Abstract
The maturation of human pluripotent stem cell (hPSC)-derived neurons mimics the protracted timing of human brain development, extending over months to years for reaching adult-like function. Prolonged in vitro maturation presents a major challenge to stem cell-based applications in modeling and treating neurological disease. Therefore, we designed a high-content imaging assay based on morphological and functional readouts in hPSC-derived cortical neurons which identified multiple compounds that drive neuronal maturation including inhibitors of lysine-specific demethylase 1 and disruptor of telomerase-like 1 and activators of calcium-dependent transcription. A cocktail of four factors, GSK2879552, EPZ-5676, N-methyl-d-aspartate and Bay K 8644, collectively termed GENtoniK, triggered maturation across all parameters tested, including synaptic density, electrophysiology and transcriptomics. Maturation effects were further validated in cortical organoids, spinal motoneurons and non-neural lineages including melanocytes and pancreatic β-cells. The effects on maturation observed across a broad range of hPSC-derived cell types indicate that some of the mechanisms controlling the timing of human maturation might be shared across lineages.
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Main
Recent advances in hPSC differentiation enable the derivation of a myriad of specific subtypes of neurons on demand. However, the application of this technology remains hampered by the slow maturation rates of human cells, resulting in prolonged culture periods for the emergence of disease-relevant phenotypes. Indeed, most neurological and psychiatric disorders manifest as impairments in postnatal or adult neuron functions such as synaptic connectivity1, dendritic arborization2 and electrophysiological function3. Therefore, develo** strategies to accelerate the maturation of hPSC-derived neurons is critical to realize their full potential in modeling and treating neural diseases.
Multiple cell-extrinsic factors have been identified as contributors to neuron maturation, including glial cells4, network activity5 and neurotrophic factors6. However, within a given microenvironment, cell-intrinsic maturation rates appear dominant and determined by a species-specific molecular clock, which runs particularly slowly in human neurons7,8. For example, the maturation of hPSC-derived cortical neurons transplanted into the develo** mouse brain follows human-specific timing, requiring 9 months to achieve mature, adult-like morphologies and spine function9. Similarly, the transplantation of mouse versus pig versus human midbrain dopamine neurons into the brain of Parkinsonian rats results in graft-induced functional rescue after 4 weeks, 3 months or 5 months, respectively, indicating that transplanted cells retain their intrinsic, species-specific, in vivo maturation timing rather than adopting the timing of the host10.
In the present study, we established a multi-phenotypic, image-based assay to monitor maturation in nearly pure populations of hPSC-derived, deep-layer cortical neuron cultures and applied it to screen 2,688 bioactive compounds for drivers of maturation. Among the screening hits, compounds targeting chromatin remodeling and calcium-dependent transcription were combined into a maturation cocktail that was effective across a broad range of maturation phenotypes and multiple cell types.
Results
High-content assay of neuron maturity
The phenotypic complexity of neurons makes single-readout assays unsuitable to fully capture maturation stages. Therefore, we used a multi-phenotype approach (via high-content screening (HCS)) to design an assay that monitors multiple features of neuronal maturation in parallel (Fig. 1a). Dendritic outgrowth is a widely used parameter of neuron maturity11 and can be monitored through automated tracing of microtubule-associated protein 2 (MAP2) immunostaining (Fig. 1b,c). Changes in nuclear size and morphology are also characteristic of neuron development and maturation12 and can be tracked via DAPI counterstaining (Fig. 1b,c). As an indirect measurement of neuronal function and excitability, we quantified the nuclear expression of immediate early gene (IEG) products FOS and early growth response (EGR)-1 after 2 h of KCl stimulation (Fig. 1b,d). IEGs are defined by their rapid induction without requiring new protein synthesis by stimuli that include sustained membrane depolarization in neurons13. In contrast to more traditional measures of neuronal activity such as calcium imaging and electrophysiology, IEG immunoreactivity is readily scalable as a readout for thousands of treatment conditions. However, IEGs can be triggered by stimuli other than neuronal activity, including growth factor signaling14 and cellular stress responses15. Therefore, to avoid direct activation of IEGs, we used transient compound treatment (days 7–14) and performed all measurements after removal of compounds, followed by culture in compound-free medium for an additional 7 d (days 14–21) before analysis (Fig. 1a). Furthermore, we recorded IEGs under both basal and KCl-stimulated conditions to specifically determine the depolarization-induced signal by subtracting the baseline from KCl-induced responses. Measuring maturation readouts only after compound withdrawal enabled the identification of hits that trigger a long-lasting ‘memory’ of a maturation stimulus even 1 week after compound withdrawal.
