技术资料

Rare coding mutations cause ~45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases,but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs),we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity,often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context,four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing,we used the MPRA data to develop a regression model,EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together,we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD. View Publication

Preclinical data have confirmed that human pluripotent stem cell-derived cardiomyocytes (PSC-CMs) can remuscularize the injured or diseased heart,with several clinical trials now in planning or recruitment stages. However,because ventricular arrhythmias represent a complication following engraftment of intramyocardially injected PSC-CMs,it is necessary to provide treatment strategies to control or prevent engraftment arrhythmias (EAs). Here,we show in a porcine model of myocardial infarction and PSC-CM transplantation that EAs are mechanistically linked to cellular heterogeneity in the input PSC-CM and resultant graft. Specifically,we identify atrial and pacemaker-like cardiomyocytes as culprit arrhythmogenic subpopulations. Two unique surface marker signatures,signal regulatory protein ? (SIRPA)+CD90?CD200+ and SIRPA+CD90?CD200?,identify arrhythmogenic and non-arrhythmogenic cardiomyocytes,respectively. Our data suggest that modifications to current PSC-CM-production and/or PSC-CM-selection protocols could potentially prevent EAs. We further show that pharmacologic and interventional anti-arrhythmic strategies can control and potentially abolish these arrhythmias. Selvakumar,Clayton et al. use a porcine model of myocardial infarction and PSC-CM transplantation and identify atrial and pacemaker-like cardiomyocytes as the cause of engraftment arrhythmias and surface marker signatures to distinguish between arrhythmogenic and non-arrhythmogenic cardiomyocytes. View Publication

Nuclear speckles are membraneless organelles that associate with active transcription sites and participate in post-transcriptional mRNA processing. During the cell cycle,nuclear speckles dissolve following phosphorylation of their protein components. Here,we identify the PP1 family as the phosphatases that counteract kinase-mediated dissolution. PP1 overexpression increases speckle cohesion and leads to retention of mRNA within speckles and the nucleus. Using APEX2 proximity labeling combined with RNA-sequencing,we characterize the recruitment of specific RNAs. We find that many transcripts are preferentially enriched within nuclear speckles compared to the nucleoplasm,particularly chromatin- and nucleus-associated transcripts. While total polyadenylated RNA retention increases with nuclear speckle cohesion,the ratios of most mRNA species to each other are constant,indicating non-selective retention. We further find that cellular responses to heat shock,oxidative stress,and hypoxia include changes to the phosphorylation and cohesion of nuclear speckles and to mRNA retention. Our results demonstrate that tuning the material properties of nuclear speckles provides a mechanism for the acute control of mRNA localization. Here the authors study how interactions with nuclear speckles help localize mRNA in cells. They find that modifications of the proteins in these structures affects their cohesion and can modulate mRNA retention under stress. View Publication

PurposeLittle is known about the development of Bruch's membrane (BrM),the structure separating and supporting the retina and choroid,nor whether differentiation of human pluripotent stem cell (hPSC)-derived retinal pigment epithelium (RPE) accurately replicates BrM. This has relevance for tissue engineering strategies,both in the development of accurate in vitro models,and effective RPE transplant strategies. Here,we investigated BrM-associated protein production in human fetal tissue and hPSC-derived RPE.MethodsThe presence of laminin,elastin,fibronectin,and types I/III/IV collagen was examined in human fetal eyes at 6 to 21 post-conception weeks (PCWs) and hPSC-derived RPE cultures at 1 to 6 weeks in culture using immunohistochemistry/immunocytochemistry and quantitative PCR (qPCR).ResultsIn human fetal retina,laminin and fibronectin were present from 6 PCW,type IV collagen from 8 PCW,elastin from 12 PCW,type I collagen by 17 PCW,and type III collagen from 21 PCW. BrM layering was discernible from 12 PCW,becoming distinct by 17 PCW. In hPSC-derived RPE cultures,basement membranes containing laminin and fibronectin were present from week 1,type IV collagen from week 2,and type I collagen from week 4. Type III collagen was present at all timepoints,although not localized as a basement membrane. Elastin was absent at all timepoints.ConclusionsBrM-like membrane synthesis in hPSC-derived RPE largely recapitulates the temporal sequence seen in human development,excluding elastin. These support the utility of hPSC-derived RPE in in vitro systems to model RPE/retina interactions in health and disease,and inform cell therapy approaches,as de novo BrM-like membrane has the potential to support transplanted donor RPE. View Publication

