Differentiation

Inherited retinal disorders are significant contributors of blindness worldwide. Mutations in Peripherin-2 (PRPH2), a highly conserved vertebrate tetraspanin membrane protein responsible for formation and maintenance of OS morphology, have been shown to cause diverse types of inherited photoreceptor cell (PRC) disorders including but not limited to Leber congenital amaurosis, cone-rod dystrophy, and retinitis pigmentosa. In this study we used a cone-rich diurnal zebrafish model to characterize the loss of PRPH2 function. Of the four PRPH2 zebrafish orthologs only prph2a and prph2b were found to be expressed in PRCs. CRISPR-mediated single mutants of prph2a and prph2b did not yield striking rod or cone phenotypes. Double prph2a/2b mutants exhibited early loss of all cone cells, preceded by cone outer segment disorganization in the form of whorls akin to the phenotypes observed in PRPH2+/- mice. Surprisingly rod photoreceptor cells were not affected and in fact exhibited a striking lengthening of rod OSs with normal disc formation. Overgrowth of rod OSs proceeded up to 1 year, but no degeneration was observed. To determine how rod OS can persist without prhp2a/b we targeted rom1a and rom1b using CRISPR. Injection of rom1a/b crRNA resulted in complete loss of both rod and cone OSs in the prph2a/b double mutants. Surprisingly, inhibition of rom1a/b alone resulted in the loss of rod but not cone OSs. These findings suggest that unlike in mammals, zebrafish rom1a/b is essential for rod OS formation while prph2a/b is essential for cone OSs.

The MAF family transcription factor Nrl is a key regulator of vertebrate rod photoreceptor formation/differentiation. The expression of Nrl in nascent photoreceptors has been proposed to act as a master regulator to initiate a rod program and to repress a default cone photoreceptor sister fate. The evidence for rod-specific expression of Nrl has been most strongly supported by mouse transgenic models that use a transcriptional promoter element for Nrl. However, this element has not been rigorously evaluated to have rod lineage-specific activity or as a validated proxy for endogenous Nrl expression, despite its wide use under this assumption. Here we identify that the Nrl promoter is not exclusively active in rod photoreceptors but is also transiently active within a high proportion of the differentiating cone photoreceptor population. Thus, the Nrl promoter cannot be used to distinguish rods from cones at developmental timepoints. Furthermore, multiple lines of evidence using immunofluorescence and reanalysis of published single cell RNA-seq/ATAC-seq datasets support the presence of endogenous Nrl gene expression in early differentiating cone photoreceptors. Taken together, these results suggest that proposed gene regulatory networks that position Nrl as a master regulator of rod versus cone fate are inadequate as currently constructed. This impacts our understanding of visual system evolution and has implications for the development of therapeutic strategies of cell replacement for human blindness.

Background: Viable pediatric human growth plate (GP) tissue is rarely available for translational research, limiting direct investigation of human longitudinal bone growth and pediatric growth disorders. In this proof-of-concept study, we aimed to determine whether it is feasible to establish a clinically integrated ex vivo human GP model using tissue obtained during routine percutaneous epiphysiodesis (PE) procedures in adolescents treated for extreme tall stature or leg length difference due to trauma. Methods: GP tissue and cells were collected during PE and processed using protocols adapted from established methods of human osteoarthritic cartilage processing within the RAAK study. Feasibility was assessed by evaluating tissue collection, cell isolation, contamination rate, monolayer expansion, and generation of three-dimensional cartilage pellets. Proliferation of GP-derived chondrocytes was compared with osteoarthritis-derived articular chondrocytes, and histological assessment was performed to evaluate cartilage-like matrix formation. Results: Across consecutive surgical procedures, viable GP tissue could be obtained reproducibly, with only few samples failing to yield cells and no relevant contamination issues. Isolated GP chondrocytes expanded successfully in two-dimensional culture and showed a strong early proliferative response compared with RAAK-derived chondrocytes. In addition, GP-derived cells formed three-dimensional organoids and histology confirmed cartilage-like matrix deposition supporting their capacity to generate neo-cartilage tissue in vitro. Conclusion: This study demonstrates feasibility to obtain, culture, and functionally assess viable human GP tissue from routine PE surgery. As such, the Leiden ex vivo human GP model provides a unique platform to study local mechanisms of endochondral bone growth, link genetic determinants of height to functional GP biology, and support future therapeutic research in pediatric growth disorders.

