Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts.

Single-cell RNA-sequencing analysis is one of the most effective tools for understanding specific cellular states. The use of single cells or pooled cells in RNA-seq analysis requires the isolation of cells from a tissue or culture. Although trypsin or more recently cold-active protease (CAP) has been used for cell dissociation, the extent to which the gene expression changes are suppressed has not been clarified. To this end, we conducted detailed profiling of the enzyme-dependent gene expression changes in mouse skeletal muscle progenitor cells, focusing on the enzyme treatment time, amount and temperature. We found that the genes whose expression was changed by the enzyme treatment could be classified in a time-dependent manner and that there were genes whose expression was changed independently of the enzyme treatment time, amount and temperature. This study will be useful as reference data for genes that should be excluded or considered for RNA-seq analysis using enzyme isolation methods.

Discriminative feature of cells characterizes cell populations of interest by a small subset of genes.

Organisms are composed of various cell types with specific states. To obtain a comprehensive understanding of the functions of organs and tissues, cell types have been classified and defined by identifying specific marker genes. Statistical tests are critical for identifying marker genes, which often involve evaluating differences in the mean expression levels of genes. Differentially expressed gene (DEG)-based analysis has been the most frequently used method of this kind. However, in association with increases in sample size such as in single-cell analysis, DEG-based analysis has faced difficulties associated with the inflation of P-values. Here, we propose the concept of discriminative feature of cells (DFC), an alternative to using DEG-based approaches. We implemented DFC using logistic regression with an adaptive LASSO penalty to perform binary classification for discriminating a population of interest and variable selection to obtain a small subset of defining genes. We demonstrated that DFC prioritized gene pairs with non-independent expression using artificial data and that DFC enabled characterization of the muscle satellite/progenitor cell population. The results revealed that DFC well captured cell-type-specific markers, specific gene expression patterns, and subcategories of this cell population. DFC may complement DEG-based methods for interpreting large data sets. DEG-based analysis uses lists of genes with differences in expression between groups, while DFC, which can be termed a discriminative approach, has potential applications in the task of cell characterization. Upon recent advances in the high-throughput analysis of single cells, methods of cell characterization such as scRNA-seq can be effectively subjected to the discriminative methods.

Comparison of the primary cesarean hysterotomy scars after single- and double-layer interrupted closure.

INTRODUCTION: It is unclear whether hysterotomy closure techniques can affect niche development. Therefore, this study aimed to analyze the effect of single-layer and double-layer interrupted closures of hysterotomy incisions during primary cesarean section on the formation of uterine niches. MATERIAL AND METHODS: A prospective cohort study of women undergoing primary cesarean section was performed between June 2011 and July 2014. Saline contrast sonohysterography was used to measure the niche depth and residual myometrium. The ratio of the niche depth to the sum of the niche depth and residual myometrium thickness (niche ratio) was calculated. RESULTS: Niches were identified in 14/58 (24.1%) women with single-layer sutures and 55/209 (26.3%) women with double-layer sutures (p = 0.74). Single-layer closure was associated with more than a five-fold increase in the odds of a niche ratio ≥0.4 (odds ratio 5.59; 95% CI 1.71-18.28). CONCLUSION: Single-layer closure may be associated with an increased risk of larger niches (niche ratio ≥0.4), although it may not increase the overall frequency of niche formation.

Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.

The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.

Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states.

Cell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.

Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle.

MyoD, a myogenic differentiation protein, has been studied for its critical role in skeletal muscle differentiation. MyoD-expressing myoblasts have a potency to be differentiated with proliferation of ectopic cells. However, little is known about the effect on chromatin structure of MyoD binding in proliferative myoblasts. In this study, we evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing. Genome-wide analysis of histone modifications was performed in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle. We found that MyoD-bound genome regions had elevated levels of active histone modifications, such as H3K4me1/2/3 and H3K27ac, compared with MyoD-unbound genome regions during the cell cycle. We also demonstrated that the elevated H3K4me2/3 modification level was maintained during the cell cycle, whereas the H3K27ac and H3K4me1 modification levels decreased to the same level as MyoD-unbound genome regions during the later phases. Immunoblot analysis revealed that MyoD abundance was high in the G1 phase then decreased in the S and G2/M phases. Our results suggest that MyoD binding formed selective epigenetic memories with H3K4me2/3 during the cell cycle in addition to myogenic gene induction via active chromatin formation coupled with transcription.

Oral delivery of diclofenac sodium using a novel solid-in-oil suspension.

