Transcriptome analysis of skeletal muscle in dermatomyositis, polymyositis, and dysferlinopathy, using a bioinformatics approach.

Background: Polymyositis (PM) and dermatomyositis (DM) are two distinct subgroups of idiopathic inflammatory myopathies. Dysferlinopathy, caused by a dysferlin gene mutation, usually presents in late adolescence with muscle weakness, degenerative muscle changes are often accompanied by inflammatory infiltrates, often resulting in a misdiagnosis as polymyositis. Objective: To identify differential biological pathways and hub genes related to polymyositis, dermatomyositis and dysferlinopathy using bioinformatics analysis for understanding the pathomechanisms and providing guidance for therapy development. Methods: We analyzed intramuscular ribonucleic acid (RNA) sequencing data from seven dermatomyositis, eight polymyositis, eight dysferlinopathy and five control subjects. Differentially expressed genes (DEGs) were identified by using DESeq2. Enrichment analyses were performed to understand the functions and enriched pathways of DEGs. A protein-protein interaction (PPI) network was constructed, and clarified the gene cluster using the molecular complex detection tool (MCODE) analysis to identify hub genes. Results: A total of 1,048, 179 and 3,807 DEGs were detected in DM, PM and dysferlinopathy, respectively. Enrichment analyses revealed that upregulated DEGs were involved in type 1 interferon (IFN1) signaling pathway in DM, antigen processing and presentation of peptide antigen in PM, and cellular response to stimuli in dysferlinopathy. The PPI network and MCODE cluster identified 23 genes related to type 1 interferon signaling pathway in DM, 4 genes (PDIA3, HLA-C, B2M, and TAP1) related to MHC class 1 formation and quality control in PM, and 7 genes (HSPA9, RPTOR, MTOR, LAMTOR1, LAMTOR5, ATP6V0D1, and ATP6V0B) related to cellular response to stress in dysferliniopathy. Conclusion: Overexpression of genes related to the IFN1 signaling pathway and major histocompatibility complex (MHC) class I formation was identified in DM and PM, respectively. In dysferlinopathy, overexpression of HSPA9 and the mTORC1 signaling pathway genes was detected.

Gas Chromatography with Flame-Ionization Detection-Based Analysis of Sugar Contents in Korean Agricultural Products for Patients with Galactosemia.

Patients with galactosemia accumulate galactose in their bodies, requiring a lifelong galactose-restricted diet. Therefore, accurate information on the galactose content in commercial agro-food resources is essential. The HPLC method generally used for sugar analysis has low separation and detection sensitivity. Here, we sought to establish an accurate analytical method for determining the galactose content in commercial agro-food resources. To that aim, we employed gas chromatography with flame-ionization detection to detect trimethylsilyl-oxime (TMSO) sugar derivatives (concentration: ≤0.1 mg/100 g). The galactose content in 107 Korean agro-food resources reflecting intake patterns was then analyzed. The galactose content in steamed barley rice was 5.6 mg/100 g, which was higher than that in steamed non-glutinous and glutinous rice. Moist-type and dry-type sweet potatoes, blanched zucchini, and steamed Kabocha squash had high galactose content (36.0, 12.8, 23.1, and 61.6 mg/100 g, respectively). Therefore, these foods are detrimental to patients with galactosemia. Among fruits, avocado, blueberry, kiwi, golden kiwifruit, and sweet persimmon had galactose contents of ≥10 mg/100 g. Dried persimmon had 132.1 mg/100 g and should therefore be avoided. Mushrooms, meat, and aquatic products showed low galactose content (≤10 mg/100 g), making them safe. These findings will help patients to manage their dietary galactose intake.

MicroRNA-dependent inhibition of WEE1 controls cancer stem-like characteristics and malignant behavior in ovarian cancer.

Cancer stem-like cells (CSCs) have been suggested to be responsible for chemoresistance and tumor recurrence owing to their self-renewal capacity and differentiation potential. Although WEE1 is a strong candidate target for anticancer therapies, its role in ovarian CSCs is yet to be elucidated. Here, we show that WEE1 plays a key role in regulating CSC properties and tumor resistance to carboplatin via a microRNA-dependent mechanism. We found that WEE1 expression is upregulated in ovarian cancer spheroids because of the decreased expression of miR-424 and miR-503, which directly target WEE1. The overexpression of miR-424/503 suppressed CSC activity by inhibiting WEE1 expression, but this effect was reversed on the restoration of WEE1 expression. Furthermore, we demonstrated that NANOG modulates the miR-424/503-WEE1 axis that regulates the properties of CSCs. We also demonstrated the pharmacological restoration of the NANOG-miR-424/503-WEE1 axis and attenuation of ovarian CSC characteristics in response to atorvastatin treatment. Lastly, miR-424/503-mediated WEE1 inhibition re-sensitized chemoresistant ovarian cancer cells to carboplatin. Additionally, combined treatment with atorvastatin and carboplatin synergistically reduced tumor growth, chemoresistance, and peritoneal seeding in the intraperitoneal mouse models of ovarian cancer. We identified a novel NANOG-miR-424/503-WEE1 pathway for regulating ovarian CSCs, which has potential therapeutic utility in ovarian cancer treatment.