a, Outline of screening protocol in hPSC-derived excitatory cortical neurons. 2SMAD-I, dual-SMAD inhibition. b, Example of input immunofluorescent images. Top, unstimulated neurons at day 21 post-plating. Bottom, neurons that received 50 mM of KCl 2 h before fixation. c, Automated analysis of neuron morphology. Left, nuclei detection mask from the DAPI channel. Right, automated neurite tracing from the MAP2 channel. d, Quantification of neuron excitability by applying an intensity threshold to FOS and EGR-1 channels within the nuclear mask. e, Left, PCA of screened compound library computed from six maturity parameters: nucleus area, nucleus roundness, total neurite length, number of neurite segments, FOS+ cell fraction and EGR-1+ cell fraction (z-scores averaged from n = 2 independent screens). Left, PCA plot of 2,343 nontoxic library compounds (out of 2,688 total compounds tested) with phenotypic clustering of maturation-enhancing (orange), maturation-inhibiting (blue) and non-neuronal proliferation-enhancing (gray) compounds. PC1 is primarily driven by the results from IEG induction and neurite growth, whereas PC2 is mainly driven by the nuclear size/roundness data. Right, representative screen images and ten representative hit compounds within each cluster. Scale bars, 50 μm.
Although these readouts are pan-neuronal, and therefore appropriate across different neuronal lineages, we chose cortical neurons for the screen for both technical and biological reasons. Cortical neurons can be derived at high efficiency in the absence of expensive recombinant proteins and their even cell distribution in two-dimensional (2D) culture, free of clusters, makes them amenable to high-throughput imaging. They also represent a brain region that follows a particularly protracted timing of development and a region of great importance to human neurological disease. Our cortical neuron differentiation protocol yields enriched populations of post-mitotic deep-layer T-brain 1-positive (TBR1+) cells, which can be scaled, cryopreserved and directly thawed for use in large-scale assays (Supplementary Fig. 1a–e). To benchmark assay performance in mature cells, we employed primary embryonic rat cortical neurons, which quickly and reliably develop mature-like functionality in vitro16. At 14 d after plating, rat neurons displayed large and round nuclei (130 μm2, 0.93 roundness index), extensive neurite growth (>2,500 μm per neuron) and almost 100% of the neurons showed KCl-induced IEG responses (Supplementary Fig. 1f–j). In contrast, in hPSC-derived cortical neurons, these properties only very gradually emerged over a 50-d culture period and never reached the maturity of their rodent counterparts (Supplementary Fig. 1k–n). These results indicate that our multi-phenotypic assay reliably captures aspects of maturation in rat and hPSC-derived cortical neurons.
Chemical screen for maturation enhancers
We next applied our maturity assay to screen a library of 2,688 bioactive compounds in hPSC-derived cortical neurons (Supplementary Fig. 2a). The library was applied at 5 μM and standard scores (z-scores) of duplicate screen runs were averaged for analysis. Viability was determined by quantifying intact nuclei and 325 toxic compounds with a viability z-score <−2 were excluded from further analysis (Supplementary Fig. 2b). For HCS hit selection, we applied principal component analysis (PCA) to six maturity z-scores to identify hit patterns for compounds, avoiding single threshold hit discrimination (Fig. 1e, left). The six parameters were: nucleus size and roundness, total neurite length and branching (number of segments per cell), and fractions of KCl-induced FOS+ and EGR-1+ cells. We identified three phenotypic clusters of compounds by PCA: maturation enhancers (hits); maturation suppressors, consisting mostly of inhibitors of the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT)/mechanistic target of rapamycin (mTOR) axis; and inducers of proliferation of a non-neuronal contaminant population, which were highly enriched for transcription growth factor (TGF)-β signaling inhibitors as well as inhibitors of ρ-associated protein kinase (ROCK) and other signaling pathways (Fig. 1e, right). We selected 32 compounds within the mature cluster (PC1 > 4) for validation. Although PCA identifies compounds with the greatest overall maturation effect, we reasoned that compounds with strong effects on single parameters could also be of interest. We therefore added the top five highest scoring compounds for each, total neurite length and double FOS+/EGR-1+ cells, excluding compounds already selected by PCA (Supplementary Fig. 3a). As single-parameter readouts are susceptible to false positives, we excluded drugs with known maturation-independent effects, such as the microtubule stabilizers docetaxel and paclitaxel. Neurite-only hits included inhibitors of Aurora kinase, in agreement with recent phenotypic screens targeting this phenotype17,18. Using such combined criteria, we selected 42 primary hits for follow-up studies (Supplementary Table 1).
