Search Results (1,102)

Background: Point mutations in mitochondrial DNA (mtDNA) cause a range of neurometabolic disorders that currently have no curative treatments. The m.8993T>G mutation in the Homo sapiens MT-ATP6 gene leads to neurogenic muscle weakness, ataxia, and retinitis pigmentosa (NARP) when heteroplasmy exceeds approximately 70%. Methods: We engineered a split DddA-derived cytosine base editor (DdCBE), each half fused to programmable TALE DNA-binding domains and a mitochondrial targeting sequence, to correct the m.8993T>G mutation in patient-derived induced pluripotent stem cells (iPSCs). Seven days after plasmid delivery, deep amplicon sequencing showed 35 ± 3% on-target C•G→T•A conversion at position 8993, reducing mutant heteroplasmy from 80 ± 2% to 45 ± 3% with less than 0.5% editing at ten predicted off-target loci. Results: Edited cells exhibited a 25% increase in basal oxygen consumption rate, a 50% improvement in ATP-linked respiration, and a 2.3-fold restoration of ATP synthase activity. Directed neural differentiation yielded 85 ± 2% Nestin-positive progenitors compared to 60 ± 2% in unedited controls. Conclusions: Edits remained stable over 30 days in culture. These results establish mitochondrial base editing as a precise and durable strategy to ameliorate biochemical and cellular defects in NARP patient cells. Full article

Proteomics of dystrophic muscle samples is limited by the amount of protein that can be extracted from patient biopsies. Cells and tissues derived from patient-derived induced pluripotent stem cells (iPSCs) can be an expandable alternative source. We have patterned iPSCs from three Duchenne muscular dystrophy (DMD) patient lines into skeletal muscle cells using a two-dimensional as well as our three-dimensional organoid differentiation system. Probes with sufficient protein amounts could be extracted and prepared for mass spectrometry. In total, 3007 proteins in 2D and 2709 proteins in 3D were detected in DMD patient probes. A total of 83 proteins in 2D and 338 proteins in 3D can be described as differentially expressed between DMD and control patient probes in a post hoc test. We have identified and we propose Myosin-9, Collagen 18A, Tropomyosin 1, BASP1, RUVBL1, and NCAM1 as proteins specifically altered in their expression in DMD for further investigation. Proteomics of skeletal muscle organoids resulted in greater consistency of results between cell lines in comparison to the two-dimensional myogenic differentiation protocol. Full article

Background/Objectives: Dilated cardiomyopathy (DCM) is a prevalent and life-threatening heart muscle disease often caused by titin (TTN) truncating variants (TTNtv). While TTNtvs are the most common genetic cause of heritable DCM, the precise downstream regulatory mechanisms linking TTN deficiency to cardiac dysfunction and maladaptive fibrotic remodeling remain incompletely understood. This study aimed to identify key epigenetic regulators of TTN-mediated gene expression and explore their potential as therapeutic targets, utilizing human patient data and in vitro models. Methods: We analyzed RNA sequencing (RNA-seq) data from left ventricles of non-failing donors and cardiomyopathy patients (DCM, HCM, PPCM) (GSE141910). To model TTN deficiency, we silenced TTN in human iPSC-derived cardiomyocytes (iPSC-CMs) and evaluated changes in cardiac function genes (MYH6, NPPA) and fibrosis-associated genes (COL1A1, COL3A1, COL14A1). We further tested the effects of TMP-195, a class IIa histone deacetylase (HDAC) inhibitor, and individual knockdowns of HDAC4/5/7/9. Results: In both human patient data and the TTN knockdown iPSC-CM model, TTN deficiency suppressed MYH6 and NPPA while upregulating fibrosis-associated genes. Treatment with TMP-195 restored NPPA and MYH6 expression and suppressed collagen genes, without altering TTN expression. Among the HDACs tested, HDAC5 knockdown was most consistently associated with improved cardiac markers and reduced fibrotic gene expression. Co-silencing TTN and HDAC5 replicated these beneficial effects. Furthermore, the administration of TMP-195 enhanced the modulation of NPPA and COL1A1, though its impact on COL3A1 and COL14A1 was not similarly enhanced. Conclusions: Our findings identify HDAC5 as a key epigenetic regulator of maladaptive gene expression in TTN deficiency. Although the precise mechanisms remain to be clarified, the ability of pharmacological HDAC5 inhibition with TMP-195 to reverse TTN-deficiency-induced gene dysregulation highlights its promising translational potential for TTN-related cardiomyopathies. Full article

