Using the yeast vacuole as a system to test the lipidic drivers of membrane heterogeneity in living cells.

The biophysical drivers of membrane lateral heterogeneity, often termed lipid rafts, have been largely explored using synthetic liposomes or mammalian plasma membrane-derived giant vesicles. Yeast vacuoles, an organelle comparable to mammalian lysosomes, is the only in vivo system that shows stable micrometer scale phase separation in unperturbed cells. The ease of manipulating lipid metabolism in yeast makes this a powerful system for identifying lipids involved in the onset of vacuole membrane heterogeneity. Vacuole domains are induced by stationary stage growth and nutritional starvation, during which they serve as a docking and internalization site for lipid droplet energy stores. Here we describe methods for characterizing vacuole phase separation, its physiological function, and its lipidic drivers. First, we detail methodologies for robustly inducing vacuole domain formation and quantitatively characterizing during live cell imaging experiments. Second, we detail a new protocol for biochemical isolation of stationary stage vacuoles, which allows for lipidomic dissection of membrane phase separation. Third, we describe biochemical techniques for analyzing lipid droplet internalization in vacuole domains. When combined with genetic or chemical perturbations to lipid metabolism, these methods allow for systematic dissection of lipid composition in the structure and function of ordered membrane domains in living cells.

Precision Medicine in Parkinson's Disease Using Induced Pluripotent Stem Cells.

Parkinson's disease (PD) is one of the most devastating neurological diseases; however, there is no effective cure yet. The availability of human induced pluripotent stem cells (iPSCs) provides unprecedented opportunities to understand the pathogenic mechanism and identification of new therapy for PD. Here a new model system of PD, including 2D human iPSC-derived midbrain dopaminergic (mDA) neurons, 3D iPSC-derived midbrain organoids (MOs) with cellular complexity, and more advanced microphysiological systems (MPS) with 3D organoids, is introduced. It is believed that successful integrations and applications of iPSC, organoid, and MPS technologies can bring new insight on PD's pathogenesis that will lead to more effective treatments for this debilitating disease.

Intracellular sphingolipid sorting drives membrane phase separation in the yeast vacuole.

The yeast vacuole membrane can phase separate into ordered and disordered domains, a phenomenon that is required for micro-lipophagy under nutrient limitation. Despite its importance as a biophysical model and physiological significance, it is not yet resolved if specific lipidome changes drive vacuole phase separation. Here we report that the metabolism of sphingolipids (SLs) and their sorting into the vacuole membrane can control this process. We first developed a vacuole isolation method to identify lipidome changes during the onset of phase separation in early stationary stage cells. We found that early stationary stage vacuoles are defined by an increased abundance of putative raft components, including 40% higher ergosterol content and a nearly 3-fold enrichment in complex SLs (CSLs). These changes were not found in the corresponding whole cell lipidomes, indicating that lipid sorting is associated with domain formation. Several facets of SL composition-headgroup stoichiometry, longer chain lengths, and increased hydroxylations-were also markers of phase-separated vacuole lipidomes. To test SL function in vacuole phase separation, we carried out a systematic genetic dissection of their biosynthetic pathway. The abundance of CSLs controlled the extent of domain formation and associated micro-lipophagy processes, while their headgroup composition altered domain morphology. These results suggest that lipid trafficking can drive membrane phase separation in vivo and identify SLs as key mediators of this process in yeast.

Polytypic Two-Dimensional FeAs with High Anisotropy.

In the realm of two-dimensional (2D) crystal growth, the chemical composition often determines the thermodynamically favored crystallographic structures. This relationship poses a challenge in synthesizing novel 2D crystals without altering their chemical elements, resulting in the rarity of achieving specific crystallographic symmetries or lattice parameters. We present 2D polymorphic FeAs crystals that completely differ from bulk orthorhombic FeAs (Pnma), differing in the stacking sequence, i.e., polytypes. Preparing polytypic FeAs outlines a strategy for independently controlling each symmetry operator, which includes the mirror plane for 2Q-FeAs (I4/mmm) and the glide plane for 1Q-FeAs (P4/nmm). As such, compared to bulk FeAs, polytypic 2D FeAs shows highly anisotropic properties such as electrical conductivity, Young's modulus, and friction coefficient. This work represents a concept of expanding 2D crystal libraries with a given chemical composition but various crystal symmetries.

Multi-omic analysis of selectively vulnerable motor neuron subtypes implicates altered lipid metabolism in ALS.

