技术资料

Genetic variants often produce complex phenotypic effects that confound current assays and predictive models. We developed Variant in situ sequencing (VIS-seq),a pooled,image-based method that measures variant effects on molecular and cellular phenotypes in diverse cell types. Applying VIS-seq to ~3,000 LMNA and PTEN variants yielded high-dimensional morphological profiles that captured variant-driven changes in protein abundance,localization,activity and cell architecture. We identified gain-of-function LMNA variants that reshape the nucleus and autism-associated PTEN variants that mislocalize. Morphological profiles predicted variant pathogenicity with near-perfect accuracy and distinguished autism-linked from tumor syndrome-linked PTEN variants. Most variants impacted a multidimensional continuum of phenotypes not recapitulated by any single functional readout. By linking protein variation to cell images at scale,we illuminate how variant effects cascade from molecular to subcellular to cell morphological phenotypes,providing a framework for resolving the complexity of variant function. View Publication

A limited number of accessible and representative models of human trophoblast cells currently exist for the study of placentation. Current stem cell models involve either a transition through a naïve stem cell state or precise dynamic control of multiple growth factors and small-molecule cues. Here,we demonstrated that a simple five-day treatment of human induced pluripotent stem cells with two small molecules,retinoic acid (RA) and Wnt agonist CHIR 99021 (CHIR),resulted in rapid,synergistic upregulation of CDX2. Transcriptomic analysis of RA + CHIR-treated cells showed high similarity to primary trophectoderm cells. Multipotency was verified via further differentiation towards cells with syncytiotrophoblast or extravillous trophoblast features. RA + CHIR-treated cells were also assessed for the established criteria defining a trophoblast cell model,and they possess all the features necessary to be considered valid. Collectively,our data demonstrate a facile,scalable method for generating functional trophoblast-like cells in vitro to better understand the placenta. View Publication

This paper presents a 360°,size-adjustable microelectrode array (MEA) system for the long-term electrophysiological monitoring of cerebral organoids derived from human pluripotent stem cells. The system consists of eight independently positionable multielectrode probes,each carrying eight electrodes arranged vertically. This configuration resulted in 64 recording channels surrounding the organoid. The multielectrode probes were mounted on custom-designed miniature manipulators with three degrees of freedom. This setup enabled positioning and contact with organoids of varying sizes (approximately 1–3.7 mm in diameter). The design allowed circumferential access and facilitated standard incubator-based cultivation without disrupting the recording setup. Fabricated using flexible printed circuit technology,this MEA system offers relatively low production costs. It is also amenable to widespread implementation in laboratory settings. Experimental results demonstrated the successful recording of neuronal activity,including spike detection and signal stability,over 2 weeks of continuous organoid culture. These results suggests that the three-dimensional system provides broad spatial coverage and supports long-term monitoring for basic biomedical research. It also holds potential for future applications such as biohybrid computing. View Publication

THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation,which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing,in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent,species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members,implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead,mis-splicing was detected in human and mouse neural tissue,revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together,these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology. THOC6 is required for TREX tetramer formation. Analysis of pathogenic THOC6 variants differentiate the conserved mRNA export functions of TREX dimers and RNA processing functions of TREX tetramers underlying THOC6 Intellectual Disability Syndrome. View Publication