Human induced pluripotent cells (hiPSCs), generated in vitro, represent a groundbreaking tool for tissue regeneration and repair. Understanding the metabolic intricacies governing hiPSCs is crucial for optimizing their performance across diverse environmental conditions and improving production strategies. To this end, in this work, we introduce hiPSCGEM01, the first genome-scale, context-specific metabolic model (GEM) uniquely tailored to fibroblast-derived hiPSCs, marking a clear distinction from existing models of embryonic and cancer stem cells. hiPSCGEM01 was developed using relevant genome expression data carefully selected from the Gene Expression Omnibus (GEO), and integrated with the RECON 3D framework, a comprehensive genome-scale metabolic model of human metabolism. Redundant and unused reactions and genes were identified and removed from the model. Key reactions, including those facilitating the exchange and transport of metabolites between extracellular and intracellular environments, along with all metabolites required to simulate the growth medium, were integrated into hiPSCGEM01. Finally, blocked reactions and dead-end metabolites were identified and adequately solved. Knockout simulations combined with flux balance analysis (FBA) were employed to identify essential genes and metabolites within the metabolic network, providing a comprehensive systems-level view of fibroblast-derived hiPSC metabolism. Notably, the model uncovered the unexpected involvement of nitrate and xenobiotic metabolism—pathways not previously associated with hiPSCs—highlighting potential novel mechanisms of cellular adaptation that merit further investigation. hiPSCGEM01 establishes a robust platform for in silico analysis and the rational optimization of in vitro experiments. Future applications include the evaluation and refinement of culture media, the design of new formulations, and the prediction of hiPSC responses under varying growth conditions, ultimately advancing both experimental and clinical outcomes. Full article

High variability in stem cell research is a well-known limiting phenomenon, with technical variation across experiments and laboratories often surpassing variation caused by genotypic effects of induced pluripotent stem cell (iPSC) lines. Evaluation of kidney organoid protocols and culture conditions across laboratories remains scarce in the literature. We used the original air-medium interface protocol to evaluate kidney organoid success rate and reproducibility with several human iPSC lines, including a novel patient-derived GRACILE syndrome iPSC line. Organoid morphology was assessed with light microscopy and immunofluorescence-stained maturing glomerular and tubular structures. The protocol was further adapted to four microplate-based high-throughput approaches utilizing spheroid culture steps. Quantitative high-content screening analysis of the nephrin-positive podocytes and ECAD-positive tubular cells revealed that the choice of approach and culture conditions were significantly associated with structure development. The culture approach, iPSC line, experimental replication, and initial cell number explained 35–77% of the variability in the logit-transformed proportion of nephrin and ECAD-positive area, when fitted into multiple linear models. Our study highlights the benefits of high-throughput culture and multivariate techniques to better distinguish sources of technical and biological variation in morphological analysis of organoids. Our microplate-based high-throughput approach is easily adaptable for other laboratories to combat organoid size variability. Full article