BackgroundThe causal relationship between the activation of nuclear factor erythroid 2-related factor 2 (NRF2) and the preservation of SERCA2a function in mitigating myocardial ischemia–reperfusion (mI/R) injury,along with the associated regulatory mechanisms,remains incompletely understood. This study aims to unravel how NRF2 directly or indirectly influences SERCA2a function and its regulators,phospholamban (PLN) and Dwarf Open Reading Frame (DWORF),by testing the pharmacological repositioning of AEOL-10150 (AEOL) in the context of mI/R injury.MethodsC57BL6/J,Nrf2 knockout (Nrf2?/?),and wild-type (Nrf2+/+) mice,as well as human induced pluripotent stem cell-derived cardiomyocytes (hiPSCMs) were subjected to I/R injury. Gain/loss of function techniques,RT-qPCR,western blotting,LC/MS/MS,and fluorescence spectroscopy were utilized. Cardiac dimensions and function were assessed by echocardiography.ResultsIn the early stages of mI/R injury,AEOL administration reduced mitochondrial ROS production,decreased myocardial infarct size,and improved cardiac function. These effects were due to NRF2 activation,leading to the overexpression of the micro-peptide DWORF,consequently enhancing SERCA2a activity. The cardioprotective effect induced by AEOL was diminished in Nrf2?/? mice and in Nrf2/Dworf knockdown models in hiPSCMs subjected to simulated I/R injury. Our data show that AEOL-induced NRF2-mediated upregulation of DWORF disrupts the phospholamban-SERCA2a interaction,leading to enhanced SERCA2a activation and improved cardiac function.ConclusionsTaken together,our study reveals that AEOL-induced NRF2-mediated overexpression of DWORF enhances myocardial function through the activation of the SERCA2a offering promising therapeutic avenues for mI/R injury.Supplementary InformationThe online version contains supplementary material available at 10.1186/s10020-025-01242-1. Highlights• Novel AEOL-10150 therapeutic potential. AEOL-10150 demonstrates promise in activating NRF2 and mitigating myocardial ischemia-reperfusion injury.• DWORF overexpression breakthrough. Overexpression of DWORF significantly contributes to preserving cardiac function and reducing myocardial injury through the NRF2-DWORF pathway.• Enhanced cardiac protection mechanisms. The study highlights the dual role of AEOL-10150 and DWORF in enhancing cardiac protection and preventing heart failure.• Future research directions. Additional studies are required to validate the long-term efficacy of AEOL-10150 and the regulatory effects of NRF2-DWORF axis in clinical applications.Supplementary InformationThe online version contains supplementary material available at 10.1186/s10020-025-01242-1. View Publication

Human pluripotent stem cells (hPSCs) and their differentiated derivatives represent valuable tools for studying development,modeling diseases,and advancing cell therapy. Recent improvements in genome engineering allow for precise modifications of hPSCs,further enhancing their utility in basic and translational research. Here we describe a Recombinase-Mediated Cassette Exchange (RMCE) platform in hPSCs that allows for the highly efficient,rapid,and specific integration of transgenes. The RCME-mediated DNA integration process is nearly 100% efficient,without negatively affecting the pluripotency or karyotypic stability of hPSCs. Taking advantage of this convenient system,we first established a dual inducible expression system based on the Tet-On and Cumate-On systems,allowing for the inducible expression of two transgenes independently. Secondly,we incorporated a Tet-on inducible system,driving the expression of three genes simultaneously. However,two genes also contain independent degron sequences,allowing for precise control over the expression of each gene individually. We demonstrated the utility of these systems in hPSCs,as well as their functionality after differentiation into cells that were representative of the three germ layers. Lastly,we used the triple inducible system to investigate the lineage commitment induced by the pancreatic transcription factors NKX6.1 and PDX1. We found that controlled dual expression,but not individual expression,biases hPSC embryoid body differentiation towards the pancreatic lineage by inducing the expression of the NeuroD program. In sum,we describe a novel genetic engineering platform that allows for the efficient and fast integration of any desired transgene(s) in hPSCs using RMCE. We anticipate that the ability to modulate the expression of three transgenes simultaneously will further accelerate discoveries using stem cell technology. View Publication