BackgroundThe expansion of GGC repeats (typically exceeding 60 repeats) in the 5’ untranslated region (UTR) of the NOTCH2NLC gene (N2C) is linked to N2C-related repeat expansion disorders (NREDs),such as neuronal intranuclear inclusion disease (NIID),frontotemporal dementia (FTD),essential tremor (ET),and Parkinson’s disease (PD). These disorders share common clinical manifestations,including parkinsonism,dementia,seizures,and muscle weakness. Intermediate repeat sizes ranging from 40 to 60 GGC repeats,particularly those with AGC-encoded serine insertions,have been reported to be associated with PD; however,the functional implications of these intermediate repeats with serine insertion remain unexplored.MethodsHere,we utilized cellular models harbouring different sizes of N2C variant 2 (N2C2) GGC repeat expansion and CRISPR-Cas9 engineered transgenic mouse models carrying N2C2 GGC intermediate repeats with and without serine insertion to elucidate the underlying pathophysiology associated with N2C intermediate repeat with serine insertion in NREDs.ResultsOur findings revealed that the N2C2 GGC intermediate repeat with serine insertion (32G13S) led to mitochondrial dysfunction and cell death in vitro. The neurotoxicity was influenced by the length of the repeat and was exacerbated by the presence of the serine insertion. In 12-month-old transgenic mice,32G13S intensified intranuclear aggregation and exhibited early PD-like characteristics,including the formation of ?-synuclein fibers in the midbrain and the loss of tyrosine hydroxylase (TH)-positive neurons in both the cortex and striatum. Additionally,32G13S induced neuronal hyperexcitability and caused locomotor behavioural impairments. Transcriptomic analysis of the mouse cortex indicated dysregulation in calcium signaling and MAPK signaling pathways,both of which are critical for mitochondrial function. Notably,genes associated with myelin sheath components,including MBP and MOG,were dysregulated in the 32G13S mouse. Further investigations using immunostaining and transmission electron microscopy revealed that the N2C intermediate repeat with serine induced mitochondrial dysfunction-related hypermyelination in the cortex.ConclusionsOur in vitro and in vivo investigations provide the first evidence that the N2C-GGC intermediate repeat with serine promotes intranuclear aggregation of N2C,leading to mitochondrial dysfunction-associated hypermyelination and neuronal hyperexcitability. These changes contribute to motor deficits in early PD-like neurodegeneration in NREDs.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13024-024-00780-2. View Publication

During a heart attack,ischemia causes losses of billions of cells; this is especially concerning given the minimal regenerative capability of cardiomyocytes (CMs). Heart remuscularization utilizing stem cells has improved cardiac outcomes despite little cell engraftment,thereby shifting focus to cell-free therapies. Consequently,we chose induced pluripotent stem cells (iPSCs) given their pluripotent nature,efficacy in previous studies,and easy obtainability from minimally invasive techniques. Nonetheless,using iPSC secretome-based therapies for treating injured CMs in a clinical setting is ill-understood. We hypothesized that the iPSC secretome,regardless of donor health,would improve cardiovascular outcomes in the CM model of ischemia–reperfusion (IR) injury. Episomal-generated iPSCs from healthy and dilated cardiomyopathy (DCM) donors,passaged 6–10 times,underwent 24 h incubation in serum-free media. Protein content of the secretome was analyzed by mass spectroscopy and used to treat AC16 immortalized CMs during 5 h reperfusion following 24 h of hypoxia. IPSC-derived secretome content,independent of donor health status,had elevated expression of proteins involved in cell survival pathways. In IR conditions,iPSC-derived secretome increased cell survival as measured by metabolic activity (p < 0.05),cell viability (p < 0.001),and maladaptive cellular remodelling (p = 0.052). Healthy donor-derived secretome contained increased expression of proteins related to calcium contractility compared to DCM donors. Congruently,only healthy donor-derived secretomes improved CM intracellular calcium concentrations (p < 0.01). Heretofore,secretome studies mainly investigated differences relating to cell type rather than donor health. Our work suggests that healthy donors provide more efficacious iPSC-derived secretome compared to DCM donors in the context of IR injury in human CMs. These findings illustrate that the regenerative potential of the iPSC secretome varies due to donor-specific differences. View Publication

The overproduction of reactive oxygen species (ROS) and mitochondrial dysregulation are regarded as key mechanisms in the progression of cardiac remodelling in cardiometabolic diseases including heart failure. Conventional treatments are often ineffective as they do not specifically target the underlying pathological mechanisms. Mitoquinone mesylate (MitoQ),a mitochondrial-targeted antioxidant has been reported to be protective against vascular dysfunction in hypertension,diabetic kidney disease and alcohol-induced liver damage. However,the cardioprotective potential of MitoQ to limit oxidative stress-induced mitochondrial remodelling in cardiomyocytes has not been fully resolved. We sought to investigate the effect of MitoQ and its mitochondrial-targeting moiety dodecyl-triphenylphosphonium (dTPP) on hydrogen peroxide-induced overproduction of ROS,mitochondrial dysregulation and cell death in H9C2 rat cardiomyoblasts (H9C2-rCM) and human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM). Cardiomyocytes were exposed to acute or chronic treatment (5–60 min or 48 h) of vehicle control (0.0001 % Ultrapure Milli-Q water),hydrogen peroxide (100 ?M) ± MitoQ (1 ?M) or dTPP (1 ?M) control. Hydrogen peroxide-induced overproduction of ROS,extracellular superoxide,mitochondrial ROS,mitochondrial hyperpolarisation and cell death were significantly blunted by MitoQ,but not dTPP,suggesting that the coenzyme Q10 moiety of MitoQ is protective under these conditions. Interestingly,both MitoQ and dTPP exhibited a pro-mitochondrial fusion effect by preserving mitochondrial network and reducing mitochondrial fragmentation in oxidative stress conditions. Overall,our findings confirm the cytoprotective potential of MitoQ to limit oxidative stress-induced adverse mitochondrial remodelling and dysregulation that is clinically observed in cardiometabolic-induced cardiac dysfunction in the failing heart. Graphical abstractBioRender Scientific Image and Illustration Software were used to generate the graphical abstract.Unlabelled Image Highlights•Oxidative stress is a key driver of mitochondrial dysregulation and cell death in cardiomyocytes.•MitoQ exhibits cytoprotection against elevated ROS production in human cardiomyocytes.•Mitochondrial structure and regulation were preserved in human cardiomyocytes with MitoQ treatment. View Publication

