技术资料

The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases,thereby facilitating the identification of alternative splicing events and isoform expressions. Recently,numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless,there remains a deficiency in comparative studies that systemically evaluate the performance of these tools,which are implemented with different algorithms,under various simulations that encompass potential influencing factors. In this study,we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data,which represented diverse sequencing platforms generated by an in-house simulator,RNA sequins (sequencing spike-ins) data,as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS,with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data. Recently,various computational tools have emerged for detecting mRNA isoforms using long-read sequencing data. Here,the authors systemically evaluate and compare the performance of these tools. View Publication

Oxidative phosphorylation (OXPHOS) in the mitochondrial inner membrane is a therapeutic target in many diseases. Neural stem cells (NSCs) show progress in improving mitochondrial dysfunction in the central nervous system (CNS). However,translating neural stem cell-based therapies to the clinic is challenged by uncontrollable biological variability or heterogeneity,hindering uniform clinical safety and efficacy evaluations. We propose a systematic top-down design based on membrane self-assembly to develop neural stem cell-derived oxidative phosphorylating artificial organelles (SAOs) for targeting the central nervous system as an alternative to NSCs. We construct human conditionally immortal clone neural stem cells (iNSCs) as parent cells and use a streamlined closed operation system to prepare neural stem cell-derived highly homogenous oxidative phosphorylating artificial organelles. These artificial organelles act as biomimetic organelles to mimic respiration chain function and perform oxidative phosphorylation,thus improving ATP synthesis deficiency and rectifying excessive mitochondrial reactive oxygen species production. Conclusively,we provide a framework for a generalizable manufacturing procedure that opens promising prospects for disease treatment. Regulating oxidative phosphorylation and restoring redox homeostasis are crucial in neurological disorders. Here,the authors develop a top-down membrane self-assembly strategy to develop stem cell-derived artificial organelles (SAOs) that mimic mitochondrial oxidative phosphorylation without the risks associated with stem cell therapy. View Publication

Significance: Heart disease is the leading cause of death in the United States,yet research is limited by the inability to culture primary cardiac cells. Cardiomyocytes (CMs) derived from human induced pluripotent stem cells (iPSCs) are a promising solution for drug screening and disease modeling. Aim: Induced pluripotent stem cell-derived CM (iPSC-CM) differentiation and maturation studies typically use heterogeneous substrates for growth and destructive verification methods. Reproducible,tunable substrates and touch-free monitoring are needed to identify ideal conditions to produce homogenous,functional CMs. Approach: We generated synthetic polyethylene glycol-based hydrogels for iPSC-CM differentiation and maturation. Peptide concentrations,combinations,and gel stiffness were tuned independently. Label-free optical redox imaging (ORI) was performed on a widefield microscope in a 96-well screen of gel formulations. We performed live-cell imaging throughout differentiation and early to late maturation to identify key metabolic shifts. Results: Label-free ORI confirmed the expected metabolic shifts toward oxidative phosphorylation throughout the differentiation and maturation processes of iPSC-CMs on synthetic hydrogels. Furthermore,ORI distinguished high and low differentiation efficiency cell batches in the cardiac progenitor stage. Conclusions: We established a workflow for medium throughput screening of synthetic hydrogel conditions with the ability to perform repeated live-cell measurements and confirm expected metabolic shifts. These methods have implications for reproducible iPSC-CM generation in biomanufacturing. View Publication

ABSTRACTThe paradoxical exacerbation of cellular injury and death during reperfusion remains a problem in the treatment of myocardial infarction. Mitochondrial dysfunction plays a key role in the pathogenesis of myocardial ischemia and reperfusion injury. Dysfunctional mitochondria can be removed by mitophagy,culminating in their degradation within acidic lysosomes. Mitophagy is pivotal in maintaining cardiac homeostasis and emerges as a potential therapeutic target. Here,we employed beating human engineered heart tissue (EHT) to assess mitochondrial dysfunction and mitophagy during ischemia and reperfusion simulation. Our data indicate adverse ultrastructural changes in mitochondrial morphology and impairment of mitochondrial respiration. Furthermore,our pH-sensitive mitophagy reporter EHTs,generated by a CRISPR/Cas9 endogenous knock-in strategy,revealed induced mitophagy flux in EHTs after ischemia and reperfusion simulation. The induced flux required the activity of the protein kinase ULK1,a member of the core autophagy machinery. Our results demonstrate the applicability of the reporter EHTs for mitophagy assessment in a clinically relevant setting. Deciphering mitophagy in the human heart will facilitate development of novel therapeutic strategies. Summary: Mitochondrial dysfunction and lysosomal degradation of mitochondria (mitophagy) is induced after ischemia and reperfusion simulation in human engineered heart tissue,as shown with an endogenous pH-sensitive mitophagy reporter. View Publication