53BP1 is a well-established DNA damage repair factor that has recently emerged to critically regulate gene expression for tumor suppression and neural development. However,its precise function and regulatory mechanisms remain unclear. Here,we showed that phosphorylation of 53BP1 at serine 25 by ATM is required for neural progenitor cell proliferation and neuronal differentiation in cortical brain organoids. Dynamic phosphorylation of 53BP1-serine 25 controls 53BP1 target genes governing neuronal differentiation and function,cellular response to stress,and apoptosis. Mechanistically,ATM and RNF168 govern 53BP1’s binding to gene loci to directly affect gene regulation,especially at genes for neuronal differentiation and maturation. 53BP1 serine 25 phosphorylation effectively impedes its binding to bivalent or H3K27me3-occupied promoters,especially at genes regulating H3K4 methylation,neuronal functions,and cell proliferation. Beyond 53BP1,ATM-dependent phosphorylation displays wide-ranging effects,regulating factors in neuronal differentiation,cytoskeleton,p53 regulation,as well as key signaling pathways such as ATM,BDNF,and WNT during cortical organoid differentiation. Together,our data suggest that the interplay between 53BP1 and ATM orchestrates essential genetic programs for cell morphogenesis,tissue organization,and developmental pathways crucial for human cortical development. 53BP1 is a DNA damage repair factor that regulates gene expression for tumor suppression and neural development,but its precise regulatory mechanisms are unclear. This study shows that phosphorylation of 53BP1 by ATM kinase is crucial for modulating genetic programs in neural progenitors and cortical organoids. View Publication

Dysregulation of mitochondrial function has been implicated in Parkinson’s disease (PD),but the role of mitochondrial metabolism in disease pathogenesis remains to be elucidated. Using an unbiased metabolomic analysis of purified mitochondria,we identified alterations in ?-ketoglutarate dehydrogenase (KGDH) pathway upon loss of PD-linked CHCHD2 protein. KGDH,a rate-limiting enzyme complex in the tricarboxylic acid cycle,was decreased in CHCHD2-deficient male mouse brains and human dopaminergic neurons. This deficiency of KGDH led to elevated ?-ketoglutarate and increased lipid peroxidation. Treatment of CHCHD2-deficient dopaminergic neurons with lipoic acid,a KGDH cofactor and antioxidant agent,resulted in decreased levels of lipid peroxidation and phosphorylated ?-synuclein. CHCHD10,a close homolog of CHCHD2 that is primarily linked to amyotrophic lateral sclerosis/frontotemporal dementia,did not affect the KGDH pathway or lipid peroxidation. Together,these results identify KGDH metabolic pathway as a targetable mitochondrial mechanism for correction of increased lipid peroxidation and ?-synuclein in Parkinson’s disease. An unbiased metabolomic analysis identifies ?-ketoglutarate dehydrogenase metabolic pathway as a targetable mitochondrial mechanism for correction of increased lipid peroxidation in CHCHD2-linked Parkinson’s disease models. View Publication

Vascular dementia is the second most common form of dementia. Yet,the mechanisms by which cerebrovascular damage progresses are insufficiently understood. Here,we create bilateral common carotid artery stenosis in mice,which effectively impairs blood flow to the brain,a major cause of the disease. Through imaging and single-cell transcriptomics of the mouse cortex,we uncover that blood vessel venous cells undergo maladaptive structural changes associated with increased Epas1 expression and activation of developmental angiogenic pathways. In a human cell model comparing arterial and venous cells,we observe that low-oxygen condition leads to sustained EPAS1 signaling specifically in venous cells. EPAS1 inhibition reduces cerebrovascular abnormalities,microglial activation,and improves markers of cerebral perfusion in vivo. In human subjects,levels of damaged endothelial cells from venous vessels are correlated with white matter injury in the brain and poorer cognitive functions. Together,these findings indicate EPAS1 as a potential therapeutic target to restore cerebrovascular integrity and mitigate neuroinflammation. How changes in brain blood vessels lead to a chronic reduction in blood flow and,consequently,to vascular dementia is poorly understood. Here,the authors show that venous endothelial dysfunction driven by EPAS1 promotes abnormal vascular remodeling and contributes to cognitive decline. View Publication