Amyotrophic lateral sclerosis (ALS) is a devastating disorder in which motor neurons degenerate, the causes of which remain unclear. In particular, the basis for selective vulnerability of spinal motor neurons (sMNs) and resistance of ocular motor neurons to degeneration in ALS has yet to be elucidated. Here, we applied comparative multi-omics analysis of human induced pluripotent stem cell-derived sMNs and ocular motor neurons to identify shared metabolic perturbations in inherited and sporadic ALS sMNs, revealing dysregulation in lipid metabolism and its related genes. Targeted metabolomics studies confirmed such findings in sMNs of 17 ALS (SOD1, C9ORF72, TDP43 (TARDBP) and sporadic) human induced pluripotent stem cell lines, identifying elevated levels of arachidonic acid. Pharmacological reduction of arachidonic acid levels was sufficient to reverse ALS-related phenotypes in both human sMNs and in vivo in Drosophila and SOD1G93A mouse models. Collectively, these findings pinpoint a catalytic step of lipid metabolism as a potential therapeutic target for ALS.

Approaches to characterize the transcriptional trajectory of human myogenesis.

Human pluripotent stem cells (hPSCs) have attracted considerable interest in understanding the cellular fate determination processes and modeling a number of intractable diseases. In vitro generation of skeletal muscle tissues using hPSCs provides an essential model to identify the molecular functions and gene regulatory networks controlling the differentiation of skeletal muscle progenitor cells. Such a genetic roadmap is not only beneficial to understanding human myogenesis but also to decipher the molecular pathology of many skeletal muscle diseases. The combination of established human in vitro myogenesis protocols and newly developed molecular profiling techniques offers extensive insight into the molecular signatures for the development of normal and disease human skeletal muscle tissues. In this review, we provide a comprehensive overview of the current progress of in vitro skeletal muscle generation from hPSCs and relevant examples of the transcriptional landscape and disease-related transcriptional aberrations involving signaling pathways during the development of skeletal muscle cells.

Novel culture system via wirelessly controllable optical stimulation of the FGF signaling pathway for human and pig pluripotency.

Stem cell fate is largely determined by cellular signaling networks and is heavily dependent on the supplementation of exogenous recombinant proteins into culture media; however, uneven distribution and inconsistent stability of recombinant proteins are closely associated with the spontaneous differentiation of pluripotent stem cells (PSCs) and result in significant costs in large-scale manufacturing. Here, we report a novel PSC culture system via wirelessly controllable optical activation of the fibroblast growth factor (FGF) signaling pathway without the need for supplementation of recombinant FGF2 protein, a key molecule for maintaining pluripotency of PSCs. Using a fusion protein between the cytoplasmic region of the FGF receptor-1 and a light-oxygen-voltage domain, we achieved tunable, blue light-dependent activation of FGF signaling in human and porcine PSCs. Our data demonstrate that a highly controllable optical stimulation of the FGF signaling pathway is sufficient for long-term maintenance of PSCs, without the loss of differentiation potential into three germ layers. This culture system will be a cost-effective platform for a large-scale stem cell culture.

Bringing rafts to life: Lessons learned from lipid organization across diverse biological membranes.

The ability of lipids to drive lateral organization is a remarkable feature of membranes and has been hypothesized to underlie the architecture of cells. Models for lipid rafts and related domains were originally based on the mammalian plasma membrane, but the nature of heterogeneity in this system is still not fully resolved. However, the concept of lipid-driven organization has been highly influential across biology, and has led to discoveries in organisms that feature a diversity of lipid chemistries and physiological needs. Here we review several emerging and instructive cases of membrane organization in non-mammalian systems. In bacteria, several types of membrane domains that act in metabolism and signaling have been elucidated. These widen our view of what constitutes a raft, but also introduce new questions about the relationship between organization and function. In yeast, observable membrane organization is found in both the plasma membrane and the vacuole. The latter serves as the best example of classic membrane phase partitioning in a living system to date, suggesting that internal organelles are important membranes to investigate across eukaryotes. Finally, we highlight plants as powerful model systems for complex membrane interactions in multicellular organisms. Plant membranes are organized by unique glycosphingolipids, supporting the importance of carbohydrate interactions in organizing lateral domains. These examples demonstrate that membrane organization is a potentially universal phenonenon in biology and argue for the continued broadening of lipid physical chemistry research into a wide range of systems.

Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PARKIN-Deficient Human Dopamine Neurons.