Nationwide incidence of myotonic dystrophy type 1 and the status of multi-organ involvement.

PURPOSE: This study aimed to investigate the incidence of myotonic dystrophy type 1 (DM1) and the status of multi-organ involvement. METHODS: This was a nationwide, population-based, cohort study using data from the Korean National Health Claims database. All patients with DM1 from the entire population aged ≤ 80 years were included. To identify possible systemic diseases along with DM1, we searched for concurrent codes for systemic diseases. To assess the recent status of systemic evaluation, concurrent codes for various diagnostic and treatment modalities were collected. Cumulative incidence during 2016-2019 was first evaluated then systemic evaluation for those patients was assessed during 2010-2019. RESULTS: A total of 387 patients (47.8% men) during the recent 4-year study period (2016-2019) were diagnosed with DM1. The cumulative incidence in the general population was 0.77 (95% confidence interval: 0.76-0.77) per 100,000 persons. In newly developed incidental cases, cardiac involvement developed in 51.2%, pneumonia in 30.7%, diabetes in 26.9%, brain involvement in 18.1%, cataract in 13.7%, and cancers in 5.4% of total patients. Electrocardiography was performed in 93.8%, Holter in 33.9%, and echocardiography in 31.3% of the total patients for cardiac evaluation. CONCLUSIONS: The incidence estimates of DM1 in the Asian population were lower than those of Caucasians. This study provides the real situation of screening and treatment for systemic diseases related to DM1. These detailed estimates could promote an understanding of the current disease status and allow for appropriate planning within the healthcare system.

A near-complete genome sequence of mungbean (Vigna radiata L.) provides key insights into the modern breeding program.

Mungbean (Vigna radiata L.), a fast-growing legume species, is an important source of carbohydrates and proteins in developing countries of Asia. Here, we constructed a near-complete genome sequence of mungbean with a scaffold N50 value of 5.2 Mb and only a 0.4% gap, with a total scaffold size of 475 Mb. We identified several misassembled pseudomolecules (Chr03, Chr04, Chr05, and Chr08) in the previous draft assembly; Chr03, Chr04, and Chr08 were assembled into one chromosome, and Chr05 was broken into two chromosomes in the improved reference genome assembly, thus providing more accurate linkage information to breeders. Additionally, using an ultra-high-resolution linkage map constructed based on resequencing data, we identified several quantitative trait loci (QTLs) and the underlying candidate genes affecting synchronous pod maturity (SPM). Mungbean homologs of two soybean ([Glycine max (L.) Merr.] flowering genes, E3 (phytochrome A) and J (early flowering 3), were identified as candidate genes for the QTLs, and the candidate genes for plant height, node number, and SPM showed critical nucleotide substitutions between the reference cultivar and other genotypes (landraces and wild accessions). Based on the analysis of genetic diversity among 276 accessions collected from 23 countries, we identified 36 selective sweep regions and observed that the overall genetic diversity of cultivars decreased to 30% of that in wild accessions postdomestication. The near-complete genome sequence of mungbean represents an important resource for genome-assisted improvement in the mungbean breeding program.

Triggered Electrooculography for Identification of Oculomotor and Abducens Nerves during Skull Base Surgery.