Viral vector delivery of gene therapy represents a promising approach for the treatment of numerous retinal diseases. Adeno-associated viral vectors (AAV) constitute the primary gene delivery platform; however,their limited cargo capacity restricts the delivery of several clinically relevant retinal genes. In this study,we explore the feasibility of employing high-capacity adenoviral vectors (HC-AdVs) as alternative delivery vehicles,which,with a capacity of up to 36 kb,can potentially accommodate all known retinal gene coding sequences. We utilized HC-AdVs based on the classical adenoviral type 5 (AdV5) and on a fiber-modified AdV5.F50 version,both engineered to deliver a 29.6 kb vector genome encoding a fluorescent reporter construct. The tropism of these HC-AdVs was evaluated in an induced pluripotent stem cell (iPSC)-derived human retinal organoid model. Both vector types demonstrated robust transduction efficiency,with sustained transgene expression observed for up to 110 days post-transduction. Moreover,we found efficient transduction of photoreceptors and Müller glial cells,without evidence of reactive gliosis or loss of photoreceptor cell nuclei. However,an increase in the thickness of the photoreceptor outer nuclear layer was observed at 110 days post-transduction,suggesting potential unfavorable effects on Müller glial or photoreceptor cells associated with HC-AdV transduction and/or long-term reporter overexpression. These findings suggest that while HC-AdVs show promise for large retinal gene delivery,further investigations are required to assess their long-term safety and efficacy. View Publication

A distinctive feature of both type 1 and type 2 diabetes is the waning of insulin-secreting beta cells in the pancreas. New methods for direct and specific targeting of the beta cells could provide platforms for delivery of pharmaceutical reagents. Imaging techniques such as Positron Emission Tomography (PET) rely on the efficient and specific delivery of imaging reagents,and could greatly improve our understanding of diabetes etiology as well as providing biomarkers for viable beta-cell mass in tissue,in both pancreas and in islet grafts.The DiGeorge Syndrome Critical Region Gene 2 (DGCR2) protein has been suggested as a beta-cell specific protein in the pancreas,but so far there has been a lack of available high-affinity binders suitable for targeted drug delivery or molecular imaging. Affibody molecules belong to a class of small affinity proteins with excellent properties for molecular imaging. Here,we further validate the presence of DGCR2 in pancreatic and stem cell (SC)-derived beta cells,and then describe the generation and selection of several Affibody molecules candidates that target human DGCR2. Using an in-house developed directed evolution method,new DGCR2-binding Affibody molecules were generated and evaluated for thermal stability and affinity. The Affibody molecules variants were further developed as targeting agents for delivering imaging reagents to beta cell. The Affibody molecule ZDGCR2:AM106 displayed nanomolar affinity,suitable stability and biodistribution,with negligible toxicity to islets,qualifying it as a suitable lead candidate for further development as a tool for specific delivery of drugs and imaging reagents to beta cells.Supplementary InformationThe online version contains supplementary material available at 10.1038/s41598-024-84574-y. View Publication

Fellows et al. report that individual dynein motors can move the entire axon length during retrograde transport. They find factors LIS1 and NDEL1,needed for transport initiation,also move with cargos. In the anterograde direction,dynein and its cofactor dynactin are transported separately,keeping them apart until required. Axonal transport is essential for neuronal survival. This is driven by microtubule motors including dynein,which transports cargo from the axon tip back to the cell body. This function requires its cofactor dynactin and regulators LIS1 and NDEL1. Due to difficulties imaging dynein at a single-molecule level,it is unclear how this motor and its regulators coordinate transport along the length of the axon. Here,we use a neuron-inducible human stem cell line (NGN2-OPTi-OX) to endogenously tag dynein components and visualize them at a near-single molecule regime. In the retrograde direction,we find that dynein and dynactin can move the entire length of the axon (>500 µm). Furthermore,LIS1 and NDEL1 also undergo long-distance movement,despite being mainly implicated with the initiation of dynein transport. Intriguingly,in the anterograde direction,dynein/LIS1 moves faster than dynactin/NDEL1,consistent with transport on different cargos. Therefore,neurons ensure efficient transport by holding dynein/dynactin on cargos over long distances but keeping them separate until required. View Publication