To validate primary hits, the 42 compounds were subjected to the maturity assay in triplicate at the screening concentration (5 μM) and ranked by their effect on 4 maturity parameters: nucleus size and roundness, total neurite length and double positivity for KCl-induced FOS/EGR-1 cells (Supplementary Fig. 3b). The 22 compounds with the highest mean normalized score over dimethyl sulfoxide (DMSO) across all parameters underwent additional dose–response studies (Fig. 2a), resulting in the identification of four compounds with the most pronounced, dose-dependent effects on the mean maturation score (Fig. 2b). These compounds consisted of two inhibitors of lysine-specific demethylase 1 (LSD1/KDM1A), an inhibitor of disruptor of telomerase-like 1 (DOT1L) and an L-type calcium channel (LTCC) agonist. As the screen was run at a concentration susceptible to off-target effects, we conducted dose–curve experiments including independent compounds targeting DOT1L and LTCC, observing dose-dependent improvements across all maturation parameters (Supplementary Fig. 4). The identification of two additional LSD1 inhibitors as hits in the primary screen obviated this step for this target.
a, Ranking of primary hits by the mean of four maturity parameters (nucleus size and roundness, neurite length and KCl-induced double FOS+/EGR-1+ cells) normalized to DMSO (n = 3 microplate wells). The 22 top-ranked compounds were selected for validation. b, Dose–response validation of 22 screen hits comparing the mean of 4 maturity parameters normalized to DMSO (n = 15 microplate wells from 3 independent differentiations). c–f, Comparison of confirmed hits GSK2879552 (G), EPZ-5676 (E), Bay K 8644 (K) and a combination of the three (G + E + K) across maturity parameter IEG induction (c), neurite growth (d), nucleus size (e) and nucleus area (f) (n = 8 microplate wells from 2 independent experiments). g–j, Comparison of three-hit drug combination (G + E + K) to the same with the addition of NMDA across maturity parameter IEG induction (g), neurite growth (h), nucleus size (i) and nucleus roundness (j) (n = 8 microplate wells from 2 independent differentiations). k, Top, representative images of cortical neurons treated with DMSO or maturation-promoting cocktail GENtoniK. Bottom, formulation of GENtoniK. In a and b, Brown–Forsythe and Welch’s ANOVA with Dunnett’s T3 multiple-comparison test were used. In c–j, two-tailed Welch’s t-test was used; asterisks indicate statistical significance. Mean values are represented by a bar graph (a) or a line (c–j). Error bars represent s.e.m. Scale bars, 50 μm.
Small-molecule cocktail promotes neuron maturity
LSD1 is a histone 3 demethylase at lysines 4 and 9, and a switch of specificity between these two substrates has been previously linked to neuron differentiation19,20. DOT1L is the sole methyltransferase targeting lysine 79 within the globular domain of histone 3 (ref. 21). LTCCs are involved in calcium-dependent transcription and play important roles in neuron development22. We reasoned that transcriptional induction by the LTCC agonist might act independently and further potentiate the effect of chromatin remodeling by epigenetic regulators such as LSD1 and DOT1L. Accordingly, we next sought to determine whether a combination of hits can further enhance neuron maturation. As two of the confirmed hits target LSD1, we decided to pursue only one of them, GSK2879552, for combinatorial experiments, because it displayed a stronger combined effect than OG-L002 (Fig. 2b). A combination of the three-hit compounds significantly increased IEG induction, neurite growth and nucleus size, but not nucleus roundness, compared with single-compound treatments (Fig. 2c–f).
In addition to LTCCs, calcium-dependent transcription is initiated through activation of N-methyl-d-aspartate (NMDA)-type glutamate receptors23, which have also been shown to participate in neuron maturation24. The compound NMDA itself was among the primary hits but, although significant, it was not among the 22 top hits in the single-agent validation study (Fig. 2a). Given its known role in activity-dependent transcription, we next tested whether the addition of NMDA could further enhance maturation in the presence of the above three-hit combination. We observed significant improvements across all maturity parameters (Fig. 2g–j) and nominated the resulting four drugs (GSK2879552, EPZ-5676, NMDA and Bay K 8644) as a maturation-promoting cocktail, naming it GENtoniK (Fig. 2k).