Acute liver failure (ALF) is a hepatology emergency with rapid hepatic destruction,multiple organ failures,and high mortality. Despite decades of research,established ALF has minimal therapeutic options. Here,we report that the small bioactive compound SCM-198 increases the survival of male ALF mice to 100%,even administered 24?hours after ALF establishment. We identify adiponectin receptor 2 (AdipoR2) as a selective target of SCM-198,with the AdipoR2 R335 residue being critical for the binding and signaling of SCM-198-AdipoR2 and AdipoR2 Y274 residue serving as a molecular switch for Ca2+ influx. SCM-198-AdipoR2 binding causes Ca2+ influx and elevates the phosphorylation levels of CaMKII and NOS3 in the AdipoR2-CaM-CaMKII-NOS3 complex identified in this study,rapidly inducing nitric oxide production for liver protection in murine ALF. SCM-198 also protects human ESC-derived liver organoids from APAP/TAA injuries. Thus,selectively targeting the AdipoR2-CaM-CaMKII-NOS3 axis by SCM-198 is a rapid-acting therapeutic strategy for advanced ALF. Late-stage acute liver failure (ALF) has limited therapies. The authors show that the bioactive compound SCM-198 extends the ALF treatment window from 3 to 24?hours in mice by selectively targeting the identified AdipoR2-CaM-CaMKII-NOS3-NO axis. View Publication

ABSTRACTObjectivesAutism spectrum disorder (ASD) is a neurodevelopmental condition that affects social communication and behaviors. While previous studies using animal models have substantially expanded our knowledge about ASD,the lack of an appropriate human model system that accurately recapitulates the human?specific pathophysiology of ASD hinders the precise understanding of its etiology and the development of effective therapies. This study aims to replicate pathological phenotypes in cerebral organoids derived from idiopathic ASD patients and to conduct proof?of?concept research for the development of ASD therapeutics.MethodsWe conducted an in vitro disease modeling study using cerebral organoids derived from three idiopathic ASD patients. Additionally,we performed organoid?based phenotypic drug screening to identify potential therapeutic compounds that could ameliorate the phenotypes observed in cerebral organoids derived from idiopathic ASD patients.ResultsHere we show that cerebral organoids derived from idiopathic ASD patients display malformation of the ventricular zones and impaired early neuronal differentiation. Through organoid?based phenotypic drug screening,we successfully generated cerebral organoids with normal tissue architecture in which the delayed neuronal differentiation could also be accelerated. Notably,cerebral organoids from ASD patients exhibited a reduced number of GABAergic neurons compared to healthy controls,resulting in an imbalance in the excitatory and inhibitory neuron ratio. The differentiation defects into GABAergic neurons in patient?derived cerebral organoids could be rescued by treating with either IGF1 or Gabapentin,a GABA agonist.ConclusionsOur findings provide a framework for utilizing patient?derived cerebral organoids in the development of personalized pharmaceutical treatment for ASD. Summary of in vitro disease modeling and drug screening using ASD patient?derived COs. This figure highlights the major phenotypes observed in COASD and the therapeutic effects of each compound screened in this study. View Publication