Polypharmacology in Amyotrophic lateral sclerosis (ALS) demands models that capture irreducible higher-order drug co-action. We introduce a categorical–topological pipeline that encodes regimens as truncated multicomplexes with a hypergraph–simplicial envelope; irreducible effects are identified by Möbius inversion, and CatMixNet predicts dose-response under monotone calibration while aligning multimodal omics via sheaf constraints. Under face-disjoint evaluation, omics fusion reduced RMSE from 0.164 to 0.149 (≈9%), increased PR-AUC from 0.38 to 0.44, and lowered calibration error to 2.6–3.1% with <10 dose-monotonicity violations per ${10}^3$ surfaces. Triad-irreducible signal strengthened (95th percentile ${\mathsf{\Delta }}^{★}=0.151$; antagonism retained at 24%). A risk-sensitive selector produced triads with toxicity headroom and projected ALSFRS-R slope gains of +0.04–0.05 points/month. Ablations confirmed the necessity of Möbius consistency, sheaf regularization, and monotone heads. Distilled monotone splines yielded compact titration charts with mean error 0.023. The framework supplies reproducible artifacts and actionable shortlists for iPSC and SOD1 validation. Full article

Schizophrenia is a highly polygenic and clinically heterogeneous disorder. In this paper, we first review layer-specific evidence across genetics, epigenetics, transcriptomics, proteomics, and patient-derived induced pluripotent stem cell (iPSC) models, then integrate cross-layer findings. Genetics research identifies widespread risk architecture. Hundreds of loci from common, rare, and CNV analyses. Epigenetics reveals disease-associated DNA methylation and histone-mark changes. These occur at neuronally active enhancers and promoters, together with chromatin contacts that link non-coding risk to target genes. Transcriptomics show broad differential expression, isoform-level dysregulation, and disrupted co-expression modules. These alterations span synaptic signaling, mitochondrial bioenergetics, and immune programs. Proteomics demonstrates coordinated decreases in postsynaptic scaffold and mitochondrial respiratory-chain proteins in cortex, with complementary inflammatory signatures in serum/plasma. iPSC models recapitulate disease-relevant phenotypes: including fewer synaptic puncta and excitatory postsynaptic currents, electrophysiological immaturity, oxidative stress, and progenitor vulnerability. These same models show partial rescue under targeted perturbations. Integration across layers highlights convergent pathways repeatedly supported by ≥3 independent data types: synaptic signaling, immune/complement regulation, mitochondrial/energetic function, neurodevelopmental programs and cell-adhesion complexes. Within these axes, several cross-layer convergence genes/proteins (e.g., DLG4/PSD-95, C4A, RELN, NRXN1/NLGN1, OXPHOS subunits, POU3F2/BRN2, PTN) recur across cohorts and modalities. Framing results through cross-layer and shared-pathway convergence organizes heterogeneous evidence and prioritizes targets for mechanistic dissection, biomarker development, and translational follow-up. Full article

N-glycanase 1 (NGLY1) is a cytoplasmic glycoenzyme that removes N-linked glycans from misfolded glycoproteins. It plays an important role in the endoplasmic reticulum-associated degradation (ERAD) pathway in mammalian cells. NGLY1 dysfunction in humans causes NGLY1 deficiency as a rare autosomal recessive disorder that is characterized by neurodevelopmental delay, hypotonia, movement disorders, seizures, and multi-system involvement. In this review, we summarize recent advances in understanding the neural functions of NGLY1 and the neuropathological phenotypes associated with its deficiency. We discuss the molecular basis of NGLY1 deficiency in the central nervous system (CNS) and pathophysiological insights from animal and human induced pluripotent stem cell (iPSC)-based models. We also highlight emerging gene therapy approaches aimed at restoring NGLY1 activity and alleviating neurological symptoms. Full article