During development, endothelial cells (ECs) migrate into the brain and acquire blood-brain barrier (BBB) properties such as tight junctions, limited transcellular transport, and high electrical resistance. Although key signaling pathways that are active in vivo have been identified, factors critical in inducing brain EC differentiation in vitro remain unclear. Here, we describe conditions that promote brain EC-like gene expression in human pluripotent stem cell (hiPSC)-derived ECs. Activation of Wnt/{beta}-catenin signaling upregulates the brain EC marker GLUT1 (SLC2A1) while suppressing the peripheral EC marker PLVAP. Simultaneously, stimulation of STAT3 by CNTF together with TGF-{beta} inhibition increases CLDN5 expression. We further found that hiPSC-derived ECs secrete high levels of angiopoietin-2 (ANGPT2) and that razuprotafib (AKB-9778), a PTPRB (VE-PTP) inhibitor, inhibits ANGPT2 and improves monolayer integrity. These results suggest that combinatorial modulation of specific signaling pathways stimulates the differentiation of human brain ECs in vitro.

Epithelial tube morphogenesis is critical for the function of many organs. Basement membranes underlie epithelia and their remodeling is a key step to reach the correct size and shape. Key regulators that mediate basement membrane remodeling for tube elongation and branching remain largely unknown. We analyze the expression and function of AdamTS-B, a matrix metalloprotease, in the respiratory system of Drosophila. Here we show, that AdamTS-B is expressed early in tracheal development during placode formation. We generated a mutant line of AdamTS-B, which is lethal. Analysis of trachea morphogenesis in this AdamTS-B mutant reveal a function in tube elongation and cell migration. Our results suggest that AdamTS-B control BM remodeling required for organ shape.

Zebrafish bone regeneration is a highly efficient process, enabling the complete restoration of an amputated fin within few weeks. The hallmark of this epimorphic regeneration is the formation of a blastema atop of a bony fin ray. Osteoblasts near the injury site dedifferentiate and migrate off the bone to contribute to the developing blastema. We show that an injury or a blastema alone is not sufficient to trigger off-bone migration of osteoblasts. Surprisingly, we found that blastema cells themselves possess intrinsic migratory properties. Moreover, when multiple injury sites are present, a preferential distal migration could be observed. We conclude that multiple injuries are hierarchical organized, and that injuries with the highest regenerative potential take priority.

Immune checkpoint inhibitor-induced myocarditis (ICIM) is a severe immune-related adverse event with heterogeneous clinical presentations and potential genetic susceptibility. Here, we established a human induced pluripotent stem cell (iPSC) line from an ICIM patient with an HLA-type distinct from previously reported line, who developed concurrent type I diabetes following ICI treatment. This line exhibited typical morphology, normal female karyotype, pluripotency, trilineage differentiation into all three germ layers, Sendai virus clearance, and no mycoplasma contamination. Given the fulminant nature and diverse clinical presentations of ICIM, expanding the repertoire of iPSC lines are critical for investigating ICIM heterogeneity and its underlying mechanisms.

Cochlear hair cell (HC) loss is a leading cause of hearing loss in humans. HCs can be generated from adjacent supporting cells (SCs); however, this regenerative capacity is lost after the onset of hearing. Using Emx2Cre Zbtb20 knockout mice, we show that ZBTB20 deficiency delays cell-cycle exit, differentiation, and maturation of cochlear SCs. Transcriptomic analysis of postnatal cochlear sensory epithelia indicates that ZBTB20 loss postpones the downregulation of progenitor genes, including Sox11 and Hmga2, and delays activation of a maturation-specific gene program. Additionally, experiments with cochlear organoid and organotypic explant models, reveal that prolonged, and to a lesser extent acute, ZBTB20 loss increases the mitotic and HC-regenerative potential of cochlear SCs. Transcriptomic profiling shows that acute ZBTB20 loss upregulates the midkine receptor Ptprz1, and further studies show that exogenous midkine, similar to ZBTB20 loss, promotes cell-cycle reentry and proliferation in cochlear organoid cultures.

