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.

Production of a Monoclonal Antibody for Histone H2b Isoform H2b3b

H2b3b is one of the histone H2b isoforms that differs from canonical H2b by five to six amino acids. Previously, we identified H3t as the testis-specific histone H3 variant located in histone cluster 3, which is also the site of H2b3b. In this study, we produced monoclonal antibodies against H2b3b, using the iliac rat lymph node method for rat antibody and the immunochamber method for rabbit antibody. Immunoblot analysis confirmed that our antibodies could specifically discriminate between H2b3b and canonical H2b. Moreover, immunostaining revealed colocalization with a testicular stem cell marker, Plzf, but not with a meiotic marker, Sycp. This indicated that H2b3b is expressed in spermatogenic cells before meiosis. Our monoclonal antibodies enable further studies to reveal specific functions of H2b3b during spermatogenesis. We also hope that the established method will lead to the production of antibodies that can identify other H2b isoforms.

FOXK1 promotes nonalcoholic fatty liver disease by mediating mTORC1-dependent inhibition of hepatic fatty acid oxidation

Nonalcoholic fatty liver disease (NAFLD) is a chronic metabolic disorder caused by overnutrition and can lead to nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC). The transcription factor Forkhead box K1 (FOXK1) is implicated in regulation of lipid metabolism downstream of mechanistic target of rapamycin complex 1 (mTORC1), but its role in NAFLD-NASH pathogenesis is understudied. Here, we show that FOXK1 mediates nutrient-dependent suppression of lipid catabolism in the liver. Hepatocyte-specific deletion of Foxk1 in mice fed a NASH-inducing diet ameliorates not only hepatic steatosis but also associated inflammation, fibrosis, and tumorigenesis, resulting in improved survival. Genome-wide transcriptomic and chromatin immunoprecipitation analyses identify several lipid metabolism-related genes, including Ppara, as direct targets of FOXK1 in the liver. Our results suggest that FOXK1 plays a key role in the regulation of hepatic lipid metabolism and that its inhibition is a promising therapeutic strategy for NAFLD-NASH, as well as for HCC.

Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types.

For complete details on the use and execution of this protocol, please refer to Honda et al. (2021).

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Preparation of tissue sections and permeabilization

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In situ reverse transcription using photo-caged primers

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Immunostaining and UV irradiation to the ROIs

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Linear amplification of uncaged cDNAs before sequencing

Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections

Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL‐based approach for analyzing the diverse cellular dynamics at the tissue level using high‐depth epigenomic data. “ChIL for tissues” allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell‐type dynamics of tissues.

Recent advance in single-cell epigenomics

The analysis of gene expression regulation, or the epigenome analysis, at the single-cell level is at the forefront of genomics research. To elucidate the mechanisms that regulate gene expression, chromatin immunoprecipitation has been conventionally used for determining the binding sites of DNA-binding proteins, such as histones and transcription factors. Now several new approaches have been emerged to reveal epigenome states at the single-cell level. Instead of using immunoprecipitation of fragmented chromatin, in situ reactions using cells or nuclei, combining with transposase tagging and other methods, have enabled single-cell analysis. Furthermore, single-cell multiomics techniques to simultaneously profiling transcriptome and open chromatin or histone modification have been developed. These single-cell analyses have the potential to identify different cell types in a cell population and reveal the dynamic changes of gene regulation, although those technologies have not yet reached a level for general application.

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.

Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay

In eukaryotes, histone variant distribution within the genome is the key epigenetic feature. To understand how each histone variant is targeted to the genome, we developed a new method, the RhIP (Reconstituted histone complex Incorporation into chromatin of Permeabilized cell) assay, in which epitope-tagged histone complexes are introduced into permeabilized cells and incorporated into their chromatin. Using this method, we found that H3.1 and H3.3 were incorporated into chromatin in replication-dependent and -independent manners, respectively. We further found that the incorporation of histones H2A and H2A.Z mainly occurred at less condensed chromatin (open), suggesting that condensed chromatin (closed) is a barrier for histone incorporation. To overcome this barrier, H2A, but not H2A.Z, uses a replication-coupled deposition mechanism. Our study revealed that the combination of chromatin structure and DNA replication dictates the differential histone deposition to maintain the epigenetic chromatin states.