Mutations and loss of activity in PARKIN, an E3 ubiquitin ligase, play a role in the pathogenesis of Parkinson's disease (PD). PARKIN regulates many aspects of mitochondrial quality control including mitochondrial autophagy (mitophagy) and mitochondrial biogenesis. Defects in mitophagy have been hypothesized to play a predominant role in the loss of dopamine (DA) neurons in PD. Here, we show that although there are defects in mitophagy in human DA neurons lacking PARKIN, the mitochondrial deficits are primarily due to defects in mitochondrial biogenesis that are driven by the upregulation of PARIS and the subsequent downregulation of PGC-1α. CRISPR/Cas9 knockdown of PARIS completely restores the mitochondrial biogenesis defects and mitochondrial function without affecting the deficits in mitophagy. These results highlight the importance mitochondrial biogenesis versus mitophagy in the pathogenesis of PD due to inactivation or loss of PARKIN in human DA neurons.

Transcriptional landscape of myogenesis from human pluripotent stem cells reveals a key role of TWIST1 in maintenance of skeletal muscle progenitors.

Generation of skeletal muscle cells with human pluripotent stem cells (hPSCs) opens new avenues for deciphering essential, but poorly understood aspects of transcriptional regulation in human myogenic specification. In this study, we characterized the transcriptional landscape of distinct human myogenic stages, including OCT4::EGFP+ pluripotent stem cells, MSGN1::EGFP+ presomite cells, PAX7::EGFP+ skeletal muscle progenitor cells, MYOG::EGFP+ myoblasts, and multinucleated myotubes. We defined signature gene expression profiles from each isolated cell population with unbiased clustering analysis, which provided unique insights into the transcriptional dynamics of human myogenesis from undifferentiated hPSCs to fully differentiated myotubes. Using a knock-out strategy, we identified TWIST1 as a critical factor in maintenance of human PAX7::EGFP+ putative skeletal muscle progenitor cells. Our data revealed a new role of TWIST1 in human skeletal muscle progenitors, and we have established a foundation to identify transcriptional regulations of human myogenic ontogeny (online database can be accessed in http://www.myogenesis.net/).

Correlation between Spot Sign and Intracranial Hemorrhage Expansion on Dual-Phase CT Angiography.

PURPOSE: Expansion of intracranial hemorrhage (ICH) is an important predictor of poor clinical outcome. ICH expansion can be predicted with a spot sign on computed tomographic angiography (CTA). We aimed to evaluate the correlation between spot signs on CTA and ICH expansion on dual-phase CTA. METHODS: Patients with spontaneous ICH between January 2017 and April 2019 who underwent an initial CT, dual-phase CTA, and a subsequent CT were retrospectively identified. ICH expansion was defined as volume growth of >33% or >6 mL. We analyzed the presence and change in size of the spot sign in the first phase and second phase CTA. Also, we divided the morphological status of the spot sign, such as a dot-like lesion or linear contrast extravasation, in the first and second phase CTA. RESULTS: A total of 206 patients, including 38 (18.5%) with ICH expansion and 45 (21.8%) with a spot sign, qualified for analysis. Of patients with a spot sign, 26 (57.8%) had ICH expansion on subsequent CT. Increased size of a spot sign in second-phase CTA was more frequent in the ICH expansion group than in the no-expansion group (96.2% vs. 52.6%, p < 0.001). First visualization of a spot sign in the second phase was more common in the no-expansion group than in the ICH expansion group (47.4% vs. 3.8%, p < 0.001). The morphological patterns of a spot sign between the two groups were not significantly different. CONCLUSION: Spot signs on dual-phase CTA have different sizes and morphological patterns. Increased size of a spot sign in the second phase of CTA can help identify patients at risk for ICH expansion.

Experimental Investigation on 3D Graphene-CNT Hybrid Foams with Different Interactions.

