New York Stem Cell Foundation

Background: Inherited retinal dystrophies are a heterogeneous group of progressive disorders impacting photoreceptor function, often limiting the usefulness of standard electroretinography in advanced cases. Full-field stimulus test (FST) testing has become a sensitive psychophysical technique for detecting residual visual function when traditional electrophysiology is non-recordable. This study evaluated the ability of chromatic FST to differentiate rod-cone from cone photoreceptor dysfunction in patients with genetically confirmed inherited retinal dystrophies. Methods: Cross-sectional FST data were analyzed from 39 patients (mean age 45.7 ± 20.0 years) with genetically confirmed inherited retinal dystrophies at a tertiary academic center. All participants underwent standardized FST testing using white, red, and blue stimuli. Patients were classified into rod-cone dystrophy (n = 27) or cone dystrophy (n = 12) groups based on genetic and clinical criteria. Group comparisons focused on FST thresholds and especially blue-red threshold differences as markers of photoreceptor-mediated function. Bonferroni correction was applied to adjust for multiple comparisons across four primary FST parameters. Additional analyses by genotype were performed with nonparametric tests. Results: Eight different genetic mutations were represented, including Phosphodiesterase 6A (PDE6A) (n = 10), Rhodopsin (RHO) (n = 7), Phosphodiesterase 6B (PDE6B) (n = 6), Cyclic Nucleotide-Gated Channel Beta 1 (CNGB1) (n = 4), Cyclic Nucleotide-Gated Channel Alpha 3 (CNGA3) (n = 4), Nuclear Receptor Subfamily 2 Group E Member 3 (NR2E3) (n = 4), Guanylate Cyclase 2D (GUCY2D) (n = 2), and Cyclic Nucleotide-Gated Channel Beta 3 (CNGB3) (n = 2). Blue-red FST threshold differences exhibited moderate group discrimination in uncorrected analysis, with rod-cone dystrophies averaging -8.35 ± 10.37 dB and cone dystrophies -11.20 ± 14.60 dB. The area under the receiver operating characteristic curve for blue-red difference was 0.74 (95% CI: 0.59-0.90), with 75% sensitivity and 70.4% specificity at a -10 dB cutoff. However, no chromatic FST parameter maintained statistical significance between groups after Bonferroni correction. Inter-eye FST correlation was high (r = 0.758, p < 0.001), supporting test reliability. Conclusions: Chromatic FST testing provides a practical and sensitive means to assess photoreceptor function in advanced inherited retinal dystrophies, particularly when standard electrophysiologic methods are uninformative. Although the blue-red threshold difference offers moderate discrimination between rod-cone and cone dystrophies in uncorrected analysis, no chromatic parameter reached statistical significance after adjustment for multiple testing. Chromatic FST should be considered a supplementary approach for clinical monitoring and therapeutic studies in advanced retinal dystrophies, with further validation needed in larger cohorts.

Genome-wide association studies (GWAS) identified over 600 loci containing single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), most of which reside in non-coding regions. Among the set of T2D SNPs, linking causal genome variants to disease risk experimentally has remained a challenge; however, advances in synthetic mammalian genome writing techniques now enable the delivery of multiple haplotypes to human induced pluripotent stem cells (hiPSCs) to create a series of isogenic cell lines that can be differentiated and phenotyped in vitro. Here, to begin efforts in dissecting a T2D GWAS locus, we engineered an NKX6–3/ANK1 gene cluster knockout hiPSC line and introduced a landing pad facilitating the delivery of synthetic haplotype payloads. We built four haplotypes, including several that are not observed in nature, containing risk SNPs spanning the NKX6–3/ANK1 gene cluster using a method called “variant Switching Auxotrophic markers for Integration” (vSwAP-In), and integrated them precisely into hiPSCs. NKX6–3/ANK1 deletion blocked pancreatic progenitor and skeletal muscle differentiation, suggesting that NKX6–3 and ANK1 are required for early pancreatic and skeletal muscle development, and perhaps related to the existence of two nonoverlapping sets of SNPs in linkage disequilibrium that associate with the expression of the two adjacent genes. When NKX6–3/ANK1 T2D “Risk” haplotypes were reintroduced, skeletal muscle and pancreatic progenitor differentiation capabilities were restored. ANK1 expression was elevated in the ANK1 Risk and All-Risk haplotypes compared to the NKX6–3 Risk and Non-Risk haplotypes, establishing a functional experimental platform to examine risk SNP clusters in their native contexts. Overall, this work establishes a platform for the dissection of GWAS loci using synthetic haplotype genomics in hiPSCs.