Targeted inhibition of EPAS1-driven IL-31 production by a small-molecule compound

BACKGROUND

IL-31 is a major pruritogen associated with atopic dermatitis (AD). Although a specific antibody for IL-31 receptor has been shown to alleviate pruritus in patients with AD, therapeutic approaches to inhibition of IL-31 production remain unexploited. IL-31 production by T_H cells critically depends on the transcription factor EPAS1, which mediates IL31 promoter activation in collaboration with SP1.

OBJECTIVE

We aimed at developing small-molecule inhibitors that selectively block IL-31 production by T_H cells.

METHODS

We generated the reporter cell line that inducibly expressed EPAS1 in the presence of doxycycline to mediate Il31 promoter activation, and we screened 9600 chemical compounds. The selected compounds were further examined by using T_H cells from a spontaneous mouse model of AD and T_H cells from patients with AD.

RESULTS

We have identified 4-(2-(4-isopropylbenzylidene)hydrazineyl)benzoic acid (IPHBA) as an inhibitor of IL31 induction. Although IPHBA did not affect nonspecific T-cell proliferation, IPHBA inhibited antigen-induced IL-31 production by T_H cells from both an AD mouse model and patients with AD without affecting other cytokine production and hypoxic responses. In line with this, itch responses induced by adoptive transfer of IL-31-producing T_H cells were attenuated when mice were orally treated with IPHBA. Mechanistically, IPHBA inhibited the association between EPAS1 and SP1, resulting in defective recruitment of both transcription factors to the specific sites of the IL31 promoter. We also determined the structure-activity relationship of IPHBA by synthesizing and analyzing 201 analogous compounds.

CONCLUSION

IPHBA could be a potential drug leading to inhibition of EPAS1-driven IL-31 production.

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.

Subnuclear gene positioning through lamina association affects copper tolerance

The nuclear lamina plays an important role in the regulation of chromatin organization and gene positioning in animals. CROWDED NUCLEI (CRWN) is a strong candidate for the plant nuclear lamina protein in Arabidopsis thaliana but its biological function was largely unknown. Here, we show that CRWNs localize at the nuclear lamina and build the meshwork structure. Fluorescence in situ hybridization and RNA-seq analyses revealed that CRWNs regulate chromatin distribution and gene expression. More than 2000 differentially expressed genes were identified in the crwn1crwn4 double mutant. Copper-associated (CA) genes that form a gene cluster on chromosome 5 were among the downregulated genes in the double mutant exhibiting low tolerance to excess copper. Our analyses showed this low tolerance to copper was associated with the suppression of CA gene expression and that CRWN1 interacts with the CA gene locus, enabling the locus to localize at the nuclear lamina under excess copper conditions.

The nuclear lamina regulates chromatin organization and gene positioning. Here the authors show that CROWDED NUCLEI proteins contribute to the meshwork lamina structure in Arabidopsis nuclei and regulate copper tolerance by promoting lamina association and expression of copper response genes.

Autologous skeletal myoblast sheet prevents cardiomyocyte ischemia and right heart dysfunction in pressure-overloaded right heart porcine model

Introduction

Severe heart failure (HF) with congenital heart disease (CHD) have demonstrated life threatening disorder despite of remarkable progress in medical therapies. Autologous skeletal myoblast sheet transplantation therapy showed clinical efficacy for left ventricular dysfunction by cytokine paracrine effects, which are expected to be sufficiently effective against right ventricular (RV) dysfunction which is often seen in end-stage of CHD patients with severe HF.

Hypothesis

An autologous skeletal myoblast sheet transplantation alleviates RV dysfunction in a pressure-overloaded right heart in a porcine model.

Methods

Five-to-six-month-old Göttingen mini-pigs underwent pulmonary artery banding with vascular occluding system. To create the porcine model of chronic pressure-overloaded right heart, vascular occluding system was gradually inflated, over a month, to make pulmonary stenosis to banding velocity >3.0 m/s measured by echocardiography (UCG), and then fixed for another month. Two months after banding, autologous skeletal myoblast sheet was placed on the epicardium of the RV free wall and followed for 2 months. Groups were as follows: control (C, n=5), sheet implantation (S, n=5). Cardiac function was measured using UCG, cardiac computed tomography (CT), and cardiac catheterization (Cath). Two months after sheet implantation, hearts were dissected for histologic analysis.

