Stem Cell Reports

BackgroundGains of chromosome 20q11.21 are among the most common culture-acquired abnormalities in human pluripotent stem cells (hPSC), conferring a well-defined survival advantage while altering differentiation capacity. However, it remains unclear whether this advantage persists during differentiation, how the aneuploidy alters ectodermal and retinal pigment epithelium (RPE) lineage specification, and which genes within the minimal amplicon drive these effects. MethodsWe used three isogenic human embryonic stem cell line pairs (wild-type and 20q11.21 gain) and assessed their behaviour in two neuroectoderm differentiation systems: directed neuroectoderm induction (dual SMAD inhibition) and long-term spontaneous RPE differentiation. Competitive dynamics were measured in mixed cultures, and lineage outcomes were analysed using immunostaining, gene expression profiling and single-cell RNA sequencing. To identify driver genes, we generated BCL2L1 and ID1 overexpression lines and tested their effects under both directed and spontaneous differentiation conditions. ResultsAcross all lines and conditions, 20q cells expanded from a minor fraction to dominate mixed cultures, indicating that their competitive advantage persists beyond the undifferentiated state. Despite this dominance, pure 20q cells failed to specify to neuroectoderm or RPE. Single-cell transcriptomics revealed consistent diversion toward non-neural ectodermal and extraembryonic fates. Mechanistically, overexpression of BCL2L1 and ID1 alone or in combination impaired neuroectoderm specification, while synergistic effect of both genes promoted non-neural ectodermal outcomes under directed differentiation conditions. In spontaneous differentiation, both genes could disrupt differentiation. ConclusionsThe 20q11.21 gain couples a persistent survival advantage with a disruption of neural and RPE lineage competence, redirecting cells toward alternative ectodermal and extraembryonic fates. These effects arise from the combined action of two dosage-sensitive genes BCL2L1 and ID1 within the amplicon, illustrating how regional gene dosage can reshape developmental signalling responses in hPSC.

In vitro stem cell models of human gastrulation have been an advance for developmental biology, though elucidating mechanisms of germ layer formation remains challenging. While investigating whether spatially-patterned signaling is required for germ layer formation, we tested a "salt-and-pepper" signaling strategy in which WNT was optogenetically activated in a subset of human pluripotent stem cells (hPSC) uniformly mixed into an aggregate. Following mesendodermal specification, WNT-activated cells spatially segregated into a hemisphere, then underwent further differentiation and organization into mesoderm and endoderm. RNAseq-based lineage analysis revealed that WNT activation non-autonomously induced TGF{beta}/BMP signaling, leading to robust emergence of an anterior visceral endoderm-like population that patterned adjacent neural and mesendodermal fates. Transcriptional profiles and trajectories closely mirrored those observed during human gastrulation. Moreover, TGF{beta} or cadherin perturbation disrupted germ layer formation or spatial organization, respectively. This simple model thus enables mechanistic dissection of complex human lineage specifications and organization during gastrulation.

Somatic cell nuclear transfer (SCNT) holds great promise for regenerative medicine and agriculture, but its application is severely hampered by low efficiency, primarily attributable to aberrant epigenetic reprogramming. Although embryonic stem cells (ESCs) and trophoblast stem cells (TSCs) have been successfully derived from cloned embryos, an in vitro counterpart of the primitive endoderm (PrE) lineage has remained unavailable. To address this gap, this study reports the first successful establishment of extra-embryonic endoderm stem cell lines (XENs) from mouse SCNT-derived blastocysts (NT-XENs). Under conventional culture conditions, NT-XENs were generated from hybrid B6D2F1 blastocysts at a high efficiency of 55%, comparable to that of fertilization-derived XEN lines (FD-XENs, 50%), whereas derivation from inbred C57BL/6J SCNT-derived blastocysts was markedly lower (12.5%). Immunofluorescence and NanoString multiplex gene expression profiling confirmed that NT-XENs robustly expressed specific marker genes for PrE/XENs (e.g., Gata4, Gata6, Sox17), while exhibiting negligible or absent expression of pluripotency and trophoblast markers. Based on NanoString assay data, NT-XENs and FD-XENs shared highly similar global gene expression patterns, yet also exhibited some nonnegligible differences, exemplified by the differentially expressed genes (DEGs) Pecam1, Gtl2, Thbd and Xlr3b, which may suggest that the NT-XENs resided in a more differentiated state (potentially biased toward parietal endoderm (PE)) and retained SCNT-specific epigenetic imprinting errors, including aberrant X-chromosome inactivation and dysregulation of imprinted domains. In summary, this study successfully establishes NT-XEN cell lines, providing a valuable in vitro model for investigating the reprogramming scenarios of PrE lineage in SCNT and offering novel insights into the mechanisms underlying developmental failure of cloned embryos.