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease of the motor system with complex determinants,including genetic and non-genetic factors. A key pathological signature of ALS is the cytoplasmic mislocalization and aggregation of TDP-43 in affected motor neurons,which is found in 97% of cases. Recent reports have shown that mitochondrial dysfunction plays a significant role in motor neuron degeneration in ALS,and TDP-43 modulates several mitochondrial transcripts. In this study,we used induced pluripotent stem cell-derived motor neurons from ALS patients with TDP-43 mutations and a transgenic TDP-43M337V mouse model to determine how TDP-43 mutations alter mitochondrial function and axonal transport. We detected significantly reduced mitochondrial respiration and ATP production in patient induced pluripotent stem cell-derived motor neurons,linked to an interaction between TDP-43M337V with ATPB and COX5A. A downstream reduction in speed of retrograde axonal transport in patient induced pluripotent stem cell-derived motor neurons was detected,which correlated with downregulation of the motor protein complex,DCTN1/dynein. Overexpression of DCTN1 in patient induced pluripotent stem cell-derived motor neurons significantly increased the percentage of retrograde travelling mitochondria and reduced the percentage of stationary mitochondria. This study shows that ALS induced pluripotent stem cell-derived motor neurons with mutations in TDP-43 have deficiencies in essential mitochondrial functions with downstream effects on retrograde axonal transport,which can be partially rescued by DCTN1 overexpression. Dafinca et al. show that mutations in TDP-43 lead to decreased mitochondrial oxidative phosphorylation,partially due to interactions with the ATP production machinery and COX5A. These have direct effects on axonal transport,which is reduced in amyotrophic lateral sclerosis motor neurons,and overexpression of dynactin-1 significantly increases retrograde mitochondrial dynamics. View Publication

High-throughput massively parallel reporter assays (MPRAs) and phenotype-rich in vivo transgenic mouse assays are two potentially complementary ways to study the impact of noncoding variants associated with psychiatric diseases. Here,we investigate the utility of combining these assays. Specifically,we carry out an MPRA in induced human neurons on over 50,000 sequences derived from fetal neuronal ATAC-seq datasets and enhancers validated in mouse assays. We also test the impact of over 20,000 variants,including synthetic mutations and 167 common variants associated with psychiatric disorders. We find a strong and specific correlation between MPRA and mouse neuronal enhancer activity. Four out of five tested variants with significant MPRA effects affected neuronal enhancer activity in mouse embryos. Mouse assays also reveal pleiotropic variant effects that could not be observed in MPRA. Our work provides a catalog of functional neuronal enhancers and variant effects and highlights the effectiveness of combining MPRAs and mouse transgenic assays. MPRAs and in vivo transgenic mouse assays are two potentially complementary ways to assay the impact of noncoding variants. Here,authors find a strong and specific correlation between the assays in neural cells. Mouse assays also reveal pleiotropic effects not observed in MPRA. View Publication

In 2022-23,the world witnessed the largest recorded outbreak of monkeypox virus (MPXV). Neurological manifestations were reported alongside the detection of MPXV DNA and MPXV-specific antibodies in the cerebrospinal fluid of patients. Here,we analyze the susceptibility of neural tissue to MPXV using human neural organoids (hNOs) exposed to a clade IIb isolate. We report susceptibility of several cell types to the virus,including neural progenitor cells and neurons. The virus efficiently replicates in hNOs,as indicated by the exponential increase of infectious viral titers and establishment of viral factories. Our findings reveal focal enrichment of viral antigen alongside accumulation of cell-associated infectious virus,suggesting viral cell-to-cell spread. Using an mNeonGreen-expressing recombinant MPXV,we confirm cell-associated virus transmission. We furthermore show the formation of beads in infected neurites,a phenomenon associated with neurodegenerative disorders. Bead appearance precedes neurite-initiated cell death,as confirmed through live-cell imaging. Accordingly,hNO-transcriptome analysis reveals alterations in cellular homeostasis and upregulation of neurodegeneration-associated transcripts,despite scarcity of inflammatory and antiviral responses. Notably,tecovirimat treatment of MPXV-infected hNOs significantly reduces infectious virus loads. Our findings suggest that viral disruption of neuritic transport drives neuronal degeneration,potentially contributing to MPXV neuropathology and revealing targets for therapeutic intervention. The mechanisms underlying neurological complications of monkeypox virus infection remain unclear. Here,the authors investigate its neurotropic potential and show that neuritic transport of viral particles drives neuronal degeneration. View Publication