Results

Before sheet implantation, RV dysfunction was equal in groups; however, 2 months after sheet implantation, RV dysfunction and myocardial ischemia was significantly ameliorated in group S than group C. On CT, RV ejection fraction exacerbation were well controlled in Group S compared to Group C (S 44.9±2.2 vs C 31.9±2.1% [p=0.0042]). UCG and Cath revealed well maintained systolic and diastolic function in Group S compared to Group C (Tei index: S 0.42±0.06 vs C 0.70±0.07 [p=0.0240], Fraction Area Change: S 45.8±7.8 vs C 19.5±1.3% [p=0.0240], Isovolumic Relaxation Time; S 44.3±9.2 vs C 97.3±9.5 ms [p=0.0304]). On C11-Acetate Positron Emission Tomography, myocardial ischemia was more prominent in Group C compared to Group S (K mono-Rest/Stress: S 3.17±0.69 vs C 2.03±0.65 min-1 [p=0.0421], Myocardial Blood Flow-Rest/Stress: S 3.22±0.39 vs C 2.13±0.92 min-1 [p=0.0421]). In histologic analysis, Group S presented less progressed hypertrophic change in periodic acid-Schiff stain (S 13.5±0.9 vs C 18.0±3.0 μg [p=0.0240]), anti-fibrotic changes in picrosirius red stain (S 3.0±0.3 vs C 4.2±0.2% [p=0.0421]), more angiogenesis in CD31 expression (S 18.3±1.5 vs C 10.7±2.8 / 104 μm2 [p=0.0240]), and less production of reactive oxygen species in fluorescent immunostaining (S 5.9±1.7 vs C 18.4±1.7% [p=0.0304]).

Conclusion

Autologous skeletal myoblast sheet transplantation alleviates cardiomyocyte Ischemia and RV dysfunction in a porcine model of pressure-overloaded right heart.

Funding Acknowledgement

Type of funding source: None

Functional engineered heart tissue cultured in a rotating wall vessel bioreactor improve cardiac function in the distressed rat heart

Introduction

How to construct massive cardiac tissue and culture it with functional improvement may be crucial as cardiomyogenesis in failed heart. We previously presented that dynamic culture in a rotating wall vessel (RWV) bioreactor could provide a better culture environment for maintenance of the engineered 3D cardiac tissue. However, it is unknown about the effect of the tissue cultured in a RWV bioreactor on engraftment and improvement of function in the distressed rat heart.

Hypothesis

We hypothesized that the engineered 3D cardiac tissue cultured in a RWV bioreactor could improve its engraftment and lead recovery of cardiac function in rat infarction model.

Methods

We made engineered cardiac tissue by seeding 2.0 × 106 human induced pluripotent stem cell derived cardiomyocytes on the PLGA fiber sheet. It was cultured in the RWV bioreactor for seven days (RWV group). For the control, static culture has been done. After in vitro assessment, these tissues were transplanted to myocardial infarction model nude rats (sham, control, and RWV group, n=10, respectively) and cardiac performance was evaluated by ultrasonography. Four weeks after transplantation, we evaluated their hearts by histological analysis.

Results

The RWV group demonstrated maturation of cardiomyocytes evidenced by significantly higher expression of Troponin T (TnT), sarcomeric α actinin (SAA), connexin 43 (Cx43) and myosin heavy chain 7 (MYH7) than the control by Western blots (TnT; 2.7±1.0 vs. 1.0±0.4, p<0.01, SAA; 2.1±0.7 vs. 1.0±0.2, p<0.01, Cx 43; 2.0±0.6 vs. 1.0±0.1, p<0.05, MYH7; 10.9±2.7 vs. 1.0±0.1, p<0.01). In the culture supernatant, the concentration of cytokines related to angiogenesis was significantly higher in the RWV group than in the control (VEGF; 29.6±7.4 vs. 12.2±4.3pg/ml, p<0.01, HGF; 72.7±9.9 vs. 42.6±5.9pg/ml, p<0.01). Four weeks after transplantation, the left ventricular ejection fraction was significantly improved in the RWV group than in the control (RWV vs. control; 47±4.9 vs. 38±6.9%, p<0.01). On histological analysis, more engineered cardiac tissue survived in the RWV group than in the control (RWV vs. control; 7/10 vs. 3/10, p=0.18). A vascular-like structure double-stained with isolectin B4 and smooth muscle actin was partially observed in the transplanted tissue. LV remodeling exhibiting extracellular collagen deposition (fibrotic area, RWV vs. control; 17±4.3 vs. 24±5.2%, p<0.05) and cardiomyocyte hypertrophy (RWV vs. control; 16±1.7 vs. 18±2.1μm, p<0.05) was significantly attenuated in RWV group than in the control. Neovascularization was significantly noted in the RWV group compared with the control (capillary density, RWV vs. control; 545±113 vs. 356±92, p<0.01).