During embryonic development, neural crest cells (NCCs) represent a multipotent population characterized by an inherently transient nature, rapidly differentiating into various lineages. This instability has presented a fundamental challenge, as it is exceedingly difficult to maintain these cells in a stable, multipotent state in vitro. In this study, we report a robust culture system dependent on Wnt and FGF signaling that enables the long-term (>6 months) expansion of human iPSC-derived neural crest stem cells (NCSCs). These NCSCs retain their self-renewal and differentiation capacity, validated at the single-cell clonal level. ATAC-seq analysis indicated that posterior NCSCs maintain a more permissive chromatin structure at neuronal gene loci. Furthermore, ChIP-seq analysis revealed that the key transcription factor SOX10 binds to the regulatory regions of genes involved in both maintenance and differentiation. This system provides a stable source of human NCSCs, offering a valuable platform for developmental biology, disease modeling, and regenerative medicine.

Ischaemic heart disease remains the leading cause of mortality worldwide, yet no therapies prevent cardiomyocyte death during acute ischaemia-reperfusion injury (IRI). Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide a platform for modelling cardiac injury, but their immature phenotype limits the physiological fidelity of in vitro models. Here, we systematically evaluated how experimental variables used during preparation of hiPSC-CM endpoint assays influence cardiomyocyte maturation and susceptibility to IRI. Integrating literature mining, molecular profiling, statistical genetics, and functional assays, we examined the effects of replating conditions, backbone media, metabolic substrates, and signalling modulators. We define the relationship between culture conditions and metabolic supplements in determining contractile maturation and sensitivity to IRI. Notably, we show that metabolic composition of the backbone medium establishes the baseline maturation state and determines responsiveness to additional maturation cues. These findings identify metabolic environment as a dominant regulator of injury susceptibility and provide a framework for improving the physiological fidelity of hiPSC-CM models of cardiac ischaemia.

Development of motoneurons from stem cells is characterized by a change from glycolytic to oxidative metabolism. Since this transition remains poorly understood, we examined it at five distinct differentiation stages from hiPSC to motoneuron. While a direct comparison of hiPSCs and mature motoneurons confirmed the expected glycolytic-to-oxidative shift, the intermediate stages showed that the conversion was not monotonic. After an initial drop of glycolysis at the hiPSC-to-neuroepithelial transition, late neuroepithelial cells showed intermittent peaks of the glycolytic marker lactate dehydrogenase A and the metabolic regulator TIGAR. Furthermore, the lactate-produced-to-glucose-consumed ratio remained elevated. A fully oxidative phenotype was only assumed upon progress from neural progenitors to motoneurons, portrayed by a definitive drop of the lactate-produced-to-glucose-consumed ratio, an increase of mitochondrial membrane charging, and shifts from lactate dehydrogenase A to B, from pyruvate dehydrogenase to anaplerotic pyruvate carboxylase, and from Mitofusin 1 to 2. Together, our data show that metabolic maturation in human motoneurons does not occur as a simple switch. Instead, it unfolds through distinct stages in a directional yet nonlinear manner.