Hirschsprung disease (HSCR) is a severe birth defect where ganglia of the enteric nervous system (ENS) are missing from distal bowel. The aganglionic segment is also characterized by increased epithelial permeability and pro-inflammatory immune activation. These problems may sequentially lead to translocation of gut microbes into the colon wall and systemic circulation, resulting in enterocolitis and sepsis. Current HSCR treatment via surgical resection of the aganglionic segment is lifesaving but not curative, often leaving patients with persistent gastrointestinal complications including recurrent risk of enterocolitis. As alternative, we are developing a regenerative medicine strategy based on in situ stimulation of tissue-resident ENS progenitors via rectal administration of the neurotrophic factor GDNF. Here, we report that GDNF-based therapy has pleiotropic gastrointestinal effects in a mouse model of short-segment HSCR, beyond its role in ENS regeneration. Interestingly, we found that these protective effects are not restricted to the aganglionic distal colon, also positively impacting the ENS-containing proximal colon. GDNF treatment reduces bacterial translocation both locally and in peripheral organs, and this is associated with recovery of the key epithelial junction proteins CLDN3, ZO1 and DSG2. Furthermore, multiparameter flow cytometry-based analysis of 55 lymphoid and 17 myeloid cell subtypes revealed that GDNF treatment has global anti-inflammatory effects, preferentially affecting innate over adaptive immunity. Overall, these findings highlight a critical role for GDNF treatment in reestablishing proper epithelial and immune cell homeostasis, offering promising therapeutic avenues not only for HSCR but also potentially for other intestinal disorders with overlapping pathophysiology.

Reelin is a secreted extracellular matrix protein that regulates neuronal migration and layer formation in the developing brain, yet its role in retinal development remains incompletely defined. Here, we investigated Reelin function in retinal lamination using wild-type and Reeler (Reln-/-) mice, combining stage-resolved RNA in situ hybridization, immunohistochemistry, and single-nucleus RNA sequencing. We show that Reln is dynamically expressed in ganglion cell layer and inner nuclear layer neurons during retinal development and persists in discrete adult neuronal populations. Loss of Reelin leads to widespread defects in retinal organization affecting both neurons and Muller glia. In Reln-/- retinas, Muller glia exhibit reduced Glul positive extensions, indicating impaired glial scaffold maturation. Early-born neuronal populations are also disrupted, with altered spatial organization markers associated with retinal ganglion cell differentiation within the ganglion cell layer at postnatal day 9. Horizontal cells are significantly reduced with dorsal-predominant vulnerability, while cone photoreceptors are generated in normal numbers but show incomplete positioning within the outer nuclear layer. Together, these findings identify Reelin as a key regulator of retinal lamination that coordinates neuronal positioning with Muller glia morphogenesis, extending its canonical role in brain development to the vertebrate retina.

The Tbx1 gene is haploinsufficient in mice and in humans, where it causes a DiGeorge syndrome phenotype characterized by developmental deficits of the pharyngeal apparatus. TBX1 plays a critical role in the differentiation and regionalization of the cardiopharyngeal mesoderm lineage and its derivatives. Nevertheless, its regulation is incompletely understood. Here we used a combination of computational and wet-lab approaches to identify regulatory sequences of the Tbx1 gene, and we use single-cell molecular analysis as a read-out and to establish the consequences of their deletion. Results revealed a cluster of regulatory sequences with at least three distinct elements. Elimination of the entire cluster caused a near shut down of the gene, while individual deletions had milder, quantitative effects. Transcriptomic analyses of the deletion mutants revealed the down regulation of genes related to cardiopharyngeal lineage specification and, more surprisingly, up regulation and anteriorization of genes related to embryonic patterning, thereby providing a rationale for the severe dysmorphogenesis of the posterior pharyngeal apparatus observed in Tbx1 mutant mice.