Adult stem cells (SCs) transition between quiescent and active states to maintain tissue integrity, and dysregulation of this balance can lead to tissue degeneration, cancer, or premature aging. Both intrinsic factors and extrinsic niche signals influence these states; however, the molecular mechanisms that integrate extrinsic cues with intrinsic programs remain poorly understood. Here, we show that the conserved repressive histone mark, H2AK119ub, serves as a molecular switch linking inhibitory fibroblast growth factor (FGF) signals with the quiescent transcriptional program in hair follicle stem cells (HFSCs). Modulation of FGF signaling is associated with changes in H2AK119ub levels, thereby toggling HFSCs between quiescence and activation states. Mechanistically, H2AK119ub directly represses a proliferation-promoting transcriptional program preserving HFSC quiescence. Loss of H2AK119ub in HFSCs shortens the quiescent phase and induces repeated rounds of HFSC activation, ultimately leading to SC exhaustion – a hallmark of aging tissue. Analysis of other mammalian SC systems and Drosophila germline SCs confirms that H2AK119ub is a broadly conserved hallmark of quiescence and is dynamic upon SC activation. These findings reveal a signaling-epigenetic axis that controls SC quiescence and underscores the importance of the conserved role of H2AK119ub in maintaining tissue homeostasis.

Disruption of parvalbumin positive (PVALB+) cortical interneurons is implicated in the pathogenesis of schizophrenia. However, how these defects emerge during development remains poorly understood. The protracted, postnatal maturation of PVALB+ cortical interneurons has complicated human pluripotent stem cell (hPSC)-based models for studying their role in neuropsychiatric disease. Here, we present a forebrain assembloid system yielding PVALB+ cortical interneurons that match the molecular identity and distinctive electrophysiology of primary PVALB+ interneurons. We further established a series of isogenic hPSC lines carrying structural variants associated with schizophrenia and identified variant-specific phenotypes affecting cortical interneuron migration, the molecular profile of PVALB+ cortical interneurons, and their ability to regulate cortical network activity, including γ-band oscillations. These findings offer plausible mechanisms for how the disruption of cortical interneuron development may impact schizophrenia risk and provide a human experimental platform to study PVALB+ cortical interneurons in health and disease.

To compare the clinical characteristics of inherited retinal diseases (IRDs) caused by biallelic versus monoallelic variants in the RP1, BEST1, and PROM1 genes. A total of 52 patients (26 female) with genetically confirmed IRDs were retrospectively selected from the records of the Harkness Eye Institute Clinical Coordinating Center at Columbia University Irving Medical Center. In RP1, 3 individuals with biallelic variants and 22 patients with monoallelic variants classified as pathogenic or likely pathogenic were selected. In BEST1, eight individuals with biallelic variants and nine individuals with monoallelic variants classified as either pathogenic or likely pathogenic were included. In PROM1, four individuals with biallelic variants and six patients with monoallelic variants classified as pathogenic or likely pathogenic were selected. All patients underwent multimodal retinal imaging and, when available, full-field electroretinography (ffERG). In all three genes, individuals with biallelic variants had markedly earlier disease onset and more severe phenotypes. In RP1, on SD-OCT, foveal involvement was observed in all biallelic cases (3/3, 100%) and in 4/22 (18%) monoallelic cases. In BEST1, the average age of onset in the biallelic cohort was 7.12 years, and the average age was 32.7 years in the monoallelic cohort. Four of eight (50%) patients in the biallelic group were additionally found to have widespread serous lesions outside of the central macula. This finding was not observed in the monoallelic group. Three of eight (38%) biallelic BEST1 patients had moderate reductions in their photopic flicker. All monoallelic BEST1 patients had photopic responses within the normal range. PROM1 biallelic cases showed severe functional impairment on ffERG, while most monoallelic cases retained normal responses. In the biallelic cohort, four of four (100%) of patients had severely attenuated or extinguished photopic responses. In the monoallelic PROM1 group, four of five (80%) monoallelic PROM1 patients had normal photopic responses, and P2-2 had mildly attenuated photopic responses. Individuals with biallelic variants exhibited earlier disease onset, more severe retinal degeneration, and significantly reduced retinal function compared with those with monoallelic variants. These observations highlight the role of loss-of-function mechanisms in more aggressive disease courses and underscore the importance of considering zygosity when determining prognosis and planning gene-based therapies.