Studying neural-related questions is inherently challenging due to the limited number of suitable cell models. Here, we characterize a previously reported immortalized human neural stem cell line, HNSC.100, serving as a robust model for a wide range of neurobiological research questions. The cell line expresses key neural stem cell markers, including SOX2, vimentin, nestin, and allows for efficient genetic manipulation. Furthermore, HNSC.100 cells can be differentiated into neurons, astrocytes and oligodendrocytes, thereby covering a wide spectrum of major neural cell types. We established a comprehensive panel of molecular markers to validate successful differentiation, enabling precise characterization of the resulting cell population. In addition, we provide a complete dataset of RNA expression levels for all detectable genes in HSNC.100 cells. Based on this dataset, we assembled a list of expressed genes implicated in neural disorders that can be studied with this cell line. Together, we present a detailed characterization of the HNSC.100 cell line and provide new tools and reference data to facilitate its use. This resource enables researchers to evaluate the lines suitability for specific applications and to rapidly integrate HNSC.100 cells into their experimental workflows. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/700829v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@115f8b3org.highwire.dtl.DTLVardef@17adb69org.highwire.dtl.DTLVardef@dad583org.highwire.dtl.DTLVardef@f7a691_HPS_FORMAT_FIGEXP M_FIG C_FIG

Despite lacking a robust interferon response, pluripotent stem cells remain highly resistant to viral infection, in part through the constitutive expression of immune genes traditionally classified as interferon-stimulated genes. While interferon signaling has been shown to be incompatible with the maintenance of pluripotency, the molecular mechanisms underlying this relationship remain poorly understood. Here, we investigate the transcriptional response of human embryonic stem cells (hESCs) to infection with a potent activator of the interferon response, an influenza A virus mutant lacking the viral NS1 protein. Single-cell RNA sequencing revealed that while most hESCs remain unresponsive to infection, a distinct subpopulation expresses type I and III interferons. Notably, only interferon-expressing cells mounted a robust antiviral response, characterized by strong induction of interferon-stimulated genes. In contrast to the bulk hESC population, interferon responding cells exhibited reduced expression of core pluripotency factors as well as negative regulators of interferon signaling, such as SOCS1 and SPRY4. Depletion of SOCS1 enabled hESCs to respond robustly to interferon stimulation, showing that this negative regulator is a key suppressor of interferon signaling in pluripotent stem cells. We further show that SOCS1 and additional negative regulators of IFN signaling are intrinsically expressed in hESCs and are transcriptionally controlled by pluripotency factors, such as NANOG, SOX2 and OCT4. Together, our findings support a model in which pluripotency factors regulate intrinsic immune gene expression, including negative regulators of interferon signaling, thereby suppressing canonical interferon signaling to preserve pluripotency while maintaining antiviral resistance. IMPORTANCEBy combining single-cell transcriptomics with functional studies, we demonstrate that the pluripotency transcriptional program active in pluripotent stem cells coordinately regulates pluripotency factors, antiviral genes, and negative regulators of interferon signaling. This integrated control enables pluripotent stem cells to achieve effective protection against viral infection while preserving their differentiation potential, providing new insights into how innate immunity is selectively constrained in pluripotent stem cells. These findings have important implications for stem cell-based therapies, where transient modulation of antiviral responses without disrupting pluripotency could improve therapeutic efficacy. More broadly, this work advances our understanding of interferon regulation that could inform the development of antiviral strategies that enhance protective immune responses while limiting harmful or unwanted inflammatory signaling.

Ovarian cancer stem cells (CSCs) can seed recurrent drug-resistant disease. Likewise, non-CSCs can acquire CSC phenotypic properties. How this process is orchestrated is of interest to inform how it might be prevented. We tested the hypothesis that ovarian CSC and/or drug-resistant tumor cells confer stem-like properties via extracellular vesicles (EVs). We focused our investigation on how EVs might mediate EZH2 signaling to promote a phenotypic change in drug-sensitive, non-CSCs. To accomplish this, we utilized paired PARP inhibitor-sensitive and - resistant ovarian cancer (OvCa) cell lines, EZH2 knockdown lines, and patient-derived organoids (PDOs) originating from recurrent high-grade serous OvCa. Small EVs isolated from drug-sensitive, CSC and/or drug-resistant enriched cultures, PARP inhibitor (olaparib) resistant lines, or drug-treated (olaparib or carboplatin) lines were cultured with treatment naive or sensitive lines for defined time points. The impact of small EV exposure was determined by assessing cell number, metabolic activity, viability, sphere and colony-forming capacity, ALDH activity, DNA damage, and changes in associated signaling pathways. We found that EVs from CSC or drug-resistant enriched cell fractions communicate CSC-like phenotypes to the more sensitive tumor cells via EZH2 canonical and non-canonical signaling pathways, promoting stemness. We conclude that EV-mediated activation of EZH2 signaling represents a targetable mechanism contributing to stemness-associated drug resistance in OvCa. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/699925v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@6b4ffborg.highwire.dtl.DTLVardef@1501931org.highwire.dtl.DTLVardef@1a5f31aorg.highwire.dtl.DTLVardef@1fb475f_HPS_FORMAT_FIGEXP M_FIG C_FIG