Retinal development has been extensively studied and key transcriptional regulators that drive fate decisions have been identified for major cell classes. These findings were confirmed and deepened in recent years with the advance of single cell RNA sequencing (Scrase). However, many processes that guide progenitor to postmitotic cell differentiation remain elusive, especially since some genes seem to yield different cell populations without apparent correlation with expression level or timing. Here, differential transcript isoform usage might play a role in diversifying the function of developmental genes. In short-read based scRNAseq, isoforms can only be identified if a read maps to a unique sequence or exon junction. However, due to the sparsity and very short reads, these events are extremely rare. We combined a commercial scRNAseq kit, that produces barcoded, full-length cDNA with Oxford Nanopore Technologies based long-read sequencing to generate the first single cell long-read sequencing dataset of fetal human retina. It can help elucidate the role of alternative splicing in retinal development and guide the design of transcript-specific gene therapies for retinal regeneration.

The tunicate Ciona robusta offers a tractable non-vertebrate chordate model for probing gene function via tissue-specific, CRISPR/Cas9-mediated mutagenesis in F0. Building on Arcadia Sciences Zoogle platform, which identifies and ranks orthologs of human genes from various non-traditional model organisms, we carried out a pilot project to probe the developmental roles of three notochord- and endoderm-expressed candidate orthologs of human disease genes (Fcho, Pgm3, and Nckap1) alongside a fourth gene (Plastin) implicated in papilla cell elongation. This preprint compiles and updates a series of research project milestones previously posted episodically on Zenodo. Here we summarize the full results and our conclusion about this pilot project. Using CRISPR/Cas9, we found that tissue-specific knockout of Pgm3 and, to a lesser extent, Fcho caused significant defects in larval tail elongation. Separately, CRISPR knockout of Plastin, an actin-bundling gene expressed throughout the sensory-adhesive papillae of the larva, caused a subtle reduction in papilla cell elongation when combined as a duoble knockout with another actin-bundling protein-encoding gene, Villin. These results identify Pgm3 as the most promising candidate for further development as a Ciona-based model of human disease and demonstrate the utility of tissue-specific CRISPR screening for prioritizing candidate disease gene orthologs identified through comparative genomics platforms like Zoogle.

ANGPT2 is widely recognized as a critical regulator of pathological neovascularization. By analyzing scRNA-seq data from neonatal retinas, we demonstrate that Angpt2 transcripts are highly enriched in tip cells relative to other endothelial subtypes, where Angpt1/4 expression is absent. However, mechanisms underlying ANGPT2 function at angiogenic fronts remain inadequately understood. Here, we show that endothelial Angpt2 deletion severely disrupted retinal vascularization, characterized by neovascular tufts and micro-hemorrhage. Similar angiogenic defects also occurred in the brain, but were less evident in other tissues examined. Mechanistically, ANGPT2 insufficiency attenuated retinal tip cell invasion with aberrant mural cell coverage, compromising sprouting into non-vascularized tissues. Retinal RNA-seq analysis revealed that transcripts associated with endothelial migration and junction assembly were reduced in Angpt2 mutants compared to littermate controls, while upregulated genes were enriched in hypoxia-responsive pathways and mural cell development. Notably, abnormal mural-tip cell associations were detected within 48 hours post-Angpt2 deletion, displaying also a hypoxia-driven transcriptomic signature. These closely resemble the vascular pathologies observed in human retinopathy of prematurity. In contrast, Angpt1 insufficiency or Angpt4 deficiency primarily affected venous morphogenesis. Collectively, our findings imply that ANGPT2 is essential for driving tip cell invasion during sprouting angiogenesis, and that its insufficiency triggers hypoxia-driven vascular anomalies.