SummaryCellular processes including lysosomal and mitochondrial dysfunction are implicated in the development of many diseases. Quantitative visualization of mitochondria and lysosomes is crucial to understand how these organelles are dysregulated during disease. To address a gap in live-imaging tools, we developed GEM-SCOPe (genetically encoded and modular subcellular organelle probes), a modular toolbox of fluorescent markers designed to inform on localization, distribution, turnover, and oxidative stress of specific organelles. We expressed GEM-SCOPe in differentiated astrocytes and neurons from a human pluripotent stem cell PRKN-knockout model of Parkinson’s disease and identified disease-associated changes in proliferation, lysosomal distribution, mitochondrial transport and turnover, and reactive oxygen species. We demonstrate GEM-SCOPe is a powerful panel that provides critical insight into the subcellular mechanisms underlying Parkinson’s disease in human cells. GEM-SCOPe can be expanded upon and applied to a diversity of cellular models to glean an understanding of the mechanisms that promote disease onset and progression.

The role of extracellular matrix adhesion components in modulation of the treatment sensitivity of ovarian cancer (OC) cells is not well understood. Analysis of ovarian cancer TCGA gene expression data sets revealed an inverse correlation between genes involved in cell-cycle progression and extracellular matrix interactions including laminin-binding receptor integrin β4, a major component of extracellular matrix adhesion. Gene ontology analysis also showed that in patient populations with low integrin β4 expression, cell cycle-related programs were activated, while in populations with high expression of integrin β4, the activation of these cell cycle programs was lower. Suppression of proliferation with CDK4/6 inhibitor Palbociclib stimulated integrin β4 expression and induced protection against cisplatin in cells naturally expressing low levels of integrin β4. Additionally, ovarian cancer patient-derived organoids showed reduced cisplatin sensitivity when pretreated with Palbociclib. Our data also showed that integrin β4 overexpression decreased ovarian cancer cell proliferation and at the same time, attenuated cisplatin response. Our investigations reveal that expression of integrin β4 inversely correlates with cell cycle progression programs, whether observed in expression data of OC patient samples or in various OC cell lines. Consistently with these results, the overexpression of ITGB4 gene in ovarian cancer cell lines correlated with reduced cell proliferation rates and diminished sensitivity to cisplatin, supporting the idea that integrin β4 and likely its matrix ligands play critical roles in the regulation of cellular growth and chemoresistance of ovarian cancer cells.

Disruption of parvalbumin positive (PVALB+) cortical interneurons is implicated in the pathogenesis of schizophrenia. However, how these defects emerge during brain development remains poorly understood. The protracted maturation of these cells during postnatal life has made their derivation from human pluripotent stem cells (hPSCs) extremely difficult, precluding hPSC-based disease modeling of their role in neuropsychiatric disease. Here we present a cortical assembloid system that supports the development of PVALB+ cortical interneurons which match the molecular profiles of primary PVALB+ interneurons and display their distinctive electrophysiological features. Further, we characterized cortical interneuron development in a series of CRISPR-generated isogenic structural variants associated with schizophrenia and identified variant-specific phenotypes affecting cortical interneuron migration and the molecular profile of PVALB+ cortical interneurons. These findings offer plausible mechanisms on how the disruption of cortical interneuron development may impact schizophrenia risk and provide the first human experimental platform to study of PVALB+ cortical interneurons.