Cardiovascular disease remains the leading cause of mortality worldwide, and at its molecular core lies a silent disruptor: oxidative stress. This imbalance between reactive oxygen species (ROS) and antioxidant defenses not only damages cellular components but also orchestrates a cascade of pathological events across diverse cardiac cell types. In cardiomyocytes, ROS overload impairs contractility and survival, contributing to heart failure and infarction. Cardiac fibroblasts respond by promoting fibrosis through excessive collagen deposition. Macrophages intensify inflammatory responses, such as atherosclerosis, via ROS-mediated lipid oxidation—acting both as mediators of damage and targets for antioxidant intervention. This review examines how oxidative stress affects cardiac cell types and evaluates antioxidant-based therapeutic strategies. Therapeutic approaches include natural antioxidants (e.g., polyphenols and vitamins) and synthetic agents (e.g., enzyme modulators), which show promise in experimental models by improving myocardial remodeling. However, clinical trials reveal inconsistent outcomes, underscoring translational challenges (e.g., clinical biomarkers). Emerging strategies—such as targeted antioxidant delivery, activation of endogenous pathways, and disease modeling using 3D organoids—aim to enhance efficacy. In conclusion, we spotlight innovative technologies—like lab-grown heart tissue models—that help scientists better understand how oxidative stress affects heart health. These tools are bridging the gap between early-stage research and personalized medicine, opening new possibilities for diagnosing and treating heart disease more effectively. Full article

Chemotherapy-induced neurotoxicity (CIN) is a major barrier against optimal anticancer treatment. This study investigated the neuroprotective effects of the naturally occurring antioxidant, Coenzyme Q10 (CoQ10), against CIN using a model of induced pluripotent stem cell (iPSC)-derived neurons. iPSCs have consistently proven to be reliable for disease modeling and drug discovery. We employed cell viability, oxidative stress, and mitochondrial function assays to measure the effect of 10 μM CoQ10 on iPSC-derived motor neuron progenitors (iPSC-MNPs) that were exposed to five chemotherapeutic agents: 5-Fluorouracil, methotrexate, paclitaxel (0, 1, and 10 μM) and doxorubicin, and vincristine (0, 0.1, and 1 μM). Our findings show that CoQ10 significantly reversed the reduction in cell viability inflicted by the exposure of iPSCs-MNPs to all five chemotherapeutics. Moreover, CoQ10 treatment resulted in a marked reduction in intracellular ROS levels and enhancement of mitochondrial membrane potential (MMP) in a drug- and dose-dependent manners, highlighting its role in preserving mitochondrial health. This study is the first to explore the protective effects of CoQ10 against CIN using an iPSC-derived neuronal platform, offering insights into its potential therapeutic use. Further investigation is essential to validate these findings and to determine the behavioral effects of CoQ10 in in vivo models of CIN. Full article

The incidence of kidney diseases has been increasing in the last decade due to extended lifespan, which is often related to polymorbidity. Chronic kidney disease (CKD) and acute kidney injury (AKI) are associated with high morbidity and mortality, elevated costs for renal replacement therapy, and heavy psychosomatic burden. At the same time, therapeutic options are limited to prophylactic and renoprotective medications and measurements, and they often cannot restore the impaired kidney function. With the development of cellular therapies, new perspectives arise on the horizon with promising potential, including mesenchymal stem cells (MSCs) and induced pluripotent cells (iPSCs). Here we review the current possibility of both cell types in the field of nephrology and assess their cost implication. Full article

Social communication difficulties characterize autism spectrum disorders (ASD). Gastrointestinal (GI) symptoms are more common in ASD than in the general population. The identification of GI problems in individuals with ASD is challenging due to their altered pain perception and irregular behaviors. Importantly, GI symptoms and ASD can potentially aggravate each other. However, it is unclear if GI problems cause ASD symptoms or vice versa. A crosstalk between the digestive system, gut microbiota, and the central and enteric nervous systems (CNS and ENS, respectively) has been repeatedly reported. The ENS regulates the GI tract with the CNS and the autonomic nervous system (ANS), as well as independently through specific neural circuits. Several mechanisms contribute to GI problems in ASD, including genetic mutations that affect the ENS, dysregulation of the ANS, alterations in gut microbiota, unhealthy dietary preferences, and changes in metabolomic profiles. Furthermore, studies have shown molecular and cellular differences in the GI biopsy of children with and without ASD. These findings highlight the unique nature of GI issues in ASD, underscoring the importance of further investigating the changes that occur in the digestive system and ENS in ASD models. Full article