Background Cervical spondylotic myelopathy (CSM) is the most common cause of nontraumatic spinal cord dysfunction in adults. For mild disease, guidelines recommend shared decision-making between surgery and structured rehabilitation on the basis of clinical equipoise, yet no comparative effectiveness study has reported outcomes in this population. Whether a randomized trial is feasible is unknown. Methods We conducted two cross-sectional surveys between December 2025 and July 2026: one of patients with surgeon-confirmed CSM recruited from academic outpatient spine clinics, and one of practicing neurosurgical and orthopedic spine surgeons. Respondents rated willingness to participate in (1) a randomized trial of early surgery versus observation and (2) a prospective observational study in which treatment was patient-selected. Responses of likely or very likely were classified as willing. Groups were compared using Fisher exact tests, designs within respondents using exact McNemar tests, and predictors using univariable logistic regression. Results Fifty-four patients and 52 surgeons completed the surveys. Patients were markedly less willing than surgeons to accept randomization (15 of 54, 27.8% versus 44 of 52, 84.6%; p < 0.001). Both groups accepted the observational design (39 of 54, 72.2% versus 51 of 52, 98.1%; p < 0.001), and 26 of 39 patients unwilling to be randomized were willing to enroll in an observational study (p < 0.001). Willingness to be randomized did not differ across mJOA severity (mild 30.4%, moderate 25.0%, severe 27.3%; p = 0.93). Among patients declining randomization, 85.2% cited a wish to retain control over treatment, whereas fear of surgery was cited by one respondent. Forty-five surgeons (86.5%) considered both surgery and observation reasonable, and preference was divided (46.2% favoring early surgery, 48.1% favoring initial observation). Conclusions Surgeons report equipoise and high willingness to randomize, but most patients would decline random allocation, citing a wish to retain treatment choice rather than fear or distrust. A prospective observational study appears the more feasible route to comparative evidence in mild CSM. Feasibility assessments restricted to clinicians may substantially overestimate attainable accrual.

Renal cysts are categorized as non-pathogenic simple cysts and pathogenic malignant cysts based on their pathophysiological status. Cyst formation is divided by cyst initiation and cyst progression/promotion. Pathogenic cysts are thought to be developed through continuous initiation followed by progression until pathogenic status is achieved. Although many genetic and environmental factors are identified to cause pathogenic cyst formation, the mechanisms that discriminate cyst initiation and progression are poorly understood. Using genetic mutation models of ETV transcription factors, ETV1, ETV4, and ETV5, and a pharmacological inhibitor of hedgehog signaling, cyclopamine, we identified one of the mechanisms regulating cyst initiation and progression. Nephron specific deletion of ETV4 and ETV5 initiated cyst formation. However, cyst initiation did not continue as animals grow, and a limited number of the initial cysts underwent further growth. Additional deletion of ETV1 was required for continuous initiation in addition to promotion of cyst growth. Furthermore, administration of cyclopamine attenuated promotion of cyst progression but had little effect on cyst initiation. Therefore, we provide evidence that cyst initiation and progression is genetically and molecularly distinct and can be modulated. This information provides new insight into how to control renal cyst initiation and progression and can be used to suppress pathogenic cyst growth.

Objective White smoke inhalation injury (WSI) causes severe acute lung damage with no specific therapy currently available. Sphingolipid metabolism is implicated in pulmonary inflammation, but its transcriptional regulatory landscape in WSI remains unexplored. This study aimed to identify key sphingolipid metabolism related genes and evaluate their regulatory roles and therapeutic potential in WSI. Methods We established a rat model of WSI and performed integrated bulk RNA sequencing, weighted gene coexpression network analysis (WGCNA), and single-cell RNA sequencing (scRNAseq) to screen for differentially expressed sphingolipid metabolism-related genes (DESRGs). Protein-protein interaction (PPI) network with four centrality algorithms was used to prioritize hub genes. In silico gene knockout and molecular docking were conducted to assess regulatory functions and identify potential drug candidates. Results We identified 22 DESRGs that were predominantly enriched in DNA replication and cell cycle pathways rather than canonical sphingolipid metabolic processes. PPI consensus prioritized three hub genes--Top2a, Ttk, and Ccna2--with Top2a exhibiting the highest expression in epithelial cells and significant downregulation after smoke exposure. ScRNAseq revealed immune cell infiltration and epithelial differentiation trajectories. Virtual knockout showed that Top2a depletion affected the largest transcriptomic fraction (~0.4%) and was enriched in lysosome biogenesis, innate immunity, phagocytosis, and lipid catabolism. Molecular docking identified thalidomide as a high affinity ligand for Top2a (Vina score: -8.5 kcal/mol). Conclusion Our multiomics integrative framework identifies Top2a as a central regulatory hub linking sphingolipid associated inflammation to epithelial responses in WSI, and nominates thalidomide as a potential drug repurposing candidate. These findings provide prioritized targets for future translational investigation.