Dysregulation of both histone methylation and calcium signaling can be associated with toxicity in neurons. To determine potentially harmful effects of GENtoniK on neuronal cultures, we conducted viability and cellular stress assays in cortical neurons from WA09 human embryonic stem cell (hESC) and GM03348-induced hPSC (hiPSC) lines. Neither individual compounds nor the complete GENtoniK cocktail increased cell death compared with DMSO in a 21-d time-course analysis measuring plasma membrane integrity at the end-point (Supplementary Fig. 5a,b). In fact, a resazurin-based assay resulted in a slightly improved viability (Supplementary Fig. 5c), possibly owing to higher respiratory rates of treated neurons caused by increased surface area and metabolism. As a readout of double-strand DNA breaks, we quantified nuclear foci containing phosphorylated ATM (serine/threonine kinase), observing no difference between DMSO and GENtoniK neurons (Supplementary Fig. 6a, at 24 h post-treatment, and Supplementary Fig. 6c, at 24 h and 7 d post-treatment), but a dramatic increase in those treated with the radiomimetic drug bleomycin as a positive control. To assess potential copy number aberrations (CNAs) induced by GENtoniK treatment, we conducted shallow whole-genome sequencing (WGS), observing no difference in copy number profiles of GENtoniK- and DMSO-treated neurons (Supplementary Fig. 6c). GENtoniK also did not cause obvious aberrations in chromatin nuclear localization, as revealed by staining for markers of heterochromatin and active chromatin H3K9me3 and H3K9ac (Supplementary Fig. 6d). Similarly, there was no loss of H3K9me3 intensity or percentage positive cells by flow cytometry upon GENtoniK treatment (Supplementary Fig. 6e–h).
GENtoniK promotes functional neuron maturation
We next validated GENtoniK on additional maturation phenotypes, independent of those assayed during primary screening. Establishing independent functional readouts was particularly important, because three of the proteins targeted by the cocktail have been reported to directly participate in IEG induction in neurons25,26,https://www.brainspan.org), genes upregulated by GENtoniK displaying an average expression that increased from early development to gestation and after birth (top). trim., trimester. Genes downregulated display higher average expression during early development and decrease over time (bottom). The black line represents smoothed mean curves with bands representing confidence intervals. In c, e–g and i–k, two-tailed Welch’s t-test was used; asterisks indicate statistical significance. Mean values are represented by a black line (c) or a bar graph (e–g and i–k). Error bars represent s.e.m.
Neurite quantification in our screen relied on the dendrite-specific marker MAP2. We next asked whether GENtoniK also enhances axonal maturation. Formation of the axon initial segment (AIS) has been used as a maturation marker in cortical neurons29. However, we observed that, in our neurons, an ANK3+ AIS is present even in untreated neurons at 21 d from plating, suggesting that it is not a limiting factor in maturation (Supplementary Fig. 8a). Expression of the pathologically relevant, four-repeat tau isoform is a feature of axonal maturity and important for disease modeling whereas the shorter three-repeat isoform is expressed during early fetal development30. Western blotting revealed increased levels of four-repeat tau in GENtoniK-treated neurons when normalized to both total tau and glyceraldehyde 3-phosphate dehydrogenase levels (Supplementary Fig. 8b–d).
Intrinsic electrophysiological features, such as passive membrane properties and the ability to fire action potentials (APs), are important functional indicators of neuronal maturation31. To assess the effect of the drug cocktail on membrane properties and excitability, we performed whole-cell, patch-clamp recordings in cortical neurons at day 28 from plating. Similar to the IEG studies, treatment was withdrawn 7 d before recordings to ensure that differences were maturation mediated and not a direct effect of NMDA or Bay K 8644. Over 90% of GENtoniK-treated neurons displayed evoked APs compared with <40% of control neurons (Fig. 3d). Among AP-firing neurons, those treated with GENtoniK displayed higher firing frequencies (Fig. 3e) and lower AP thresholds (Fig. 3f). Despite lower resting membrane potential in treated neurons (Fig. 3g), their values were still distant from the physiological range of −60 mV to −70 mV reported for the cortex in vivo32. These results indicate that GENtoniK significantly promotes excitability, but that additional, including extrinsic, factors may be required to achieve more mature resting membrane properties. Finally, to probe for functional consequences of enhanced synaptic marker expression in GENtoniK-treated neurons (Fig. 3a–d), we recorded spontaneous excitatory postsynaptic currents (sEPSCs) and found that treated neurons displayed increased sEPSC amplitudes when recorded at either –60 mV or at 0 mV (Fig. 3h–j). GENtoniK-treated neurons displayed more pronounced, synchronized bursts of sEPSCs (Fig. 3k) as further evidence of enhanced synaptic maturation.