The present work reports on a new pharmaceutical formulation for oral delivery of diclofenac sodium (DFNa), a non-steroidal anti-inflammatory drug (NSAID). Although DFNa itself is water-soluble at neutral pH, it was readily suspended in soybean oil via complex formation with an edible lipophilic surfactant and a matrix protein. The resulting solid-in-oil (S/O) suspension containing stably encapsulated DFNa in an oil phase markedly reduced the risks for gastrointestinal ulcers upon oral administration even at the LD(50) level in rats (ca. 50 mg/kg DFNa). In addition, plasma concentration of DFNa upon administration of an S/O suspension was comparable with that of the aqueous counterpart at the same DFNa dose. These results indicate the potential use of S/O suspensions as novel oil-based pharmaceutical formulations for oral delivery of water-soluble drugs without causing severe mucitis.

Serum calcium-decreasing factor, caldecrin, ameliorates muscular dystrophy in dy/dy mice.

BACKGROUND: Calcium signaling is important in muscular cells and abnormal Ca(2+) handling results in muscle damage. Caldecrin is a serum calcium-decreasing factor purified from pancreas. It is a chymotrypsin-type secretory protease, whereas the serum calcium-decreasing activity does not depend on its protease activity. Here, we evaluated the effect of caldecrin on dystrophia muscularis (dy/dy) mice. MATERIALS AND METHODS: Caldecrin gene in hemagglutinating virus of Japan envelop vector (10 µg/head) was single injected in the femoral muscle or daily intraperitoneal administration of caldecrin (100 µg/kg body weight) was given for 4 days in dy/dy mice. Progression of muscular dystrophy was assessed by blood urea nitrogen and Evans blue dye penetration assay. RESULTS: Ectopic expression of the caldecrin gene in the muscle of dy/dy mice reduced the level of blood urea nitrogen and improved the dystrophic progression similarly to that of caldecrin-injected mice. CONCLUSION: Caldecrin treatment is effective for preventing muscular dystrophy.

A novel solid-in-oil nanosuspension for transdermal delivery of diclofenac sodium.

PURPOSE: We formulated a solid-in-oil nanosuspension (SONS) as a novel transdermal delivery carrier for diclofenac sodium (DFNa). The basic transdermal characteristics of the SONS were evaluated using a Yucatan micropig (YMP) skin model. METHODS: DFNa-sucrose erucate (i.e. surfactant) complexes were prepared via the formation of a water-in-oil emulsion. The complexes were suspended in isopropyl myristate (IPM) to form a SONS. The basic transdermal characteristics of the SONS were examined using full-thickness YMP dorsal skin in a Franz-type diffusion cell. DFNa powder suspended in IPM without complex formation was used as a control. The effect of the weight ratio of surfactant to DFNa on DFNa penetration of the skin was evaluated. RESULTS: DFNa was successfully dispersed into IPM as a nanosized suspension via complex formation with sucrose erucate. The resultant SONS increased the permeability flux of DFNa across the YMP skin by up to 3.8-fold compared with the control. The size of the SONS depended on the weight ratio of the surfactant to DFNa. The optimal weight ratio for the highest DFNa permeation was 8.8, at which point the mean diameter of the SONS was 14.4 nm. CONCLUSION: The SONS formulation can enhance the percutaneous absorption of DFNa.

A solid-in-oil nanodispersion for transcutaneous protein delivery.

Transcutaneous delivery attracts much attention but remains a challenging strategy for hydrophilic macromolecular drug administration. In the present study, we demonstrated that a solid-in-oil (S/O) nanodispersion, an oil-based nanodispersion of hydrophilic drugs, effectively enhanced the permeation of proteins into the skin. All of the different model proteins, FITC-labeled insulin (MW ca. 6 kDa), enhanced green fluorescent protein (EGFP, MW ca. 27 kDa) and horseradish peroxidase (HRP, MW ca. 40 kDa), permeated through the stratum corneum of Yucatan micropig skin in vitro by forming a S/O nanodispersion. The penetrated EGFP and HRP exhibited green fluorescence and catalytic activity, respectively, suggesting that these proteins can permeate into the skin in a functional form. The results indicated the potential utility of the S/O nanodispersion as a novel vehicle for transcutaneous protein delivery.

Reduction of gastric ulcerogenicity during multiple administration of diclofenac sodium by a novel solid-in-oil suspension.

This article reports a significant reduction of gastric ulcerogenicity by complex formation of a nonsteroidal anti-inflammatory drug with surfactants. Diclofenac sodium (DFNa) was suspended in medium chain triglyceride (MCT) by forming a complex with an edible lipophilic surfactant. Two types of suspensions, prepared through a membrane emulsification with different pore sizes, were evaluated according to the degree of gastric damage following multiple oral administration in rats. It was shown that gastric ulcerogenicity of DFNa was reduced by the surfactant-drug complexes, at doses up to 12 mg/kg, whereas severe gastric damage was observed upon oral administration of the aqueous solution at doses of 6 mg/kg. Comparable blood levels of DFNa were observed after administration of solution and suspension formulations.