Background: Infertility remains a significant global health challenge, affecting approximately 15% of couples worldwide. In vitro fertilization (IVF) has transformed reproductive medicine; however, challenges such as low success rates in older patients, ovarian insufficiency, endometrial dysfunction, and male infertility continue to limit outcomes. Objective: This review aims to summarize the principles of IVF and explore the potential role of stem cells in enhancing IVF outcomes, with particular attention to applications in both women and men, as well as the accompanying ethical considerations. Summary: Stem cell research has introduced novel therapeutic opportunities, including ovarian rejuvenation, endometrial regeneration, sperm quality enhancement, and the development of synthetic embryo models. Mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs) demonstrate regenerative properties that may help to overcome current reproductive limitations. Despite encouraging findings from preclinical and early clinical studies, challenges such as tumorigenesis, genetic instability, and ethical controversies remain major barriers to translation. Conclusions: IVF continues to serve as a cornerstone of assisted reproductive technology (ART). Stem cell-based approaches represent an exciting frontier that could expand the therapeutic possibilities of IVF. Careful clinical validation, international regulatory harmonization, and robust ethical oversight will be essential to ensuring safe and equitable implementation. Full article

The high prevalence and diversity of liver diseases present a significant problem for modern healthcare. Despite FDA approval of gene therapy drugs to treat hemophilia A and B, available treatment methods for other hereditary liver diseases are mainly limited to the frequently ineffective traditional therapies and surgical intervention. In recent years, significant progress has been made in the treatment of hepatitis C, but hepatitis B is still considered an incurable disease. In this regard, the treatment of hereditary and viral liver diseases using gene or cell therapy remains relevant. This review is focused on the current state of the induced pluripotent stem cells (iPSCs) field in the context of modeling and treatment of hereditary, viral, and some other liver diseases, both ex vivo and in vivo. Here we present a detailed discussion of the possible ways of modeling liver diseases ex vivo using iPSCs (reprogramming of patient somatic cells and genetic engineering (GE) of healthy iPSCs), summarize gene editing (GE) and non-GE approaches for the treatment of liver diseases, and demonstrate that iPSCs and their derivatives are widely used to treat liver diseases in vivo. Taken together, we are presenting a comprehensive analysis of 2D and 3D iPSC-based products in the context of liver diseases, discussing the advantages and disadvantages of this platform, including the comparison with other types of stem cells and animal models. This analysis may help understand not only the potential but also the limitations associated with the use of iPSCs in the context of various types of liver diseases. Full article

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder that poses an increasing burden on society. It is characterized by the presence of neurofibrillary tangles (NFTs) and amyloid-beta (Aβ) plaques. AD is a multifactorial disease, with one of the strongest genetic risk factors being the APOE4 allele. In this study, we investigated the impact of APOE4 on NF-κB signaling in induced pluripotent stem (iPS) cells. Our results indicate that APOE4 may influence the subcellular localization of the pluripotency marker OCT4, showing a predominantly nuclear localization in APOE4 cells, whereas it appears cytoplasmic in APOE3 cells. Additionally, NF-κB activation via its canonical subunits is blunted in APOE4 cells. Interestingly, APOE4 cells still exhibit increased transcription of key hyperinflammatory markers CCL2, CXCL10 and COX2, which are known NF-κB target genes, and exhibit a significantly higher rate of apoptosis compared to APOE3 cells—independent of TNF-α stimulation. Moreover, an elevated incidence of DNA double-strand breaks was observed in APOE4 cells. However, the precise molecular mechanisms by which APOE4 suppresses NF-κB activation while simultaneously promoting inflammation and apoptosis remain unclear. Further research is required to elucidate these underlying pathways. Full article