Due to the exceptional properties of graphene, numerous possibilities for real applications in various fields have been provided. However, it is a challenge to fabricate bulk graphene materials with properties arising from the nature of individual graphene sheets, and which assemble into monolithic three-dimensional structures. If 3D structured graphene foam were made instead of 2D structured graphene, it is expected that it would be a facile fabrication, with relatively low cost with the possibility of scale-up, and would maintain the intrinsic properties of graphene. To solve the weaknesses of 2D structured graphene, this study aimed to fabricate a 3D graphene-carbon nanotubes (CNT) hybrid foam. In this study, CNT was used to reinforce the graphene foams. In addition, two different surfactants, known as sodium dodecylbenzene sulphonate (SDBS) and cetyltrimethylammonium bromide (CTAB), were applied to help CNT dispersion. The π⁻π interaction was induced by SDBS/CNT, while ionic interaction was derived from CTAB/CNT. To confirm the charge effect with different surfactants, SEM, Zeta-potential, FT-IR, Raman spectroscopy, and compression tests were performed. When using a cationic surfactant, CTAB, compressive modulus, and strength increased due to the formation of relatively strong ionic bonding.

Scopoletin Stimulates Melanogenesis via cAMP/PKA Pathway and Partially p38 Activation.

Scopoletin was recently shown to stimulate melanogenesis through cAMP-response element-binding protein (CREB) phosphorylation. In this study, we investigated the molecular events of melanogenesis-induced by scopoletin. After exposure to scopoletin, the protein levels of tyrosinase and tyrosianse related protein-1 (TRP-1) were significantly increased in B16F10 cells. The mRNA levels of tyrosinase and microphthalmia-associated transcription factor (MITF) were also enhanced by scopoletin. cAMP production and phosphorylation of p38 mitogen-activated protein kinase (MAPK) were increased by scopoletin treatment. Scopoletin-mediated increase of intracellular melanin and tyrosinase expression were significantly attenuated by protein kinase A (PKA) inhibitors (H-89 and KT5720), while a protein kinase C (PKC) inhibitor (Ro-32-0432) had no effect and a p38 MAPK inhibitor (SB203580) partially blocked the scopoletin-induced intracellular melanin and tyrosinase expression. Moreover, scopoletin synergistically with cell-permeable cAMP analog (dibutyryl cAMP) significantly induced tyrosinase activity and melanin content in B16F10 cells. The silencing of p38 MAPK by small interfering RNA (siRNA) decreased the scopoletin-induced tyrosinase expression in B16F10 cells. These results suggest that scopoletin could induce melanin synthesis through the cAMP/PKA pathway and partially p38 MAPK activation in B16F10 cells.

Concordant but Varied Phenotypes among Duchenne Muscular Dystrophy Patient-Specific Myoblasts Derived using a Human iPSC-Based Model.

Duchenne muscular dystrophy (DMD) remains an intractable genetic disease. Althogh there are several animal models of DMD, there is no human cell model that carries patient-specific DYSTROPHIN mutations. Here, we present a human DMD model using human induced pluripotent stem cells (hiPSCs). Our model reveals concordant disease-related phenotypes with patient-dependent variation, which are partially reversed by genetic and pharmacological approaches. Our "chemical-compound-based" strategy successfully directs hiPSCs into expandable myoblasts, which exhibit a myogenic transcriptional program, forming striated contractile myofibers and participating in muscle regeneration in vivo. DMD-hiPSC-derived myoblasts show disease-related phenotypes with patient-to-patient variability, including aberrant expression of inflammation or immune-response genes and collagens, increased BMP/TGFß signaling, and reduced fusion competence. Furthermore, by genetic correction and pharmacological "dual-SMAD" inhibition, the DMD-hiPSC-derived myoblasts and genetically corrected isogenic myoblasts form "rescued" multi-nucleated myotubes. In conclusion, our findings demonstrate the feasibility of establishing a human "DMD-in-a-dish" model using hiPSC-based disease modeling.

Human umbilical cord blood-derived mesenchymal stem cells improve functional recovery through thrombospondin1, pantraxin3, and vascular endothelial growth factor in the ischemic rat brain.

Cell therapy is a potential therapeutic method for cerebral ischemia, which remains a serious problem. In the search for more effective therapeutic methods, many kinds of stem cells from various tissues have been developed and tested as candidate therapeutic agents. Among them, human umbilical cord blood (hUCB)-derived mesenchymal stem cells (MSCs) are widely used for cell therapy because of their genetic flexibility. To confirm that they are effective and understand how they affect ischemic neural cells, hUCB-MSCs were directly administered ipsilaterally into an ischemic zone induced by middle cerebral artery occlusion (MCAO). We found that the neurobehavioral performance of the hUCB-MSC group was significantly improved compared with that of the vehicle-injected control group. The infarct was also remarkably smaller in the hUCB-MSC group. Additionally, hUCB-MSC transplantation resulted in a greater number of newly generated cells and angiogenic and tissue repair factors and a lower number of inflammatory events in the penumbra zone. To determine why these events occurred, hUCB-MSCs were assayed under hypoxic and normoxic conditions in vitro. The results showed that hUCB-MSCs exhibit higher expression levels of thrombospondin1, pantraxin3, and vascular endothelial growth factor under hypoxic conditions than under normoxic conditions. These results were found to be correlated with our in vivo immunofluorescent staining results. On the basis of these findings, we suggest that hUCB-MSCs may have a beneficial effect on cerebral ischemia, especially through angiogenesis, neurogenesis, and anti-inflammatory effects, and thus could be used as a therapeutic agent to treat neurological disorders such as cerebral ischemia.