Human iPSC-derived neuronal networks are increasingly being employed in basic and applied research to enhance translation. Astrocytes are essential for neuronal network function, but are often not included, or replaced with mouse astrocytes, which compromises translation. Current protocols produce hiPSC-derived astrocytes by stepwise differentiation using small molecules and cytokines, or by forward programming by inducing transcription factors introduced by lentiviral transduction. Here we created a stable, inducible hiPSC line capable of producing iAstrocytes by introducing the transcription factors NFIB and SOX9 into the AAVS1 locus of the BIHi005-A hiPSC line. iAstrocytes induced from this line upregulated astrocytic genes over four weeks in culture, expressed GFAP and S100B and exhibited spontaneous calcium waves and responses to ATP and CPA. In co-cultures, iAstrocytes supported the growth and function of mature iNeuron networks. Pre- and post-synaptic markers and synchronous neuronal activity measured by high-density multi-electrode array recordings and neuronal calcium imaging, appeared by four weeks. The use of iAstrocytes will help to standardize the use of human astrocytes to support human neural networks and enhance translation.

Facial development is highly sensitive to genetic and environmental perturbation, with craniofacial malformation associated with over one-third of congenital birth defects. The face arises during an early and largely inaccessible window of embryonic development, with a large contribution from transient and multipotent cranial neural crest cells (CNCCs). Assessment of the molecular and cellular mechanisms driving normal and disordered human facial development therefore relies greatly on the use of in vitro cellular models. Here, we adapted a neurosphere-based CNCC differentiation protocol to facilitate robust quantification of early specification and migration events. Introduction of single-cell aggregation with arrayed plating enabled standardisation of neurosphere size, growth and patterning. Inclusion of fibronectin coating enhanced the efficiency of neurosphere attachment and synchronicity of CNCC migration timing. To demonstrate application of the Array-CNCC method, we developed a strategy for mosaic co-culture, which can facilitate differentiation of wildtype untreated cells directly alongside cells exposed to distinct drug treatments or genetic alterations. Finally, we present a screening approach which we use to test the impact of distinct extracellular matrix components on neurosphere morphology, CNCC migration and gene expression. Together, the Array-CNCC method is highly amenable to quantitative phenotyping and screening approaches, enabling enhanced craniofacial disease modelling with both cellular and molecular readouts.

Interspecies chimeras comprising human tissues have potential for use in disease modeling and regenerative medicine. Here, we successfully transplanted human induced pluripotent stem cell (iPSC)-derived PDX1+ pancreatic progenitor cells into Pdx1-deficient mouse embryos via intraplacental injection. The engrafted human cells predominantly localized to the duodenum, produced insulin, and extended the lifespan of Pdx1-/- mice by up to 10 days after birth. Transcriptomic analyses confirmed human pancreatic gene expression in human cells engrafted into the mouse duodenum. Our findings demonstrated the feasibility of generating interspecies chimeras with functional human pancreatic cells through in utero transplantation of lineage-committed progenitors. This approach circumvents developmental barriers while minimizing ethical concerns associated with PSCs. However, the incomplete rescue of the Pdx1-/- phenotype highlights the need for further research to enhance human cell engraftment and tissue integration. Overall, this study provides a foundation for developing human-animal chimera models for studying human development and regenerative therapies.