BackgroundThioredoxin-interacting protein (TXNIP) plays a role in regulating endoplasmic reticulum (ER) and oxidative stress,which disrupt glucose homeostasis in diabetes. However,the impact of TXNIP deficiency on the differentiation and functionality of human stem cell-derived somatic metabolic cells remains unclear.MethodsWe used CRISPR-Cas12a genome editing to generate TXNIP-deficient (TXNIP?/?) H1 human embryonic stem cells (H1-hESCs). These cells were differentiated into hepatocyte-like cells (HLCs) and stem-cell-derived insulin-producing islets (SC-islets). The maturation and functionality TXNIP?/? and TXNIP+/+ SC-islets were assessed by implantation under the kidney capsule of male or female NOD-SCID mice.ResultsTXNIP deficiency significantly increased H1-hESC proliferation without affecting pluripotency,viability,or differentiation potential into HLCs and SC-islets. Bulk RNA-sequencing of thapsigargin-treated TXNIP?/? and TXNIP+/+ hESCs revealed differential expression of stress-responsive genes,with enriched apoptosis-related pathways in TXNIP+/+ cells,but minimal transcriptional changes specific to TXNIP deficiency. In HLCs,TXNIP deletion reduced albumin secretion and insulin signalling,as indicated by decreased AKT phosphorylation,while showing no differences in glycolytic activity or lipid metabolism markers. Under thapsigargin-induced ER stress,TXNIP?/? HLCs exhibited transiently reduced eIF2? phosphorylation and lower BiP expression,suggesting compromised adaptive responses to prolonged stress. SC-islets derived from TXNIP?/? hESCs showed comparable viability,endocrine cell composition,and cytokine responses to TXNIP+/+ islets. Following IFN? or IFN? treatment,STAT1 phosphorylation was increased in TXNIP?/? SC-islets,indicating that IFN signalling remained intact despite TXNIP deficiency. Upon implantation into NOD-SCID mice,both TXNIP?/? and TXNIP+/+ SC-islets produced human C-peptide and responded to glucose stimulation. However,TXNIP?/? SC-islets did not demonstrate enhanced glycaemic control or glucose-stimulated insulin secretion compared to controls.ConclusionsOur study demonstrates that TXNIP deficiency does not improve the differentiation or functionality of HLCs and SC-islets. We present the generation and characterisation of TXNIP?/? and TXNIP+/+ H1-hESCs,HLCs,and SC-islets as valuable models for future studies on the role of TXNIP in metabolic cell biology.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13287-025-04314-5. View Publication

MicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in post-transcriptional gene regulation. Poly(A) RNA polymerase D5 (PAPD5) catalyzes the addition of adenosine to the 3? end of miRNAs. In this study,we demonstrate that the Yin Yang 1 protein,a transcriptional repressor of PAPD5,is recruited to both RNA foci and protein aggregates,resulting in an upregulation of PAPD5 expression in Huntington’s disease (HD). Additionally,we identify a subset of PAPD5-regulated miRNAs with increased adenylation and reduced expression in our disease model. We focus on miR-7-5p and find that its reduction causes the activation of the TAB2-mediated TAK1–MKK4–JNK pro-apoptotic pathway. This pathway is also activated in induced pluripotent stem cell-derived striatal neurons and post-mortem striatal tissues isolated from HD patients. In addition,we discover that a small molecule PAPD5 inhibitor,BCH001,can mitigate cell death and neurodegeneration in our disease models. This study highlights the importance of PAPD5-mediated miRNA dysfunction in HD pathogenesis and suggests a potential therapeutic direction for the disease. PAPD5 is responsible for adenylation of microRNAs. Here,the authors show that elevated level of PAPD5 enhances the adenylation and reduced expression of miR-7-5p. As a result,expression of TAB2,a target of miR-7-5p,is induced triggering neuronal apoptosis in Huntington’s disease. View Publication