Conclusion

Functional engineered 3D cardiac tissue cultured in a RWV bioreactor could induce angiogenesis and improved its engraftment, leading significant improvement of cardiac function in rat infarction model.

Dynamic culture in a RWV bioreactor

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Japan Society for the Promotion of Science

Cholesterol uptake capacity: a new measure of HDL functionality as a predictor of subsequent revascularization in patients undergoing percutaneous coronary intervention

Background

Recent studies have demonstrated the importance of high-density lipoprotein (HDL) functionality in the development of de novo coronary artery disease by using the cholesterol-efflux capacity, a measure of the ability of HDL to promote cholesterol removal from lipid-laden macrophages. Recently, we developed a rapid cell-free assay system to directly evaluate the capacity of HDL to accept additional cholesterol; the measurement of the cholesterol-uptake capacity (CUC) enables HDL functionality to be readily evaluated in our daily practice. However, prognostic implication of CUC measurement at the timing of percutaneous coronary intervention (PCI) remains unclear.

Purpose

We aimed to evaluate the association between baseline CUC and revascularization during follow-up in the patients who underwent PCI.

Methods

We retrospectively reviewed the patients who underwent PCI with follow-up coronary angiography (CAG) or ischemic-driven revascularization. The patients who had the frozen blood samples of which CUC were measurable at the index PCI and follow-up CAG or revascularization were enrolled. We excluded the patients under hemodialysis.

Results

Among a total of 703 consecutive patients who underwent PCI between Dec 2014 and Mar 2019, we finally enrolled 74 patients who underwent ischemic-driven revascularization (revascularization group) and 183 patients who underwent follow-up CAG without revascularization (non-revascularization group).There were no significant difference in baseline traditional cardiovascular risk factors between the groups. However, the presence of diabetes was significantly more frequent in the revascularization group (63.5% vs 41.0%; P=0.001) than in the non-revascularization group. CUC at the index PCI was significantly lower in the revascularization group than in the non-revascularization group (87.0±19.5 vs 93.9±19.2; P=0.004). Multivariate logistic regression analysis revealed that impaired HDL functionality assessed by decreased CUC level at the index PCI (odds ratio; 0.984, 95% confidence interval; 0.969–1.000) was independently associated with subsequent revascularization after PCI. Indeed, there was a graded inverse association between increasing tertiles of CUC levels and the incidence of revascularization during a median follow-up of 881 days (Figure). Especially in the subgroup analysis of non-diabetic patients, decreased CUC level at the index PCI was independently associated with subsequent revascularization (odds ratio; 0.947, 95% confidence interval; 0.915–0.981), while not in diabetic population.

Conclusion

Serum CUC level at the index procedure was associated with subsequent revascularization especially in non-diabetic patients who underwent PCI.

Funding Acknowledgement

Type of funding source: None

Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input

Cell identity is determined by the selective activation or silencing of specific genes via transcription factor binding and epigenetic modifications on the genome. Chromatin immunoprecipitation (ChIP) has been the standard technique for mapping the sites of transcription factor binding and histone modification. Recently, alternative methods to ChIP have been developed for addressing the increasing demands for low-input epigenomic profiling. Chromatin integration labeling (ChIL) followed by sequencing (ChIL-seq) has been demonstrated to be particularly useful for epigenomic profiling of low-input samples or even single cells because the technique amplifies the target genomic sequence before cell lysis. After labeling the target protein or modification in situ with an oligonucleotide-conjugated antibody (ChIL probe), the nearby genome sequence is amplified by Tn5 transposase-mediated transposition followed by T7 RNA polymerase-mediated transcription. ChIL-seq enables the detection of the antibody target localization under a fluorescence microscope and at the genomic level. Here we describe the detailed protocol of ChIL-seq with assessment methods for the key steps, including ChIL probe reaction, transposition, in situ transcription and sequencing library preparation. The protocol usually takes 3 d to prepare the sequencing library, including overnight incubations for the ChIL probe reaction and in situ transcription. The ChIL probe can be separately prepared and stored for several months, and its preparation and evaluation protocols are also documented in detail. An optional analysis for multiple targets (multitarget ChIL-seq) is also described. We anticipate that the protocol presented here will make the ChIL technique more widely accessible for analyzing precious samples and facilitate further applications.

Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells

Transcriptional bursting is the stochastic activation and inactivation of promoters, contributing to cell-to-cell heterogeneity in gene expression. However, the mechanism underlying the regulation of transcriptional bursting kinetics (burst size and frequency) in mammalian cells remains elusive. In this study, we performed single-cell RNA sequencing to analyze the intrinsic noise and mRNA levels for elucidating the transcriptional bursting kinetics in mouse embryonic stem cells. Informatics analyses and functional assays revealed that transcriptional bursting kinetics was regulated by a combination of promoter- and gene body-binding proteins, including the polycomb repressive complex 2 and transcription elongation factors. Furthermore, large-scale CRISPR-Cas9-based screening identified that the Akt/MAPK signaling pathway regulated bursting kinetics by modulating transcription elongation efficiency. These results uncovered the key molecular mechanisms underlying transcriptional bursting and cell-to-cell gene expression noise in mammalian cells.

Association of Muscle Strength and Gait Speed with Cross-Sectional Muscle Area Determined by Mid-Thigh Computed Tomography - A Comparison with Skeletal Muscle Mass Measured by Dual-Energy X-Ray Absorptiometry

BACKGROUND

Muscle mass is often mentioned not to reflect muscle strength. For muscle mass assessment skeletal muscle index (SMI) is often used. We have reported that dual-energy X-ray absorptiometry (DXA)-derived SMI does not change with age in women, whereas the cross-sectional muscle area (CSMA) derived from computed tomography (CT) does.

OBJECTIVES

The present study aimed to compare CT and DXA for the assessment of muscle tissue.

DESIGN AND SETTING

Cross-sectional study in the local residents.

PARTICIPANTS

A total of 1818 subjects (age 40-89 years) randomly selected from community dwellers underwent CT examination of the right mid-thigh to measure the cross-sectional muscle area (CSMA). Skeletal muscle mass (SMM) was measured by DXA. The subjects performed physical function tests such as grip strength, knee extension strength, leg extension strength, and gait speed. The correlation between CT-derived CSMA and DXA-derived SMM along with their association with physical function was examined.

RESULTS

After controlling for related factors, the partial correlation coefficient of muscle cross-sectional area (CSA) with physical function was larger than that of DXA-derived SMM for gait speed in men (p=0.002) and knee extension strength in women (p=0.03). The partial correlation coefficient of quadriceps (Qc) CSA with physical function was larger than that of DXA-derived SMM for leg extension power in both sexes (p=0.01), gait speed in men (p<0.001), and knee extension strength in women (p<0.001).

CONCLUSION

Mid-thigh CT-derived CSMA, especially Qc CSA, showed significant associations with grip strength, knee extension strength, and leg extension power, which were equal to or stronger than those of DXA-derived SMM in community-dwelling middle-aged and older Japanese people. The mid-thigh CSMA may be a predictor of mobility disability, and is considered to be useful in the diagnosis of sarcopenia.

Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells

We previously demonstrated that CRM1, a major nuclear export factor, accumulates at Hox cluster regions to recruit nucleoporin-fusion protein Nup98HoxA9, resulting in robust activation of Hox genes (Oka et al., 2016). However, whether this phenomenon is general to other leukemogenic proteins remains unknown. Here, we show that two other leukemogenic proteins, nucleoporin-fusion SET-Nup214 and the NPM1 mutant, NPM1c, which contains a nuclear export signal (NES) at its C-terminus and is one of the most frequent mutations in acute myeloid leukemia, are recruited to the HOX cluster region via chromatin-bound CRM1, leading to HOX gene activation in human leukemia cells. Furthermore, we demonstrate that this mechanism is highly sensitive to a CRM1 inhibitor in leukemia cell line. Together, these findings indicate that CRM1 acts as a key molecule that connects leukemogenic proteins to aberrant HOX gene regulation either via nucleoporin-CRM1 interaction (for SET-Nup214) or NES-CRM1 interaction (for NPM1c).

