Masahito Yoshihara

Proliferative vitreoretinopathy (PVR) remains associated with a poor prognosis despite advances in vitreoretinal surgery. In the absence of effective adjunctive therapies, this study aimed to characterize vitreous metabolic alterations in PVR to better understand its pathophysiology. Untargeted metabolomic profiling was conducted on vitreous humor samples from 38 eyes that underwent surgery: PVR (grade C, n = 10), rhegmatogenous retinal detachment (RRD; grades A and B, n = 18), and controls undergoing intraocular lens (IOL) scleral fixation (n = 10). Metabolites were analyzed using capillary electrophoresis-mass spectrometry. Metabolic profiles were compared pairwise among the three groups with multiple testing correction, and pathway enrichment analysis was performed. RRD demonstrated no disease-specific metabolic signature relative to controls after multiple testing correction. In contrast, PVR exhibited a distinct metabolic profile compared with both RRD and controls. Pathway enrichment analysis revealed upregulation of amino acid and nitrogen metabolism-including arginine and proline metabolism, glycine and serine metabolism, the urea cycle, ammonia recycling, alanine metabolism, and the malate-aspartate shuttle-consistent with increased biosynthetic demand. Pathways related to fibrosis and stress responses were also enriched. This study shows that PVR exhibits a unique metabolic signature distinct from RRD, characterized by the activation of metabolic pathways that support increased energy demand, cellular proliferation, stress responses, and fibrotic remodeling. These findings provide insights into the metabolic mechanisms associated with the progression from RRD to PVR, suggesting potential therapeutic targets to prevent fibrosis and aberrant cell proliferation.

Cells of the retina, photoreceptors especially, are highly metabolically active with substantial energy requirements. Accordingly, the effective delivery of oxygen and nutrients to the retina via the retinal vasculature is key to tissue function. Indeed, a disturbed retinal blood supply, especially if prolonged, can result in a loss of vision. Vascular endothelial cells, which form the inner lining of blood vessels, are pivotal in ensuring a healthy blood circulation in many tissues, including the light-sensitive retina at the back of the eye. However, the mechanism by which vascular endothelial cells maintain a functional retina (and aid the healing of a damaged one) is not understood. Here, through single-cell RNA sequencing, colony-forming assays and lineage tracing analysis, we provide data that point to a new regulatory system by which vascular endothelial cells are supplied to the retina by a reservoir of stem/progenitor cells in the optic nerve.

During eye development, surface ectoderm cells that express PAX6 differentiate into corneal, limbal and conjunctival epithelia. However, several aspects of this differentiation process -- such as the developmental origin of the limbal epithelium and the mechanisms that underlie PAX6-mediated lineage specification -- are not properly understood. To explore these issues, we used single-cell RNA sequencing to study ocular surface epithelial cells derived from human induced pluripotent stem cells. Our analysis reveals that the corneal and conjunctival epithelial cell lineages originate from the surface ectoderm, and that the conjunctival lineage contributes to limbal epithelial cell populations. We also show that primordial conjunctival epithelial cells express limbal epithelial markers before lineage bifurcation. Finally, the activity and expression of PAX6 are highest in corneal epithelial cells, followed by those of the limbal epithelium and conjunctival epithelium, suggesting that lineage-specific differentiation is regulated by levels of PAX6 activity. These findings provide deeper understanding of the early-stage human ocular surface development.

Genome-wide association studies (GWASs) have identified thousands of variants associated with complex phenotypes, including neuropsychiatric disorders. To better understand their pathogenesis, it is necessary to identify the functional roles of these variants, which are largely located in non-coding DNA regions. Here, we employ a human mesencephalic neuronal cell differentiation model, LUHMES, with sensitive and high-resolution methods to discover enhancers (NET-CAGE), perform DNA conformation analysis (Capture Hi-C) to link enhancers to their target genes, and finally validate selected interactions. We expand the number of known enhancers active in differentiating human LUHMES neurons to 47,350, and find overlap with GWAS variants for Parkinson’s disease and schizophrenia. Our findings reveal a fine-tuned regulation of human neuronal differentiation, even between adjacent developmental stages; provide a valuable resource for further studies on neuronal development, regulation, and disorders; and emphasize the importance of exploring the vast regulatory potential of non-coding DNA and enhancers.