At the Wisconsin National Primate Research Center, we have identified a family of rhesus carrying the microtubule-associated protein tau (MAPT) R406W mutation linked to frontotemporal dementia (FTD). Rhesus induced pluripotent stem cells (RhiPSCs) derived from these monkeys present a unique opportunity for in vitro modeling and comparison with cells derived from MAPT R406W human carriers. Here, we report the development of a reproducible method to generate RhiPSCs compliant with the standards of the International Society for Stem Cell Research (ISSCR) to support in vitro modeling of FTD-MAPT R406W. Our stepwise approach identified efficient methods for fibroblast derivation, fibroblast reprogramming to RhiPSC, and RhiPSC maintenance over continued culture. To derive fibroblasts from MAPT wild type (WT) and R406W monkeys, a combination of manual processing and overnight enzymatic digestion was required to maximize the number of low passage fibroblasts available for reprogramming. Fibroblast reprogramming to RhiPSC using Sendai viral vectors versus oriP/EBNA1 episomal plasmids revealed the latter as most efficient. Electroporation conditions for oriP/EBNA1 reprogramming were optimized to maximize plasmid uptake and cell survival. Ultimately, eight RhiPSC lines were derived from 4 donor rhesus monkeys (n=2 WT, n=2 R406W; two clonal lines per donor) and fully characterized according to ISSCR standards. RhiPSC stemness and genetic stability was best maintained on mouse embryonic fibroblast feeders in Universal Primate Pluripotency Stem Cell medium, as opposed to Essential 12 medium supplemented with IWR1, which produced cytogenetic abnormalities. Rhesus neural progenitor cells were generated using a monolayer protocol and expressed PAX6 and NESTIN after 21 days of differentiation. Our reliable method will be useful to labs seeking to derive RhiPSCs for preclinical studies. Overall, the RhiPSCs generated from MAPT R406W carriers will be a critical resource for evaluating the molecular underpinnings of tau-related neurodegeneration across primate species.

Neuromodulators influence critical functions of the developing human brain and regulate behavioral states. Dysfunction of neuromodulatory systems is often involved in neuropsychiatric disease and many drugs for these conditions act on these signaling pathways. Recent advances in stem cell biology have made it possible to derive a wide range of cells across the developing human nervous system in regionalized organoids and to functionally integrate them into assembloids, however they currently do not systematically incorporate neuromodulation. Here, we generated human midbrain-hindbrain organoids (hMHO) from human induced pluripotent stem (hiPS) cells and fused them with human cortical organoids (hCO) to form neuromodulatory assembloids (hNMA). We focus on serotonin (5-hydroxytryptamine, 5-HT) as one key neuromodulator and found characteristic gene expression patterns and electrophysiological properties of serotonergic neurons (5-HT neurons) in the hMHO. In hNMA, 5-HT neurons projected into hCO, released 5-HT and modulated cortical network activity. To explore the applicability of this system in human disease, we studied 22q11.2 deletion syndrome (22q11.2DS), a common microdeletion associated with high risk for neuropsychiatric disease and defects in 5-HT signaling. We found aberrant 5-HT dynamics in hNMA from patient hiPS cell lines that were rescued by administration of a selective serotonin reuptake inhibitor (SSRI). Taken together, hNMA can be used to study human 5-HT dynamics and uncover disease phenotypes which could facilitate therapeutic development.

Macrophages are innate immune cells present in most tissues of the body, whose molecular programs are determined by their ontogeny and environment. From the earliest stages of embryonic development, macrophages are recruited into developing tissues where they support organogenesis with trophic factors such as WNT, VEGF and PDGF. While macrophage subsets have been described in different tissues at single cell resolution, little is known about transcript isoforms and proteoforms that underpin their differentiation and function. Here we assessed enhancer, promoter, transcript and proteomic variation as pluripotent stem cells differentiate to macrophages, identifying over 200 previously uncharacterised genes and over 20,000 new mRNA isoforms, updating our current understanding of the human genome, its regulation and potential output. Newly discovered myeloid-expressed transcripts and proteins were enriched for motifs associated with secreted proteins, and these included previously uncharacterised isoforms of growth factors, in which we predict N-terminal changes impact on their location and function. Activation of primary adult monocytes and monocyte-derived macrophages was also characterised by the expression of diverse transcript isoforms, largely arising from alternate transcription initiation sites and predicted to impact on the acute response to bacterial or fungal stimuli. Understanding the full spectrum of gene products expressed by these cells further extends our understanding of the phenotypic plasticity and trophic potential of macrophages in human development and may lead to the discovery of new clinical targets for tissue engineering or immune-related studies. Graphical AbstractIn this manuscript, Berrocal-Rubio and colleagues examined the differentiation of human macrophages using an iPSC model of tissue macrophage biology. Combining long-read sequencing technology with promoter profiling identified over 17, 700 genes implicated in pluripotency-myeloid specification. 7% of transcripts profiled from previously characterised genes were predicted to encode new proteins, and a further 3% of transcripts were derived from genes newly discovered in this project. They confirmed that a high proportion of these alternate transcripts were detectable in primary monocytes but also discovered that activation of primary monocytes led to further alternate promoter usage, with the potential to further diversify the innate immune responses to a broad set of pathogens. The newly described macrophage genes and transcripts encoded proteins enriched for motifs associated with secreted peptides. These data suggest that alternate transcription of macrophage genes leads to new effectors of innate immune function, that include a substantially expanded number of growth factors or secreted proteins. Created in BioRender. Berrocal, M. (2025) https://BioRender.com/d0n47le O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC="FIGDIR/small/703142v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@454cf0org.highwire.dtl.DTLVardef@1be28e8org.highwire.dtl.DTLVardef@16fb2e8org.highwire.dtl.DTLVardef@4aca30_HPS_FORMAT_FIGEXP M_FIG C_FIG