OBJECTIVE: Electrooculography (EOG) records eyeball movements as changes in the potential difference between the negatively charged retina and the positively charged cornea. We aimed to investigate whether reliable EOG waveforms can be evoked by electrical stimulation of the oculomotor and abducens nerves during skull base surgery. METHODS: We retrospectively reviewed the records of 18 patients who had undergone a skull base tumor surgery using EOG (11 craniotomies and seven endonasal endoscopic surgeries). Stimulation was performed at 5 Hz with a stimulus duration of 200 µs and an intensity of 0.1-5 mA using a concentric bipolar probe. Recording electrodes were placed on the upper (active) and lower (reference) eyelids, and on the outer corners of both eyes; the active electrode was placed on the contralateral side. RESULTS: Reproducibly triggered EOG waveforms were observed in all cases. Electrical stimulation of cranial nerves (CNs) III and VI elicited positive waveforms and negative waveforms, respectively, in the horizontal recording. The median latencies were 3.1 and 0.5 ms for craniotomies and endonasal endoscopic surgeries, respectively (p=0.007). Additionally, the median amplitudes were 33.7 and 46.4 µV for craniotomies and endonasal endoscopic surgeries, respectively (p=0.40). CONCLUSION: This study showed reliably triggered EOG waveforms with stimulation of CNs III and VI during skull base surgery. The latency was different according to the point of stimulation and thus predictable. As EOG is noninvasive and relatively easy to perform, it can be used to identify the ocular motor nerves during surgeries as an alternative of electromyography.

Transcriptomic and biochemical analyses of the accumulation of sucrose in mungbean (Vigna radiata (L.) Wilczek) leaves after pod removal.

KEY MESSAGE: Synchronous pod maturity is critical for increasing grain yield. The candidate genes involved in synchronous pod maturity were identified through RNA-seq and HPLC. Mungbean (Vigna radiata [L.] Wilczek), an important source of carbohydrate and protein in Asia, is characterized by nonsynchronous pod maturity; consequently, harvesting is labor intensive. Because pod maturity is associated with synthesis and remobilization of sucrose, we examined changes in sucrose levels and transcriptome in leaf (source) tissues after pod (sink) removal using two genotypes, VC1973A and V2984; VC1973A had higher synchronicity in pod maturity than V2984. After pod removal, much higher number of pods were produced in V2984 than VC1973A. The sucrose content of leaf tissues significantly decreased in V2984 because it continued to utilize assimilates from leaves for producing new pods, but significantly increased in VC1973A because of the loss of sink. Transcriptome analysis revealed that the number of differentially expressed genes was approximately fourfold higher in VC1973A than in those of V2984 after pod removal. The expression of two paralogous genes (Vradi01g05010 and Vradi10g08240), encoding beta-glucosidase enzymes, significantly decreased in VC1973A after pod removal and was significantly lower in depodded VC1973A than depodded V2984, indicating these two genes may participate in sucrose utilization for seed development by regulating the level of glucose. The results of this study will help elucidate the genetic basis of synchronous pod maturity in mungbean and facilitate the development of new cultivars with synchronous pod maturity.

Genome sequence of Jatropha curcas L., a non-edible biodiesel plant, provides a resource to improve seed-related traits.

Jatropha curcas (physic nut), a non-edible oilseed crop, represents one of the most promising alternative energy sources due to its high seed oil content, rapid growth and adaptability to various environments. We report ~339 Mbp draft whole genome sequence of J. curcas var. Chai Nat using both the PacBio and Illumina sequencing platforms. We identified and categorized differentially expressed genes related to biosynthesis of lipid and toxic compound among four stages of seed development. Triacylglycerol (TAG), the major component of seed storage oil, is mainly synthesized by phospholipid:diacylglycerol acyltransferase in Jatropha, and continuous high expression of homologs of oleosin over seed development contributes to accumulation of high level of oil in kernels by preventing the breakdown of TAG. A physical cluster of genes for diterpenoid biosynthetic enzymes, including casbene synthases highly responsible for a toxic compound, phorbol ester, in seed cake, was syntenically highly conserved between Jatropha and castor bean. Transcriptomic analysis of female and male flowers revealed the up-regulation of a dozen family of TFs in female flower. Additionally, we constructed a robust species tree enabling estimation of divergence times among nine Jatropha species and five commercial crops in Malpighiales order. Our results will help researchers and breeders increase energy efficiency of this important oil seed crop by improving yield and oil content, and eliminating toxic compound in seed cake for animal feed.

Lower-extremity magnetic resonance imaging in patients with hyperkalemic periodic paralysis carrying the SCN4A mutation T704M: 30-month follow-up of seven patients.