P5391Systemic administration of high-mobility group box 1 can suppress adverse post-infarction ventricular remodeling in a rat infarction model by enhancing self-regeneration

Background

High-mobility group box 1 protein (HMGB1) reportedly enhances CXCR4-positive bone marrow-derived mesenchymal stem cell (BM-MSC) recruitment to damaged tissue to promote tissue regeneration.

Purpose

Our aim of this study is to evaluate whether systemic administration of HMGB1 might promote tissue repair in a rat myocardial infarction (MI) model.

Methods

We prepared 26 MI model rats with high ligation of the left coronary artery. Two weeks later, HMGB1 (3 mg/kg/day) or phosphate-buffered saline (control: 3 mL/kg/day) was administered for 4 days via femoral vein. Cardiac performance was evaluated by ultrasonography, left ventricular (LV) remodeling via immunostaining. We then used immunostaining to examine MSC recruitment to damaged tissue in green fluorescent protein bone marrow transplantation (GFP-BMT) model rats, and also performed intravital imaging using two-photon microscopy to visualize BM-cells recruitment in real time.

Results

Compared with control rats, there was a significant improvement in the left ventricular ejection fraction of the HMGB1 group (HMGB1 vs. control: 48.6% ± 5.5% vs. 33.6% ± 5.4%; p<0.01) at 4 weeks after each administration. LV remodeling, characterized by interstitial fibrosis, cardiomyocyte hypertrophy, and a decrease of capillary density, was significantly attenuated in the HMGB1 group compared with control rats. On QT-PCR analysis, VEGF mRNA expression was significantly higher in the HMGB1 group than in the control (border zone; 1.6±0.6 vs. 1.1±0.2; p=0.02, septal zone; 1.1±0.1 vs. 0.9±0.1; p<0.01). In GFP-BMT rats, GFP+/PDGFR+ cells were significantly mobilized to the border zone in the HMGB1 group compared with the control (1331±197 vs. 615±45 /mm2; p<0.01), leading to formation of newly developed vasculature (Figure 1). In intravital imaging, more GFP+ cells were mobilized to the infarction area in the HMGB1 group than in the control, which was further enhanced at 12h later. Additionally, SDF-1 expression in the peri-infarction area increased significantly in MI rats compared with normal rats (MI vs. normal; 2.1±0.4 vs. 0.9±0.1; p<0.01), in where some cell-adhesions of vascular endothelial cells were destroyed.

Conclusions

Systemic administration of HMGB1 mobilized BM-MSCs to the damaged myocardium via the SDF-1/CXCR4 signaling complex. Those BM-MSCs might migrate to extracellular matrix in the border zone via the gap of each endothelial cell, leading to induction of angiogenesis and reduced fibrosis.

Acknowledgement/Funding

None

Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle

In overloaded and regenerating muscle, the generation of new myonuclei depends on muscle satellite cells (MuSCs). Because MuSC behaviors in these two environments have not been considered separately, MuSC behaviors in overloaded muscle remain unexamined. Here, we show that most MuSCs in overloaded muscle, unlike MuSCs in regenerating muscle, proliferate in the absence of MyoD expression. Mechanistically, MuSCs in overloaded muscle sustain the expression of Heyl, a Notch effector gene, to suppress MyoD expression, which allows effective MuSC proliferation on myofibers and beneath the basal lamina. Although Heyl-knockout mice show no impairment in an injury model, in a hypertrophy model, their muscles harbor fewer new MuSC-derived myonuclei due to increased MyoD expression and diminished proliferation, which ultimately causes blunted hypertrophy. Our results show that sustained HeyL expression is critical for MuSC proliferation specifically in overloaded muscle, and thus indicate that the MuSC-proliferation mechanism differs in overloaded and regenerating muscle.

Biochemical analysis of nucleosome targeting by Tn5 transposase

Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5 transposase preferentially targets near the entry-exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry-exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.

Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection

BACKGROUND

We previously demonstrated that step training leads to reorganization of neuronal networks in the lumbar spinal cord of rodents after a hemisection (HX) injury and step training, including increases excitability of spinally evoked potentials in hindlimb motor neurons.

METHODS

In this study, we investigated changes in RNA expression and synapse number using RNA-Seq and immunohistochemistry of the lumbar spinal cord 23 days after a mid-thoracic HX in rats with and without post-HX step training.