Current retinal pigment epithelium (RPE) cell replacement strategies in trials for age-related macular degeneration (AMD) are based on either pluripotent stem cell (PSC) or adult RPE stem cell (RPESC) sources. We used Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) to simultaneously assess single-cell transcriptomic and surface protein information, comparing these two RPE sources. Both RPESC-RPE and PSC-RPE expressed key RPE markers and exhibited cellular heterogeneity. However, RPESC-RPE had higher expression of genes related to mature retinal functions, whereas PSC-RPE had greater expression of genes involved in stem cell development and differentiation. We identified two surface proteins that distinguished the cell types. The "dont eat me" signal, CD24, was detected robustly on adult RPESC-RPE cells, while CD57 was detected on most PSC-RPE cells. The differences in gene and surface protein expression suggest that the two RPE sources differ in functional, adhesion, and immunomodulatory properties, which may impact transplantation outcomes.

Human induced pluripotent stem cells (hiPSC) and iPSC-differentiated neural cells, in combination with CRISPR editing, are commonly used for studying neurodevelopmental and other brain disorders. Female iPSCs undergo random X-chromosome inactivation (XCI) via epigenetic silencing by noncoding X inactive specific transcript (XIST). It is known that female iPSCs may lose XIST expression, leading to XCI erosion that affects both X-linked and autosomal gene expression. However, the effects of CRSIPR editing and neural differentiation on XCI erosion in iPSC-derived neurons and how this may confound a real-world transcriptomic analysis of differentially expressed genes (DEGs) are poorly understood. Here, leveraging bulk RNA-seq of hundreds of CRISPR-edited female iPSC lines from four donor lines for 66 genes and single-cell RNA-seq of iPSC-derived neurons of a subset of 42 edited genes, we investigated the effects of XCI erosion during CRISPR editing and in iPSC-derived neurons. We found that XCI erosion was variable in CRISPR-edited female iPSCs and largely preserved in iPSC-derived neurons. Like in iPSCs, XIST in neurons predominately influenced the expression of X-linked genes; however, its effect on autosomal genes was more pronounced in single neurons. Mechanistically, XIST epigenetically causes allelic imbalance of both X-linked and autosomal genes, with the former showing stronger allele-specific expression (ASE) bias. Notably, XIST-induced ASE bias exhibited a conserved positional pattern at loci affecting neurodevelopmental genes across different female lines and cell types. Finally, we demonstrated a confounding effect of XCI erosion on DEG analyses in iPSC-derived neurons. These results have significant implications in hiPSC modeling of neurodevelopmental and other brain disorders.