Inherited non-hemolytic anemia is a group of rare bone marrow disorders characterized by erythroid defects. Although concerted efforts have been made to explore the underlying pathogenetic mechanisms of these diseases,the understanding of the causative mutations are still incomplete. Here we identify in a diseased pedigree that a gain-of-function mutation in toll-like receptor 8 (TLR8) is implicated in inherited non-hemolytic anemia. TLR8 is expressed in erythroid lineage and erythropoiesis is impaired by TLR8 activation whereas enhanced by TLR8 inhibition from erythroid progenitor stage. Mechanistically,TLR8 activation blocks annexin A2 (ANXA2)-mediated plasma membrane localization of STAT5 and disrupts EPO signaling in HuDEP2 cells. TLR8 inhibition improves erythropoiesis in RPS19+/? HuDEP2 cells and CD34+ cells from healthy donors and inherited non-hemolytic anemic patients. Collectively,we identify a gene implicated in inherited anemia and a previously undescribed role for TLR8 in erythropoiesis,which could potentially be explored for therapeutic benefit in inherited anemia. Decoding the pathogenic genes of the inherited anemia could provide us with novel regulators of pathological and physiological erythropoiesis. Here,the authors show TLR8 is expressed by erythroid cells and regulates erythropoiesis through interacting with EPO signaling. View Publication

Stem cell-derived ?-cells (SC-BCs) represent a potential source for curing diabetes. To date,in vitro generated SC-BCs display an immature phenotype and lack important features in comparison to their bona-fide counterparts. Transplantation into a living animal promotes SC-BCs maturation,indicating that components of the in vivo microenvironment trigger final SC-BCs development. Here,we investigated whether cues of the pancreas specific extracellular matrix (ECM) can improve the differentiation of human induced pluripotent stem cells (hiPSCs) towards ?-cells in vitro. To this aim,a pancreas specific ECM (PanMa) hydrogel was generated from decellularized porcine pancreas and its effect on the differentiation of hiPSC-derived pancreatic hormone expressing cells (HECs) was tested. The hydrogel solidified upon neutralization at 37 °C with gelation kinetics similar to Matrigel. Cytocompatibility of the PanMa hydrogel was demonstrated for a culture duration of 21 days. Encapsulation and culture of HECs in the PanMa hydrogel over 7 days resulted in a stable gene and protein expression of most ?-cell markers,but did not improve ?-cell identity. In conclusion,the study describes the production of a PanMa hydrogel,which provides the basis for the development of ECM hydrogels that are more adapted to the demands of SC-BCs. View Publication

The primed epiblast acts as a transitional stage between the relatively homogeneous naïve epiblast and the gastrulating embryo. Its formation entails coordinated changes in regulatory circuits driven by transcription factors and epigenetic modifications. Using a multi-omic approach in human embryonic stem cell models across the spectrum of peri-implantation development,we demonstrate that the transcription factors ZIC2 and ZIC3 have overlapping but essential roles in opening primed-specific enhancers. Together,they are essential to facilitate progression to and maintain primed pluripotency. ZIC2/3 accomplish this by recruiting SWI/SNF to chromatin and loss of ZIC2/3 or degradation of SWI/SNF both prevent enhancer activation. Loss of ZIC2/3 also results in transcriptome changes consistent with perturbed Polycomb activity and a shift towards the expression of genes linked to differentiation towards the mesendoderm. Additionally,we find an intriguing dependency on the transcriptional machinery for sustained recruitment of ZIC2/3 over a subset of primed-hESC specific enhancers. Taken together,ZIC2 and ZIC3 regulate highly dynamic lineage-specific enhancers and collectively act as key regulators of human primed pluripotency. Here the authors identify ZIC2 and ZIC3 as key regulators of human primed pluripotency which recruit BRG1 to open primed hESC-specific enhancers. View Publication