The transcription factor Growth Factor Independence 1B (GFI1B) recruits Lysine Specific Demethylase 1 A (LSD1/KDM1A) to stimulate gene programs relevant for megakaryocyte and platelet biology. Inherited pathogenic GFI1B variants result in thrombocytopenia and bleeding propensities with varying intensity. Whether these affect similar gene programs is unknow. Here we studied transcriptomic effects of four patient-derived GFI1B variants (GFI1BT174N,H181Y,R184P,Q287*) in MEG01 megakaryoblasts. Compared to normal GFI1B,each variant affected different gene programs with GFI1BQ287* uniquely failing to repress myeloid traits. In line with this,single cell RNA-sequencing of induced pluripotent stem cell (iPSC)-derived megakaryocytes revealed a 4.5-fold decrease in the megakaryocyte/myeloid cell ratio in GFI1BQ287* versus normal conditions. Inhibiting the GFI1B-LSD1 interaction with small molecule GSK-LSD1 resulted in activation of myeloid genes in normal iPSC-derived megakaryocytes similar to what was observed for GFI1BQ287* iPSC-derived megakaryocytes. Thus,GFI1B and LSD1 facilitate gene programs relevant for megakaryopoiesis while simultaneously repressing programs that induce myeloid differentiation. Using patient-derived induced pluripotent stem cells,the authors show that the transcription factor GFI1B and the lysine demethylase KDM1A/LSD1 promote gene programs while repressing those involved in myeloid differentiation. View Publication

MYBPC3,encoding cardiac myosin binding protein-C (cMyBP-C),is the most mutated gene known to cause hypertrophic cardiomyopathy (HCM). However,since little is known about the underlying etiology,additional in vitro studies are crucial to defining the underlying molecular mechanisms. Accordingly,this study aimed to investigate the molecular mechanisms underlying the pathogenesis of HCM associated with a polymorphic variant (D389V) in MYBPC3 by using isogenic human-induced pluripotent stem cell (hiPSC)-derived cardiac organoids (hCOs). The hiPSC-derived cardiomyocytes (hiPSC-CMs) and hCOs were generated from human subjects to define the molecular,cellular,functional,and energetic changes caused by the MYBPC3D389V variant,which is associated with increased fractional shortening and highly prevalent in South Asian descendants. Recombinant C0-C2,N’ region of cMyBP-C (wild-type and D389V),and myosin S2 proteins were also utilized to perform binding and motility assays in vitro. Confocal and electron microscopic analyses of hCOs generated from noncarriers (NC) and carriers of the MYBPC3D389V variant revealed the presence of highly organized sarcomeres. Furthermore,functional experiments showed hypercontractility,faster calcium cycling,and faster contractile kinetics in hCOs expressing MYBPC3D389V than NC hCOs. Interestingly,significantly increased cMyBP-C phosphorylation in MYBPC3D389V hCOs was observed,but without changes in total protein levels,in addition to higher oxidative stress and lower mitochondrial membrane potential (??m). Next,spatial mapping revealed the presence of endothelial cells,fibroblasts,macrophages,immune cells,and cardiomyocytes in the hCOs. The hypercontractile function was significantly improved after the treatment of the myosin inhibitor mavacamten (CAMZYOS®) in MYBPC3D389V hCOs. Lastly,various vitro binding assays revealed a significant loss of affinity in the presence of MYBPC3D389V with myosin S2 region as a likely mechanism for hypercontraction. Conceptually,we showed the feasibility of assessing the functional and molecular mechanisms of HCM using highly translatable hCOs through pragmatic experiments that led to determining the MYBPC3D389V hypercontractile phenotype,which was rescued by the administration of a myosin inhibitor. View Publication

The MAPT gene encodes Tau protein,a member of the large family of microtubule-associated proteins. Tau forms large insoluble aggregates that are toxic to neurons in several neurological disorders,and neurofibrillary Tau tangles represent a key pathological hallmark of Alzheimer’s disease (AD) and other tauopathies. Lowering Tau expression levels constitutes a potential treatment for AD but the mechanisms that regulate Tau expression at the transcriptional or translational level are not well understood. Natural antisense transcripts (NATs) are a particular class of long non-coding RNAs (lncRNAs) that can regulate expression of their overlapping protein-coding genes at the epigenetic,transcriptional,or translational level. We and others identified a long non-coding RNA associated with the MAPT gene,named MAPT antisense 1 (MAPT-AS1). We confirmed that MAPT-AS1 is expressed in neurons in human post mortem brain tissue. To study the role of MAPT-AS1 on MAPT expression regulation,we modulated the expression of this lncRNA in human neuroblastoma cell lines and in human induced pluripotent stem cell (iPSC) derived neurons. In contrast to previous reports,we observed no changes on MAPT mRNA or Tau protein levels upon modulation of MAPT-AS1 levels in these cellular models. Our data suggest that MAPT-AS1 does not regulate Tau expression levels in human neurons in vitro. Thus,MAPT-AS1 does not represent a valuable therapeutic target to lower Tau expression in patients affected by tauopathies including AD. View Publication