Hyperkalemic periodic paralysis (hyperKPP) is a muscle channelopathy characterized by recurrent paralytic attacks. Our previous study, in which we conducted whole-body muscle magnetic resonance imaging (MRI) in patients with hyperKPP, revealed muscle atrophy and fatty change in the lower extremity, especially in older persons. The aim of current study was to identify the progression of myopathy in hyperKPP patients had been assessed in the previous study. We performed lower-extremity muscle MRI in seven hyperKPP patients carrying the T704M mutation in the SCN4A gene at an interval of 30 months. Muscle atrophy, edematous change, fatty change, and fat fraction quantified using the Dixon technique were compared with the previous MRI findings. The lower-extremity MRI scan showed progressive muscle pathologic findings when compared with the previous study. Muscle atrophy, edematous change, and fatty change were prominent in the superficial posterior compartment of the lower leg. The follow-up lower-extremity muscle MRI findings provide evidence for chronic progressive myopathy and suggest the usefulness of MRI for assessing disease progression in patients with hyperKPP. This study is meaningful in terms of providing data showing the longitudinal changes of muscles in patients with periodic paralysis.

A PPARγ-dependent miR-424/503-CD40 axis regulates inflammation mediated angiogenesis.

Activation of the endothelium by pro-inflammatory stimuli plays a key role in the pathogenesis of a multitude of vascular diseases. Angiogenesis is a crucial component of the vascular response associated with inflammatory signaling. The CD40/CD40 ligand dyad in endothelial cells (EC) has a central role in promoting vascular inflammatory response; however, the molecular mechanism underlying this component of inflammation and angiogenesis is not fully understood. Here we report a novel microRNA mediated suppression of endothelial CD40 expression. We found that CD40 is closely regulated by miR-424 and miR-503, which directly target its 3' untranslated region. Pro-inflammatory stimuli led to increased endothelial CD40 expression, at least in part due to decreased miR-424 and miR-503 expression. In addition, miR-424 and miR-503 reduced LPS induced EC sprouting, migration and tube formation. Moreover, we found that miR-424 and miR-503 expression is directly regulated by peroxisome proliferator-activated receptor gamma (PPARγ), whose endothelial expression and activity are decreased in response to inflammatory factors. Finally, we demonstrate that mice with endothelial-specific deletion of miR-322 (miR-424 ortholog) and miR-503 have augmented angiogenic response to LPS in a Matrigel plug assay. Overall, these studies identify a PPARγ-dependent miR-424/503-CD40 signaling axis that is critical for regulation of inflammation mediated angiogenesis.

Negative regulation of NOD1 mediated angiogenesis by PPARγ-regulated miR-125a.

Infection with pathogens activates the endothelial cell and its sustained activation may result in impaired endothelial function. Endothelial dysfunction contributes to the pathologic angiogenesis that is characteristic of infection-induced inflammatory pathway activation. Nucleotide-binding oligomerization domain-containing protein 1 (NOD1) is a protein receptor which recognizes bacterial molecules and stimulates an immune reaction in various cells; however, the underlying molecular mechanisms in the regulation of inflammation-triggered angiogenesis are not fully understood. Here we report that peroxisome proliferator-activated receptor gamma (PPARγ)-mediated miR-125a serves as an important regulator of NOD1 agonist-mediated angiogenesis in endothelial cells by directly targeting NOD1. Treatment of human umbilical vein endothelial cells with natural PPARγ ligand, 15-Deoxy-Delta12,14-prostaglandin J2, led to inhibition of NOD1 expression; contrarily, protein levels of NOD1 were significantly increased by PPARγ knockdown. We report that PPARγ regulation of NOD1 expression is a novel microRNA-mediated regulation in endothelial cells. MiR-125a expression was markedly decreased in human umbilical vein endothelial cells subjected to PPARγ knockdown while 15-Deoxy-Delta12,14-prostaglandin J2 treatment increased the level of miR-125a. In addition, NOD1 is closely regulated by miR-125a, which directly targets the 3' untranslated region of NOD1. Moreover, both overexpression of miR-125a and PPARγ activation led to inhibition of NOD1 agonist-induced tube formation in endothelial cells. Finally, NOD1 agonist increased the formation of cranial and subintestinal vessel plexus in zebrafish, and this effect was abrogated by concurrent PPARγ activation. Overall, these findings identify a PPARγ-miR-125a-NOD1 signaling axis in endothelial cells that is critical in the regulation of inflammation-mediated angiogenesis.

Affinity-mediated sorting order reversal of single-walled carbon nanotubes in density gradient ultracentrifugation.