RESULTS

Gene Ontology (GO) term clustering demonstrated that expression levels of 36 synapse-related genes were increased in trained compared with nontrained rats. Many synaptic genes were upregulated in trained rats, but Lrrc4 (coding NGL-2) was the most highly expressed in the lumbar spinal cord caudal to the HX lesion. Trained rats also had a higher number of NGL-2/synaptophysin synaptic puncta in the lumbar ventral horn.

CONCLUSIONS

Our findings demonstrate clear activity-dependent regulation of synapse-related gene expression post-HX. This effect is consistent with the concept that activity-dependent phenomena can provide a mechanistic drive for epigenetic neuronal group selection in the shaping of the reorganization of synaptic networks to learn the locomotion task being trained after spinal cord injury.

Cell-autonomous and redundant roles of Hey1 and HeyL in muscle stem cells: HeyL requires Hes1 to bind diverse DNA sites

The undifferentiated state of muscle stem (satellite) cells (MuSCs) is maintained by the canonical Notch pathway. Although three bHLH transcriptional factors, Hey1, HeyL, and Hes1, are considered to be potential effectors of the Notch pathway exerting anti-myogenic effects, neither HeyL nor Hes1 inhibits myogenic differentiation of myogenic cell lines. Furthermore, whether these factors work redundantly or cooperatively is unknown. Here, we showed cell-autonomous functions of Hey1 and HeyL in MuSCs using conditional and genetic null mice. Analysis of cultured MuSCs revealed anti-myogenic activity of both HeyL and Hes1. We found that HeyL forms heterodimeric complexes with Hes1 in living cells. Moreover, our ChIP-Seq experiments demonstrated that, compared with HeyL alone, HeyL-Hes1 heterodimer bound with high affinity to specific sites in the chromatin including the cis-element of Hey1. Finally, the analyses of myogenin promoter activity showed that HeyL and Hes1 acted synergistically to suppress myogenic differentiation. Collectively, those results suggest that HeyL and Hey1 function redundantly in MuSCs, and that HeyL requires Hes1 for effective DNA binding and biological activity.

The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation

Myogenic progenitor/stem cells retain their skeletal muscle differentiation potential by maintaining myogenic transcription factors such as MyoD. However, the mechanism of how MyoD expression is maintained in proliferative progenitor cells has not been elucidated. Here, we found that MyoD expression was reduced at the mRNA level by cell cycle arrest in S and G2 phases, which in turn led to the absence of skeletal muscle differentiation. The reduction of MyoD mRNA was correlated with the reduced expression of factors regulating RNA metabolism, including methyltransferase like 3 (Mettl3), which induces N⁶-methyladenosine (m⁶A) modifications of RNA. Knockdown of Mettl3 revealed that MyoD RNA was specifically downregulated and that this was caused by a decrease in processed, but not unprocessed, mRNA. Potential m⁶A modification sites were profiled by m⁶A sequencing and identified within the 5' untranslated region (UTR) of MyoD mRNA. Deletion of the 5' UTR revealed that it has a role in MyoD mRNA processing. These data showed that Mettl3 is required for MyoD mRNA expression in proliferative myoblasts.

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration

Regulation of gene expression requires selective incorporation of histone H3 variant H3.3 into chromatin. Histone H3.3 has several subsidiary variants but their functions are unclear. Here we characterize the function of histone H3.3 sub-variant, H3mm7, which is expressed in skeletal muscle satellite cells. H3mm7 knockout mice demonstrate an essential role of H3mm7 in skeletal muscle regeneration. Chromatin analysis reveals that H3mm7 facilitates transcription by forming an open chromatin structure around promoter regions including those of myogenic genes. The crystal structure of the nucleosome containing H3mm7 reveals that, unlike the S57 residue of other H3 proteins, the H3mm7-specific A57 residue cannot form a hydrogen bond with the R40 residue of the cognate H4 molecule. Consequently, the H3mm7 nucleosome is unstable in vitro and exhibited higher mobility in vivo compared with the H3.3 nucleosome. We conclude that the unstable H3mm7 nucleosome may be required for proper skeletal muscle differentiation.

Incorporation of histone H3 variant H3.3 into chromatin regulates transcription. Here the authors find that H3.3 sub-variant H3mm7 is required for skeletal muscle regeneration and that H3mm7 nucleosomes are unstable and exhibit higher mobility, with H3mm7 promoting open chromatin around promoters.