GENtoniK induces immature to mature shift in transcription
We next conducted RNA sequencing (RNA-seq) to assess global changes in gene expression induced by GENtoniK. In accordance with a dual effect of the cocktail on chromatin state and calcium influx, we treated hPSC cortical neurons with either of the two epigenetic factors, the two compounds affecting calcium signaling or the full GENtoniK cocktail (Supplementary Fig. 9a). Genes differentially expressed in GENtoniK were similarly regulated by treatment with the two epigenetic drugs, but to a lesser magnitude, which is consistent with the hypothesis that calcium influx potentiates transcriptional changes facilitated by chromatin remodeling (Supplementary Fig. 9b–d). Although both calcium signaling modulators were identified as maturation enhancers in our protein-based screen, their combined effect on gene expression was modest 7 d after treatment withdrawal (Supplementary Fig. 9b).
Gene ontology (GO) analyses of transcripts downregulated by GENtoniK revealed enrichment in immature, early, post-mitotic neuron functions, including migration and axon guidance, as well as transcriptional regulation (Fig. 3l and Supplementary Fig. 9e). Upregulated genes were enriched for transcripts related to mature neuron function, including chemical synaptic transmission and transmembrane ion transport (Fig. 3l and Supplementary Fig. 9f). Although previous studies indicate a switch from glycolytic to oxidative metabolism in maturing neurons33,34, we observed enrichment in both glycolysis and oxidative phosphorylation, as well as fatty acid metabolism in treated cells (Supplementary Fig. 10).
To match the transcriptional data with temporal changes in gene expression during cortical neuron development in vitro, we plotted differentially expressed genes against the CORTECON dataset35. Genes upregulated by GENtoniK showed a time-dependent increase in expression on extended in vitro culture (Fig. 3m), as expected for maturation-related transcripts. However, the CORTECON data do not allow precise staging of GENtoniK-treated neurons. To match in vitro transcriptional data with in vivo changes in gene expression, we mapped differentially expressed genes against the BrainSpan Transcriptome database of the Develo** Human Brain36. Most genes upregulated by GENtoniK showed an increase in gene expression from early to late gestation (Fig. 3n, top). In contrast, genes downregulated by the treatment were more highly expressed during early embryonic brain development, with decreasing levels toward birth and postnatal stages (Fig. 3n, bottom). There were no changes in markers of neuronal and glial subtype identity in GENtoniK-treated neurons (Supplementary Fig. 11a).
Recent studies reported transcriptional signatures of cell stress that may interfere with the development and maturation of cortical organoids37. Gene expression analysis in GENtoniK-treated neurons did not reveal any enrichment for genes associated with the integrated stress response (Supplementary Fig. 11b). Finally, neuronal maturation has been linked to developmental switches from fetal to adult variants of specific transcripts. One such example is the switch from NMDAR subunits GRIN2B to GRIN2A38. Our RNA-seq results revealed significant decreases in the fetal GRIN2B subunit in GENtoniK-treated neurons from three of four independent hPSC lines. However, we did not observe a significant upregulation of the adult GRIN2A subunit (Supplementary Fig. 11c), suggesting that longer-term GENtoniK treatment, more extended culture periods or additional factors may be required to trigger a complete switch to adult-like NMDAR subunits.