Sorted single-walled carbon nanotubes (SWNTs) are of paramount importance for their utilization in high-end optoelectronic applications. Sodium cholate (SC)-based density gradient ultracentrifugation (DGU) has been instrumental in isolating small diameter (d t) SWNTs. Here, we show that SWNTs wrapped by flavin mononucleotide (FMN) as a dispersing agent are sorted in DGU, and show sorting order reversal behavior, departing from prototypical SC-SWNT trends. Larger d t SWNTs are sorted in lower density (ρ), and buoyant ρ distribution of FMN-SWNT ranges from 1.15-1.25 g cm(-3). Such a nanotube layering pattern originates from both the binding affinity between FMN and SWNT and the less-susceptible hydrated volume of remote phosphate sidechains of FMN according to nanotube d t change.

Translational genomics for plant breeding with the genome sequence explosion.

The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

Serum interleukin-27 expression in patients with myasthenia gravis.

Myasthenia gravis (MG)(1) is an autoimmune disease directed at the neuromuscular junction, and cytokines are thought to contribute to its immunopathogenesis. Interleukin-27 (IL-27)(2) plays a complex and pleiotropic role in immune responses associated with T helper cells. To assess the role of IL-27 in MG, we determined serum IL-27 levels in MG patients (n=32) compared to healthy controls (n=50). The median serum IL-27 level was significantly higher in MG patients (35.947pg/mL) than in controls (19.885pg/mL). Furthermore, serum IL-27 was significantly higher in early onset MG. This study suggests the possibility that IL-27 might contribute to MG pathogenesis or immunoregulation.

Posterior reversible encephalopathy syndrome as an initial neurological manifestation of primary Sjögren's syndrome.

It is well known that patients with peripheral neuropathy along with autonomic involvement can also exhibit autonomic hyperactivity. There are rare cases in which these patients developed posterior reversible encephalopathy syndrome (PRES). Patients with primary Sjögren's syndrome (pSS) may be more likely to exhibit autonomic hypofunction rather than autonomic hyperfunction, which is a rare event. In the present work, we report the first known case of PRES as an initial neurological manifestation of pSS.

Novel glycosylated VEGF decoy receptor fusion protein, VEGF-Grab, efficiently suppresses tumor angiogenesis and progression.

Antiangiogenic therapies targeting VEGFA have been commonly used in clinics to treat cancers over the past decade. However, their clinical efficacy has been limited, with drawbacks including acquisition of resistance and activation of compensatory pathways resulting from elevated circulating VEGFB and placental growth factor (PlGF). To bypass these disadvantages, we developed a novel glycosylated soluble decoy receptor fusion protein, VEGF-Grab, that can neutralize VEGFA, VEGFB, and PlGF. VEGF-Grab has the second and third immunoglobulin (Ig)-like domains of VEGF receptor 1 (VEGFR1) fused to IgG1 Fc, with three potential glycosylation sites introduced into the third Ig-like domain of VEGF-Grab by mutagenesis. Compared with VEGF-Trap, VEGF-Grab showed more potent decoy activity against VEGF and PlGF, mainly attributed to the VEGFR1 backbone. Most importantly, the negatively charged O-glycans attached to the third Ig-like domain of VEGFR1 counterbalanced the originally positively charged VEGFR1 backbone, minimizing nonspecific binding of VEGF-Grab to the extracellular matrix, and resulting in greatly improved pharmacokinetic profile. These advancements led to stronger and more durable antiangiogenic, antitumor, and antimetastatic efficacy in both implanted and spontaneous tumor models as compared with VEGF-Trap, while toxicity profiles were comparable with VEGF-Trap. Collectively, our results highlight VEGF-Grab as a promising therapeutic candidate for further clinical drug development.

Compound heterozygous mutations of TYMP as underlying causes of mitochondrial neurogastrointestinal encephalomyopathy (MNGIE).

Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE), an autosomal recessive multiorgan disease, frequently associated with mutations in the thymidine phosphorylase (TYMP) gene. TYMP encodes thymidine phosphorylase (TP), which has an essential role in the nucleotide salvage pathway for mitochondrial DNA (mtDNA) replication. This study reports an MNGIE patient with novel compound heterozygous missense mutations (Thr151Pro and Leu270Pro) in TYMP. Each mutation was inherited from one parent. Neither mutation was found in the controls and the mutation sites were well conserved between different species. Neither large deletion nor causative point mutations were found in the mtDNA. The patient presented with MNGIE symptoms, including gastrointestinal discomfort, external ophthalmoplegia, pigmentary retinopathy and demyelinating type diffuse sensory motor polyneuropathy. The patient demonstrated an early-onset but mild phenotype, with 9.6% TP activity; therefore, patients with these compound heterozygous mutations may exhibit a mild phenotype with a variable onset age according to TP activity level.