Association of vitamin B12 deficiency and metformin use in patients with type 2 diabetes.

We evaluated the prevalence of vitamin B12 deficiency and associated factors in type 2 diabetes patients using metformin. A total of 799 type 2 diabetes patients using metformin was enrolled. Vitamin B12 and folate levels were quantified by chemiluminescent enzyme immunoassay. Vitamin B12 deficiency was defined as vitamin B12 ≤ 300 pg/mL without folate deficiency (folate > 4 ng/mL). The prevalence of vitamin B12 deficiency in metformin-treated type 2 diabetes patients was 9.5% (n = 76), and the mean vitamin B12 level was 662.5 ± 246.7 pg/mL. Vitamin B12 deficient patients had longer duration of metformin use (P < 0.001) and higher daily metformin dose (P < 0.001) than non-deficient patients. Compared with daily metformin dose of ≤ 1,000 mg, the adjusted odds ratio for 1,000-2,000 mg, and ≥ 2,000 mg were 2.52 (95% CI, 1.27-4.99, P = 0.008) and 3.80 (95% CI, 1.82-7.92, P < 0.001). Compared with metformin use of < 4 yr, the adjusted odds ratios for 4-10 yr, and ≥ 10 yr were 4.65 (95% CI, 2.36-9.16, P < 0.001) and 9.21 (95% CI, 3.38-25.11, P < 0.001), respectively. In conclusion, our study indicates that patients with type 2 diabetes treated with metformin should be screened for vitamin B12 deficiency, especially at higher dosages (> 1,000 mg) and longer durations (≥ 4 yr) of treatment.

Large-scale screening using familial dysautonomia induced pluripotent stem cells identifies compounds that rescue IKBKAP expression.

Patient-specific induced pluripotent stem cells (iPSCs) represent a novel system for modeling human genetic disease and could provide a source of cells for large-scale drug-discovery screens. Here we demonstrate the feasibility of performing a primary screen in neural crest precursors derived from iPSCs that were generated from individuals with familial dysautonomia (FD), a rare, fatal genetic disorder affecting neural crest lineages. We tested 6,912 small-molecule compounds and characterized eight that rescued expression of IKBKAP, the gene responsible for FD. One of the hits, SKF-86466, was found to induce IKBKAP transcription through modulation of intracellular cAMP levels and PKA-dependent CREB phosphorylation. SKF-86466 also rescued IKAP protein expression and the disease-specific loss of autonomic neuronal marker expression. Our data implicate alpha-2 adrenergic receptor activity in regulating IKBKAP expression and demonstrate that small-molecule discovery using an iPSC-based disease model can identify candidate drugs for potential therapeutic intervention.

Construction of an expression system for the secretory production of recombinant α-agarase in yeast.

α-Agarase hydrolyzes the α-1,3 linkage of agarose yielding agaro-oligosaccharides. It is less well characterized than ß-agarase. AgaA gene (2.3 kb ORF), encoding the α-agarase from Thalassomonas JAMB A33, was subcloned into both a constitutive and an inducible expression vector. Both the constructed plasmids, pVT-AgaA (ADH1 promoter) and pYInu-AgaA (GAL10 promoter), were transformed into Saccharomyces cerevisiae SEY2102 and FY833 and pPIC9-AgaA harboring the AOX1 promoter was transformed into Pichia pastoris GS115. The recombinant α-agarases were over-expressed with activities from 0.3 to 1.6 unit/ml, the highest being in the SEY2102/pYInu-AgaA transformant. Most of the recombinant α-agarase was extracellular because each plasmid possesses a signal sequence for the secretory production of α-agarase. In contrast, the Pichia host-vector expression system was unsuitable for the production of recombinant α-agarase. This is the first report of recombinant production of α-agarase in yeast for industrial use.