We next performed CUT&RUN chromatin profiling on histone marks downstream of the epigenetic factors targeted by the cocktail. Although LSD1 can switch its substrate to H3K9 in the mature neuron-specific variant, we focused on its canonical target H3K4, reasoning that maturation-enhancing inhibition probably targets the immature form. H3K4me2 was widespread in the genome, with the highest enrichment in the promoter region and near the transcription start site (Supplementary Fig. 12a). In contrast, H3K79me2 was enriched at a much smaller subset of genes, where it extended into the transcribed region (Supplementary Fig. 12b). Both H3K4 and H3K79 2-methylation were more highly enriched at GENtoniK-downregulated versus GENtoniK-upregulated genes (Supplementary Fig. 12c). Genes associated with H3K79 peaks showed near-identical ontology enrichment to those downregulated with GENtoniK by RNA-seq, including terms for neuron migration, chromatin modification and RNA-processing gene categories (Supplementary Fig. 12d–g). Chromatin-regulating genes associated with H3K79me2 peaks include the GENtoniK target LSD1 (Supplementary Fig. 12f), whereas messenger RNA-processing genes with H3K79me2 peaks, such as NOVA2 and CELF1 (Supplementary Fig. 12g), are known to participate in cortical neuron development39,40. These results indicate that H3K79 methylation may play a role in maintaining immature gene expression programs and that loss of this mark might facilitate neuronal maturation in GENtoniK-treated cells.
GENtoniK enhances maturation across neuronal culture systems
We next tested the efficacy of GENtoniK across additional hPSC lines and hPSC-derived cell types. As our primary screen was carried out in a female hESC line H9 (WA09), we first replicated key maturation readouts in cortical neurons derived from male and female induced PSC (iPSC) lines. We confirmed the effect of GENtoniK on both IEG induction and neurite outgrowth across iPSC lines from five donors (Supplementary Fig. 13a–e). Functional maturation was assessed by validating changes in synaptic markers and changes in maturation-associated gene expression. We observed a robust increase in total number of assembled synapses relative to DMSO controls in GENtoniK-treated neurons across iPSC lines (Supplementary Fig. 14a–c). Finally, bulk RNA-seq analysis of iPSC neurons showed an upregulation in gene expression pathways associated with maturation, including chemical synaptic transmission, and downregulation of genes associated with immature post-mitotic neurons, including axon guidance (Supplementary Fig. 15a,c,e). Comparison with the Brainspan Human Developmental Atlas (Brainspan.com) showed that genes upregulated by GENtoniK were enriched in postnatally associated transcripts, whereas genes downregulated by GENtoniK were primarily associated with early prenatal development (Supplementary Fig. 15b,d,f). Collectively, these results confirm that GENtoniK promotes the maturation of hPSC-derived neurons, independent of biological sex or hESC versus iPSC origin.
Alternative maturation strategies are routinely employed in neuronal cultures, including the addition of trophic factors such as brain-derived neurotrophic factor (BDNF), and the use of culture medium with more physiological levels of glucose and ion concentrations (BrainPhys)41. We conducted time-course experiments to assess the efficacy and compatibility of GENtoniK with existing maturation approaches. GENtoniK in standard neurobasal medium (without neurotrophic factors) robustly induced several neuronal maturation parameters at levels above control or BrainPhys plus BDNF conditions. Treatment with GENtoniK in combination with BrainPhys and neurotrophic factors showed an additional, albeit modest, increase in maturation (Supplementary Fig. 16). More detailed electrophysiological and transcriptional studies will be required to fully define the complementary and synergistic effect of GENtoniK and BrainPhys on neuronal maturation.
Self-organizing 3D culture systems such as neural organoids have become a widely used model system to study human brain development and disease. Similar to 2D culture systems, human 3D organoids are subject to slow maturation rates42. We observed that forebrain organoids treated with GENtoniK, from day 15 to day 50 of derivation, displayed an increased density of SYN1 puncta (Fig. 4a,b), decreased expression of immature neuron marker DCX (Supplementary Fig. 17a) and increased number of cells with nuclear expression of EGR-1 and FOS (Fig. 4c,d and Supplementary Fig. 17a) at day 60 without inducing obvious changes in the cortical layer identity (Supplementary Fig. 17b). For these studies, organoids were not subjected to KCl stimulation before IEG immunostaining, thus indicating higher levels of spontaneous activity after GENtoniK treatment. To confirm this effect functionally, we next conducted calcium imaging in intact organoids loaded with the calcium indicator Fluo-4 AM. In agreement with the IEG results, regions of interest (ROIs) within GENtoniK-treated organoids displayed an increased number of spontaneous calcium spikes (Fig. 4e,f and Supplementary Videos 1 and 2).
