single corneal stem cells reveals compartmentalized organization of the limbal niche

(2021) Olivia Farrelly et al.   Cell Stem Cell

Employing core regulatory circuits to define cell identity

(2021) Nathalia Almeida et al.   EMBO JOURNAL

A single cell atlas of human cornea that defines its development, limbal progenitor cells and their interactions with the immune cells

(2021) Joseph Collin et al.   Ocular Surface

Single-cell transcriptomics identifies limbal stem cell population and cell types mapping its differentiation trajectory in limbal basal epithelium of human cornea

(2021) De-Quan Li et al.   Ocular Surface

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

(2021) Madhav Mantri et al.   Nature Communications

Comparative Transcriptomic Analysis of the Hematopoietic System between Human and Mouse by Single Cell RNA Sequencing

(2021) Shouguo Gao et al.   Cells

A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre

(2021) Matteo A. Molè et al.   Nature Communications

Molecular characteristics and spatial distribution of adult human corneal cell subtypes

(2021) Ann J. Ligocki et al.   Scientific Reports

Canonical NF-κB signaling maintains corneal epithelial integrity and prevents corneal aging via retinoic acid

(2021) Qian Yu et al.   eLife

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

(2021) Trygve E Bakken et al.   eLife

A single-cell guide to retinal development: Cell fate decisions of multipotent retinal progenitors in scRNA-seq

(2021) Fion Shiau et al.   DEVELOPMENTAL BIOLOGY

Multi-species single-cell transcriptomic analysis of ocular compartment regulons

(2021) Pradeep Gautam et al.   Nature Communications

Confronting false discoveries in single-cell differential expression

(2021) Jordan W. Squair et al.   Nature Communications

Single cell transcriptomics reveals the heterogeneity of the human cornea to identify novel markers of the limbus and stroma

(2021) Pere Català et al.   Scientific Reports

Multiocular organoids from human induced pluripotent stem cells displayed retinal, corneal, and retinal pigment epithelium lineages

(2021) Helena Isla-Magrané et al.   Stem Cell Research & Therapy

Corneal epithelial differentiation of human pluripotent stem cells generates ABCB5+ and ∆Np63α+ cells with limbal cell characteristics and high wound healing capacity

(2021) Meri Vattulainen et al.   Stem Cell Research & Therapy

The protective and pathogenic roles of CXCL17 in human health and disease: Potential in respiratory medicine

(2020) José Alberto Choreño-Parra et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Fuchs endothelial corneal dystrophy: The vicious cycle of Fuchs pathogenesis

(2020) Stephan Ong Tone et al.   PROGRESS IN RETINAL AND EYE RESEARCH

Bowman's layer in the cornea– structure and function and regeneration

(2020) Steven E. Wilson   EXPERIMENTAL EYE RESEARCH

Ocular surface ectoderm instigated by WNT inhibition and BMP4

(2020) Yuki Kobayashi et al.   Stem Cell Research

CXCL14 Maintains hESC Self-Renewal through Binding to IGF-1R and Activation of the IGF-1R Pathway

(2020) Chih-Lun Cheng et al.   Cells

A Quantitative Proteome Map of the Human Body

(2020) Lihua Jiang et al.   CELL

Update on the genetics of keratoconus

(2020) Yelena Bykhovskaya et al.   EXPERIMENTAL EYE RESEARCH

Corneal development: Role of the periocular mesenchyme and bi-directional signaling

(2020) Haydn Walker et al.   EXPERIMENTAL EYE RESEARCH

Transfer learning efficiently maps bone marrow cell types from mouse to human using single-cell RNA sequencing

(2020) Patrick S. Stumpf et al.   Communications Biology

UBE2C Functions as a Potential Oncogene by Enhancing Cell Proliferation, Migration, Invasion and Drug Resistance in Hepatocellular Carcinoma Cells

(2019) Yu Xiong et al.   BIOSCIENCE REPORTS

Single-Cell Profiles of Retinal Ganglion Cells Differing in Resilience to Injury Reveal Neuroprotective Genes

(2019) Nicholas M. Tran et al.   NEURON

The Spectrum of PAX6 Mutations and Genotype-Phenotype Correlations in the Eye

(2019) Dulce Lima Cunha et al.   Genes

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

(2018) Bruce A. Rheaume et al.   Nature Communications

Corneal-Committed Cells Restore the Stem Cell Pool and Tissue Boundary following Injury

(2018) Waseem Nasser et al.   Cell Reports

Tumor suppressor RARRES1- A novel regulator of fatty acid metabolism in epithelial cells

(2018) Sara Maimouni et al.   PLoS One

SOX2 regulates P63 and stem/progenitor cell state in the corneal epithelium

(2018) Swarnabh Bhattacharya et al.   STEM CELLS

Visualizing the Contribution of Keratin-14+ Limbal Epithelial Precursors in Corneal Wound Healing

(2018) Mijeong Park et al.   Stem Cell Reports

Differences in the Activity of Endogenous Bone Morphogenetic Protein Signaling Impact on the Ability of Induced Pluripotent Stem Cells to Differentiate to Corneal Epithelial-Like Cells