Mueller glial reprogramming studies demonstrate that mammalian Mueller glia can be induced to proliferate and/or engage in neural differentiation, as occurs naturally in teleost fish. A major objective is the identification of combined strategies that promote both robust proliferation and neurogenesis. These studies would benefit from a translatable screening platform that enables controlled perturbation, maintained tissue context and longitudinal analysis, such as 3D culture for first tier analysis of reprogramming strategies. Here, we validate a 3D retinal culture for Mueller glial reprogramming studies by recapitulating key signatures of an in vivo reprogramming paradigm. Next, we find that electrical stimulation (E-stim) as a tunable, extrinsic cue is sufficient to activate endogenous Ascl1 expression, indicating a state transition favorable for neurogenesis, while Mueller glia-specific p27Kip1 inactivation promotes robust, prolonged proliferation. Utilization of the lineage-tracing proliferation-history reporter H3.1-iCOUNT enabled longitudinal proliferation analysis and assessment of reprogramming outcomes within the proliferative, Mueller-derived population. With this model, we find that E-stim and p27Kip1 inactivation in combination (ESPI) increases proliferation, endogenous Ascl1 expression, and neurogenesis of Mueller-derived cells across modalities. Together, this work establishes a 3D culture framework for discovery of combinatorial reprogramming strategies within a proliferative context and identifies ESPI as an efficient approach to proliferative, neurogenic Mueller glial reprogramming.

Human pluripotent stem cell (hPSC)-derived retinal organoids provide an in vitro system for generating retinal ganglion cells (RGCs), yet the cellular composition and developmental fidelity of RGC-enriched cultures remain insufficiently characterised. Here, we tested an RGC-enriched approach involving dissociation of hPSC-derived retinal organoids at day 40, corresponding to peak expression of RGC markers, followed by two-dimensional culture conditions intended to enrich for RGC survival. Flow cytometry was used to assess the expression of RGC markers, including POU4F, ISL1, SNCG, and THY1. Across four samples, POU4F expression ranged from 79-95%, ISL1 from 18-58%, SNCG from 22%-91% and THY1 from 3%-29%, indicating substantial variability between markers and samples. Single-cell RNA sequencing analysis of 73,642 cells identified multiple retinal lineages, including retinal progenitors, RGCs, photoreceptor-committed cells, amacrine and horizontal cells, and retinal pigment epithelium (RPE), as well as off-target populations comprising HOX-enriched posterior neural cells and other cell types. Cellular composition varied across samples. Transcriptomically defined RGCs accounted for 19-45% of cells across samples, with different subtypes identified. These findings indicate that marker-based assessments alone may overestimate RGC identity and provide a detailed single-cell characterisation of cellular heterogeneity in RGC-enriched retinal organoid cultures.

Parvalbumin-expressing cortical interneurons play a critical role in maintaining the balance between excitatory and inhibitory signalling and are essential for cognition, with dysfunction implicated in numerous brain disorders. Although human pluripotent stem cells have enabled the generation of diverse human neuronal types in vitro, including cortical interneurons, parvalbumin-expressing interneurons - unlike somatostatin-expressing interneurons - remain difficult to generate reliably and consistently. Here, we demonstrate the efficient and reproducible generation of parvalbumin-expressing cortical interneurons in vitro within 50 days of differentiation. Parvalbumin mRNA and protein were detected without forced gene expression, cell sorting, rodent co-culture or intracerebral transplantation, approaches commonly required by previous protocols. Single-cell transcriptomic analyses validated neuronal identity and authenticity, revealing enrichment for gene expression signatures of parvalbumin-expressing cortical interneurons in vivo. Together, these findings establish a robust method that facilitates interneuron research by enabling the reliable generation of authentic human parvalbumin-expressing cortical interneurons within a short time frame. eTOC blurbAzzouni et al. present a rapid and reproducible protocol for generating authentic human parvalbumin-expressing cortical interneurons from pluripotent stem cells in just 50 days, without forced gene expression or co-culture. Single-cell transcriptomics confirm robust acquisition of in vivo-like PVALB interneuron identity, enabling new opportunities for human interneuron research. HighlightO_LIOptimising SHH and WNT modulators enables consistent PVALB interneuron generation. C_LIO_LI10% of cells express PVALB mRNA within 50 days of 2D differentiation from hPSCs. C_LIO_LIPVALB expression occurs without gene forcing, sorting, co-culture or grafting. C_LIO_LIComparison of gene expression to in vivo interneurons confirms PVALB authenticity. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=192 SRC="FIGDIR/small/710579v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1a53d13org.highwire.dtl.DTLVardef@14cd131org.highwire.dtl.DTLVardef@3a0f9corg.highwire.dtl.DTLVardef@1d7034d_HPS_FORMAT_FIGEXP M_FIG C_FIG