a–f, GENtoniK treatment inducing synaptogenesis and spontaneous activity in cortical organoids. a, Representative images of immunofluorescent staining for SYN1 and MAP2 in day-60 organoids. b, Quantification of total SYN1 puncta per field (n = 8 cryosections randomly sampled from n = 20 organoids). c, Representative images of immunofluorescence staining for EGR-1 and MAP2 in unstimulated day-60 organoids. d, Quantification of EGR-1+ cells per field (n = 8 cryosections randomly sampled from n = 20 organoids). e, Representative confocal images with ROI traces of calcium imaging with Fluo-4 AM in whole day-60 cortical organoids that received treatment with DMSO (left) or GENtoniK (right). Traces show a 20-min time course captured at 0.2 ps. The red lines represent counted spikes. f, Quantification of total spikes per ROI in 20-min recordings of Fluo-4 AM calcium transients (n = 45 DMSO ROIs and 47 GENtoniK ROIs from 4 organoids per condition). g–m, GENtoniK promoting maturation of hPSC-derived SMNs. g, Representative high-content maturation assay images of ISL1/2+ SMNs (day 40 of hPSC differentiation). h–j, Quantification showing GENtoniK-improved KCl-induction of FOS+ cells (h), total neurite length (n = 12 for both conditions) (i) and nucleus area (n = 12 for both conditions) (j) in SMNs (n = 12 for DMSO and n = 11 for GENtoniK). k–m, GENtoniK treatment increasing firing rates and inducing spontaneous bursting activity on SMNs plated on high-density multielectrode arrays. k, Sample single-channel trace of GENtoniK-treated SMNs illustrating spike detection. l, Time-course analysis of average firing rates in SMNs plated on high-density microelectrode arrays (HD-MEAs), calculated from 60 s of activity in the 1/64th most active electrodes (n = 128 electrodes from 2-MEA probes). m, Representative 60-s spike rastergrams (top) and average firing rates (middle) of SMNs plated on HD-MEAs. Only GENtoniK-treated SMNs displayed spontaneous bursting events (orange bars). Bottom, array heatmap of a 4-s bursting event. In b, d, f, h–j and l, two-tailed Welch’s t-test was used. Asterisks indicate statistical significance. Mean values are represented by a black line. Errors represent s.e.m. Scale bars, 50 μm.
We next addressed whether the treatment could drive the maturation of hPSC-derived neurons outside the forebrain by deriving spinal motoneurons (SMNs). ISL1+ SMNs treated with GENtoniK displayed a highly significant increase across all the maturity parameters tested (Fig. 4g–j). We observed that SMNs exhibit robust levels of spontaneous activity when cultured on high-density multielectrode arrays (Fig. 4k). In a time-course experiment, average firing rates were increased modestly in the presence of the drug cocktail (possibly via direct ion channel activation effect). In contrast, a more pronounced effect was observed starting 6 d after treatment withdrawal, indicating that the treatment triggered a long-lasting maturation effect (Fig. 4l). Notably, only SMNs pretreated with GENtoniK exhibited highly synchronous bursts of activity in the 0.8- to 0.6-Hz range (Fig. 4m and Supplementary Video 3), reminiscent of central pattern generator activity in the embryonic spinal cord43.
GENtoniK enhances cell function in non-neuronal lineages
Slow maturation rates of hPSC-derived cells are a common problem across lineages beyond neurons. To assess the potential of GENtoniK in other cell types, we next tested neural crest-derived melanocytes, which produce the pigment melanin in a differentiation/maturation-dependent manner. The production and secretion of melanin from melanocytes is responsible for human skin and hair color, and hPSCs/melanocytes have been used to model various pigmentation disorders44. Using our established differentiation protocol, treatment of hPSC-derived melanocytes with GENtoniK, starting at day 11, induced a dramatic increase in pigmentation at day 33 of differentiation versus untreated melanocytes (Supplementary Fig. 18).
Finally, we tested GENtoniK on a cell type derived from a different germ layer, hPSC-derived. insulin-secreting, pancreatic β-like cells. These cells arise from definitive endoderm and are of great interest for develo** cell-based treatments for type 1 diabetes45. Although many protocols have been reported, one limitation is the generation of a subset of glucagon-positive (GCG+), insulin-positive (INS+) polyhormonal cells46. Flow cytometry analysis revealed that GENtoniK treatment decreased the number of GCG+ cells among INS+ cells (Supplementary Fig. 19b,c). The β-like cells treated with GENtoniK from day 20 to day 27 of differentiation displayed evidence of improved maturation, including increased total insulin content, fraction of insulin granules and KCl-induced insulin secretion at day 29 (Supplementary Fig. 19d–i). These results suggest that GENtoniK can trigger aspects of cellular function, differentiation or maturation also in non-neural lineages.