The dog, Canis lupus familiaris, is an important model for studying human diseases. Unlike many model organisms, the dog genome has a comparatively poor functional annotation, which hampers gene discovery for development, morphology, disease, and behavior. To fill this gap, we established a comprehensive tissue biobank for both the dog and wolf samples. The biobank consists of 5485 samples representing 132 tissues from 13 dogs, 12 dog embryos, and 24 wolves. In a subset of 100 tissues from nine dogs and 12 embryos, we characterized gene expression activity for each promoter, including alternative and novel, i.e., previously not annotated, promoter regions, using the 5’ targeting RNA sequencing technology STRT2-seq. We identified over 100,000 promoter region candidates in the recent canine genome assembly, CanFam4, including over 45,000 highly reproducible sites with gene expression and respective tissue enrichment levels. We provide a promoter and gene expression atlas with interactive, open data resources, including a data coordination center and genome browser track hubs. We demonstrated the applicability of Dog Genome Annotation (DoGA) data and resources using multiple examples spanning canine embryonic development, morphology and behavior, and diseases across species.

Meconium, a non-invasive biomaterial reflecting prenatal substance accumulation, could provide valuable insights into neonatal health. However, the comprehensive protein profile of meconium across gestational ages remains unclear. Here, we conducted an extensive proteomic analysis of first meconium from 259 newborns across varied gestational ages to delineate protein composition and elucidate its relevance to neonatal diseases. The first meconium samples were collected, with the majority obtained before feeding, and the mean time for the first meconium passage from the anus was 11.9 ± 9.47 h. Our analysis revealed 5370 host-derived meconium proteins, which varied depending on sex and gestational age. Specifically, meconium from preterm infants exhibited elevated concentrations of proteins associated with the extracellular matrix. Additionally, the protein profiles of meconium also exhibited unique variations depending on both specific diseases, including gastrointestinal diseases, congenital heart diseases, and maternal conditions. Furthermore, we developed a machine learning model to predict gestational ages using meconium proteins. Our model suggests that newborns with gastrointestinal diseases and congenital heart diseases may have immature gastrointestinal systems. These findings highlight the intricate relationship between clinical parameters and meconium protein composition, offering potential for a novel approach to assess neonatal gastrointestinal health.

Background: Tumors possess incessant growth features, and expansion of their masses demands sufficient oxygen supply by red blood cells (RBCs). In adult mammals, the bone marrow (BM) is the main organ regulating hematopoiesis with dedicated manners. Other than BM, extramedullary hematopoiesis is discovered in various pathophysiological settings. However, whether tumors can contribute to hematopoiesis is completely unknown. Accumulating evidence shows that, in the tumor microenvironment (TME), perivascular localized cells retain progenitor cell properties and can differentiate into other cells. Here, we sought to better understand whether and how perivascular localized pericytes in tumors manipulate hematopoiesis. Methods: To test if vascular cells can differentiate into RBCs, genome‐wide expression profiling was performed using mouse‐derived pericytes. Genetic tracing of perivascular localized cells employing NG2‐CreERT2:R26R‐tdTomato mouse strain was used to validate the findings in vivo. Fluorescence‐activated cell sorting (FACS), single‐cell sequencing, and colony formation assays were applied for biological studies. The production of erythroid differentiation‐specific cytokine, erythropoietin (EPO), in TME was checked using quantitative polymerase chain reaction (qPCR), enzyme‐linked immunosorbent assay (ELISA, magnetic‐activated cell sorting and immunohistochemistry. To investigate BM function in tumor erythropoiesis, BM transplantation mouse models were employed. Results: Genome‐wide expression profiling showed that in response to platelet‐derived growth factor subunit B (PDGF‐B), neural/glial antigen 2 (NG2) ⁺ perivascular localized cells exhibited hematopoietic stem and progenitor‐like features and underwent differentiation towards the erythroid lineage. PDGF‐B simultaneously targeted cancer‐associated fibroblasts to produce high levels of EPO, a crucial hormone that necessitates erythropoiesis. FACS analysis using genetic tracing of NG2 ⁺ cells in tumors defined the perivascular localized cell‐derived subpopulation of hematopoietic cells. Single‐cell sequencing and colony formation assays validated the fact that, upon PDGF‐B stimulation, NG2 ⁺ cells isolated from tumors acted as erythroblast progenitor cells, which were distinctive from the canonical BM hematopoietic stem cells. Conclusions: Our data provide a new concept of hematopoiesis within tumor tissues and novel mechanistic insights into perivascular localized cell‐derived erythroid cells within TME. Targeting tumor hematopoiesis is a novel therapeutic concept for treating various cancers that may have profound impacts on cancer therapy.

Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell’s immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and a mutant with altered cilia (RFX2 -/-), we discovered an early-differentiation “ciliary time window” during which transient cilia promote axon outgrowth, branching and arborization. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in “mild” impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.