Sensitive detection of fluorescence in western blotting by merging images

The western blotting technique is widely used to analyze protein expression levels and protein molecular weight. The chemiluminescence method is mainly used for detection due to its high sensitivity and ease of manipulation, but it is unsuitable for detailed analyses because it cannot be used to detect multiple proteins simultaneously. Recently, more attention has been paid to the fluorescence detection method because it is more quantitative and is suitable for the detection of multiple proteins simultaneously. However, fluorescence detection can be limited by poor image resolution and low detection sensitivity. Here, we describe a method to detect fluorescence in western blots using fluorescence microscopy to obtain high-resolution images. In this method, filters and fluorescent dyes are optimized to enhance detection sensitivity to a level similar to that of the chemiluminescence method.

Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis

Cellular differentiation is associated with dynamic chromatin remodeling in establishing a cell-type-specific epigenomic landscape. Here, we find that mouse testis-specific and replication-dependent histone H3 variant H3t is essential for very early stages of spermatogenesis. H3t gene deficiency leads to azoospermia because of the loss of haploid germ cells. When differentiating spermatogonia emerge in normal spermatogenesis, H3t appears and replaces the canonical H3 proteins. Structural and biochemical analyses reveal that H3t-containing nucleosomes are more flexible than the canonical nucleosomes. Thus, by incorporating H3t into the genome during spermatogonial differentiation, male germ cells are able to enter meiosis and beyond.

Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells

Chromatin reorganization is necessary for pluripotent stem cells, including embryonic stem cells (ESCs), to acquire lineage potential. However, it remains unclear how ESCs maintain their characteristic chromatin state for appropriate gene expression upon differentiation. Here, we demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the differentiation potential of mouse ESCs. Chd2-depleted ESCs showed suppressed expression of developmentally regulated genes upon differentiation and subsequent differentiation defects without affecting gene expression in the undifferentiated state. Furthermore, chromatin immunoprecipitation followed by sequencing revealed alterations in the nucleosome occupancy of the histone variant H3.3 for developmentally regulated genes in Chd2-depleted ESCs, which in turn led to elevated trimethylation of the histone H3 lysine 27. These results suggest that Chd2 is essential in preventing suppressive chromatin formation for developmentally regulated genes and determines subsequent effects on developmental processes in the undifferentiated state.

Periostin Promotes Scar Formation through the Interaction between Pericytes and Infiltrating Monocytes/Macrophages after Spinal Cord Injury

Scar formation is a prominent pathological feature of traumatic central nervous system (CNS) injury, which has long been implicated as a major impediment to the CNS regeneration. However, the factors affecting such scar formation remain to be elucidated. We herein demonstrate that the extracellular matrix protein periostin (POSTN) is a key player in scar formation after traumatic spinal cord injury (SCI). Using high-throughput RNA sequencing data sets, we found that the genes involved in the extracellular region, such as POSTN, were significantly expressed in the injured spinal cord. The expression of POSTN peaked at 7 days after SCI, predominantly in the scar-forming pericytes. Notably, we found that genetic deletion of POSTN in mice reduced scar formation at the lesion site by suppressing the proliferation of the pericytes. Conversely, we found that recombinant POSTN promoted the migration capacity of the monocytes/macrophages and increased the expression of tumor necrosis factor-α from the monocytes/macrophages in vitro, which facilitated the proliferation of pericytes. Furthermore, we revealed that the pharmacological blockade of POSTN suppressed scar formation and improved the long-term functional outcome after SCI. Our findings suggest a potential mechanism whereby POSTN regulates the scar formation after SCI and provide significant evidence that POSTN is a promising therapeutic target for CNS injury.

Identification of Immunoglobulin Gene Sequences from a Small Read Number of mRNA-Seq Using Hybridomas

Identification of immunoglobulin genes in hybridomas is essential for producing antibodies for research and clinical applications. A couple of methods such as RACE and degenerative PCR have been developed for determination of the Igh and Igl/Igk coding sequences (CDSs) but it has been difficult to process a number of hybridomas both with accuracy and rapidness. Here, we propose a new strategy for antibody sequence determination by mRNA-seq of hybridomas. We demonstrated that hybridomas highly expressed the Igh and Igl/Igk genes and that de novo transcriptome assembly using mRNA-seq data enabled identification of the CDS of both Igh and Igl/Igk accurately. Furthermore, we estimated that only 30,000 sequenced reads are required to identify immunoglobulin sequences from four different hybridoma clones. Thus, our approach would facilitate determining variable CDSs drastically.