(2017) Taty Anna Kamarudin et al.   STEM CELLS

Establishment of Novel Limbus-Derived, Highly Proliferative ABCG2+/ABCB5+ Limbal Epithelial Stem Cell Cultures

(2017) Eung Kweon Kim et al.   Stem Cells International

Induced pluripotent stem cell-derived limbal epithelial cells (LiPSC) as a cellular alternative for in vitro ocular toxicity testing

(2017) Edith Aberdam et al.   PLoS One

Cornea organoids from human induced pluripotent stem cells

(2017) James W. Foster et al.   Scientific Reports

Characterization of slow cycling corneal limbal epithelial cells identifies putative stem cell markers

(2017) R. Sartaj et al.   Scientific Reports

Insulin-like growth factor-1 signaling in renal cell carcinoma

(2016) Adam F. Tracz et al.   BMC CANCER

Stathmin-dependent molecular targeting therapy for malignant tumor: the latest 5 years’ discoveries and developments

(2016) Rong Biaoxue et al.   Journal of Translational Medicine

Co-ordinated ocular development from human iPS cells and recovery of corneal function

(2016) Ryuhei Hayashi et al.   NATURE

Human limbal mesenchymal stem cells express ABCB5 and can grow on amniotic membrane

(2016) Bakiah Shaharuddin et al.   Regenerative Medicine

Upregulation of E2F8 promotes cell proliferation and tumorigenicity in breast cancer by modulating G1/S phase transition

(2016) Liping Ye et al.   Oncotarget

Sphere-forming cells from peripheral cornea demonstrate the ability to repopulate the ocular surface

(2016) Jeremy John Mathan et al.   Stem Cell Research & Therapy

Neural crest derivatives in ocular development: Discerning the eye of the storm

(2015) Antionette L. Williams et al.   BIRTH DEFECTS RESEARCH PART C-EMBRYO TODAY-REVIEWS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Lineage tracing in the adult mouse corneal epithelium supports the limbal epithelial stem cell hypothesis with intermittent periods of stem cell quiescence

(2015) Natalie J. Dorà et al.   Stem Cell Research

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

Vesicular Location and Transport of S100A8 and S100A9 Proteins in Monocytoid Cells

(2015) Paramita Chakraborty et al.   PLoS One

Stabilization of collagen nanofibers with l-lysine improves the ability of carbodiimide cross-linked amniotic membranes to preserve limbal epithelial progenitor cells

(2014) Jui-Yang Lai et al.   International Journal of Nanomedicine

Evaluation of corneal epithelial and stromal thickness in keratoconus using spectral-domain optical coherence tomography

(2014) Naoyuki Maeda et al.   JAPANESE JOURNAL OF OPHTHALMOLOGY

ABCB5 is a limbal stem cell gene required for corneal development and repair

(2014) Bruce R. Ksander et al.   NATURE

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

Differentiation of Human Limbal-Derived Induced Pluripotent Stem Cells Into Limbal-Like Epithelium

(2014) Dhruv Sareen et al.   Stem Cells Translational Medicine

Small-Molecule Induction Promotes Corneal Epithelial Cell Differentiation from Human Induced Pluripotent Stem Cells

(2014) Alexandra Mikhailova et al.   Stem Cell Reports

High Throughput Gene Expression Analysis Identifies Reliable Expression Markers of Human Corneal Endothelial Cells

(2013) Zhenzhi Chng et al.   PLoS One

Smooth Muscle α Actin (Acta2) and Myofibroblast Function during Hepatic Wound Healing

(2013) Don C. Rockey et al.   PLoS One

Correction: Transcriptional Dissection of Human Limbal Niche Compartments by Massive Parallel Sequencing

(2013) Chris Bath et al.   PLoS One

PI3-K/Akt/JNK/NF-κB is essential for MMP-9 expression and outgrowth in human limbal epithelial cells on intact amniotic membrane

(2012) Ching-Yi Cheng et al.   Stem Cell Research

Ex vivo expansion of limbal stem cells is affected by substrate properties

(2012) Roanne R. Jones et al.   Stem Cell Research

Neural crest cells organize the eye via TGF-β and canonical Wnt signalling

(2011) Timothy Grocott et al.   Nature Communications

Membrane-tethered mucins have multiple functions on the ocular surface

(2010) Bharathi Govindarajan et al.   EXPERIMENTAL EYE RESEARCH

In vitro culture and expansion of human limbal epithelial cells

(2010) Indumathi Mariappan et al.   Nature Protocols

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Lrig1 Expression Defines a Distinct Multipotent Stem Cell Population in Mammalian Epidermis

(2009) Kim B. Jensen et al.   Cell Stem Cell

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Oligopotent stem cells are distributed throughout the mammalian ocular surface

(2008) François Majo et al.   NATURE

Direct epithelial–stromal interaction in corneal wound healing: Role of EMMPRIN/CD147 in MMPs induction and beyond

(2008) Eric E. Gabison et al.   PROGRESS IN RETINAL AND EYE RESEARCH

Hes1 Regulates Corneal Development and the Function of Corneal Epithelial Stem/Progenitor Cells

(2008) Takahiro Nakamura et al.   STEM CELLS