Satellite DNA is long arrays of tandem repetitive DNA located often near the centromeres of chromosomes, whose function, or lack of, has been debated since its discovery. Although situated in heterochromatin, satellite DNA may be expressed as long noncoding RNAs (lncRNAs). Although there are a few examples of satellite lncRNAs being characterized, and functions suggested, how widespread and functionally important they may be for developmental processes is not understood. Here, we take an evolutionary approach to investigate satellite lncRNA expression in Drosophila spp. ovaries, a tissue whose development is well-characterized but where satellite expression has only been minimally explored. Using a publicly-available total RNAseq dataset, we find that 118/156 surveyed satellite DNAs were expressed across 10 species, with 33 satellites having high expression over 20 RPM. However, all but two of these expressed satellites (AAACTAC in D. virilis and ACAGACAGACAGG in D. ananassae) had higher read counts in a sister smallRNA dataset, suggesting that most satellite transcripts primarily serve as precursors for piRNA biogenesis. The two "stand-alone" lncRNAs were highly strand-biased, with 96-97% of the total reads coming from one strand. We further investigated AAACTAC expression with RNA FISH and found the transcript is specifically present in the oocyte nucleus following a dynamic spatiotemporal pattern, with the highest expression in stage 3-5 oocytes. The transcription pattern of AAACTAC is conserved in the three other virilis clade species that contain this satellite DNA. Further, we found expression of unrelated satellites in more distantly related D. borealis and littoralis both in the oocyte and the nurse cells. Overall, our work identifies a novel lncRNA AAACUAC found in the early oocyte nucleus, which is conserved across ~5 MY of evolution, and is therefore a strong candidate for the discovery of novel functions of satellite lncRNAs in development.

Activated leukocyte cell adhesion molecule A (Alcama) plays a role in axonal guidance, cell differentiation, and retinal lamination in a developing retina and was identified as a marker for activated Muller glial cells in adult zebrafish. However, its spatiotemporal localization and its involvement in retina regeneration remains unclear. Here we induced focal photoreceptor damage in zebrafish using laser photocoagulation and examined the expression and localization of Alcama at different time points post lesion. Immunohistochemistry in wild type fish and Tg(kdrl-EGFP) fish showed Alcama localized to the blood retina barrier with increased expression in Muller glial end feet and radial processes in a regenerating retina. To confirm its role in retina regeneration, alcama expression was transiently knocked down using morpholinos in adult fish. Scanning laser ophthalmoscopy, Zpr1 immunostaining and EdU staining showed delayed retina regeneration in alcama knockdown fish, indicating a possible role for Alcama in zebrafish retina regeneration.

Eph and ephrin genes encode receptor-ligand pairs that mediate contact-dependent cell signaling and are essential for nervous system development. However, less is known about the role of Ephrin signaling during adult tissue homeostasis and regeneration. Here, we investigated the role of Ephrin signaling in neural patterning in the planarian Schmidtea mediterranea. We discovered that RNAi against the Eph receptor EphR1 led to striking ectopic expression of the mechanosensory neuron markers pkd1L-2 and hmcn-1-L, without obvious disruption of the overall architecture of the central nervous system. To investigate the basis of this phenotype, we identified additional Eph receptor homologs and four putative ephrin ligands and assessed their function. An RNAi screen revealed that ephrin-1 phenocopies the defects of EphR1 RNAi. Temporal analyses of EphR1 and ephrin-1 inhibition revealed a progressive increase in pkd1L-2+ and hmcn-1-L+ cells, indicating an unappreciated role for Ephrin signaling in regulating neural patterning and cell number during adult tissue homeostasis. Together, these findings provide a framework for dissecting Ephrin-dependent mechanisms in adult tissue maintenance and regeneration.