Comparative transcriptomics of primary cells in vertebrates.

Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

Functional annotation of human long noncoding RNAs via molecular phenotyping.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.

An atlas of human long non-coding RNAs with accurate 5' ends.

Long non-coding RNAs (lncRNAs) are largely heterogeneous and functionally uncharacterized. Here, using FANTOM5 cap analysis of gene expression (CAGE) data, we integrate multiple transcript collections to generate a comprehensive atlas of 27,919 human lncRNA genes with high-confidence 5' ends and expression profiles across 1,829 samples from the major human primary cell types and tissues. Genomic and epigenomic classification of these lncRNAs reveals that most intergenic lncRNAs originate from enhancers rather than from promoters. Incorporating genetic and expression data, we show that lncRNAs overlapping trait-associated single nucleotide polymorphisms are specifically expressed in cell types relevant to the traits, implicating these lncRNAs in multiple diseases. We further demonstrate that lncRNAs overlapping expression quantitative trait loci (eQTL)-associated single nucleotide polymorphisms of messenger RNAs are co-expressed with the corresponding messenger RNAs, suggesting their potential roles in transcriptional regulation. Combining these findings with conservation data, we identify 19,175 potentially functional lncRNAs in the human genome.

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs.

The Functional ANnoTation Of the Mammalian genome (FANTOM) Consortium has continued to provide extensive resources in the pursuit of understanding the transcriptome, and transcriptional regulation, of mammalian genomes for the last 20 years. To share these resources with the research community, the FANTOM web-interfaces and databases are being regularly updated, enhanced and expanded with new data types. In recent years, the FANTOM Consortium's efforts have been mainly focused on creating new non-coding RNA datasets and resources. The existing FANTOM5 human and mouse miRNA atlas was supplemented with rat, dog, and chicken datasets. The sixth (latest) edition of the FANTOM project was launched to assess the function of human long non-coding RNAs (lncRNAs). From its creation until 2020, FANTOM6 has contributed to the research community a large dataset generated from the knock-down of 285 lncRNAs in human dermal fibroblasts; this is followed with extensive expression profiling and cellular phenotyping. Other updates to the FANTOM resource includes the reprocessing of the miRNA and promoter atlases of human, mouse and chicken with the latest reference genome assemblies. To facilitate the use and accessibility of all above resources we further enhanced FANTOM data viewers and web interfaces. The updated FANTOM web resource is publicly available at https://fantom.gsc.riken.jp/.

Determination of lower radiation dose limit for automatic measurement of adipose tissue.

The purpose of this study was to determine the lower limit of radiation dose required to measure visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) volumes when a fat quantification and noise reduction techniques (NRTs) are combined. For this purpose, we utilized CT colonography (CTC) images taken at low doses and manually segmented VAT and SAT fat volumes as ground truth. In order to derive the acceptable precision of the measurements needed to estimate the lower limit of radiation dose, we estimated the effect of different positioning during CT scanning on fat measurements using manually segmented VAT and SAT against normal dose. As a result, the acceptable accuracy of SAT and VAT was found to be 94.5% and 85.2%, respectively. Using these thresholds, the lower radiation dose limit required to accurately measure SAT using 5.25-mm slice-thick images was 1.5 mGy of size-specific dose estimates (SSDE), while the lower radiation dose limit required to accurately measure VAT was 0.4 mGy of SSDE. The lower dose limit for SAT and VAT combined was 1.5 mGy, which was equivalent to an estimated effective dose of 0.38 mSv. Alternatively, without noise reduction, SAT could not achieve acceptable accuracy even for images with a slice thickness of 5.25 mm, while VAT required noise reduction for images with a slice thickness of 1.25 mm, but could achieve acceptable accuracy without noise reduction for images with a slice thickness of 5.25 mm.

Do people who highly value happiness tend to ruminate?

Previous studies have suggested that an extremely strong desire for happiness might ironically reduce a person's well-being, particularly among Western people. According to the goal progress theory and the theory of valuing happiness, rumination might explain the relationship between valuing happiness and well-being. Based on these theoretical rationales, this study examined the following hypotheses: (1) valuing happiness is significantly associated with rumination, (2) people who experience low life stress have a stronger association between valuing happiness and rumination, and (3) people with more interdependent self-construal have a weaker association between valuing happiness and rumination. University students in Japan participated in a cross-sectional study (N = 350; Study 1) and a 4-weeks longitudinal study (N = 329; Study 2). They responded to a packet of questionnaires assessing valuing happiness, trait rumination, depressive symptoms, negative events, and interdependent self-construal. Consistent with our hypothesis, valuing happiness was concurrently and longitudinally associated with increased rumination after controlling for depressive symptoms. However, negative events did not moderate the association between valuing happiness and rumination. Furthermore, Study 1, but not Study 2, indicated that the association between valuing happiness and rumination was stronger among students with highly interdependent self-construal than those with less interdependent self-construal. The preset findings indicated that valuing happiness might be a factor that perpetuates rumination. More sophisticated evidence on the influence of valuing happiness on rumination can lead to effective psychotherapies for decreasing rumination and depression. Supplementary Information: The online version contains supplementary material available at 10.1007/s12144-022-04131-6.

Response inhibition deficits are positively associated with trait rumination, but attentional inhibition deficits are not: aggressive behaviors and interpersonal stressors as mediators.

Previous findings on relationships between inhibition that is a core executive function, and trait rumination have been inconsistent. This inconsistency could be overcome by investigating the association between rumination and the two subcomponents of inhibition: response inhibition and attentional inhibition. This study examined whether and how response inhibition and attentional inhibition were related to rumination as well as worry. University students in Japan (N = 213) conducted the Go/No-Go Task and the Modified Stroop Task. They also completed self-report measures of depression, trait rumination, trait worry, stressors, and aggressive behaviors. Results indicated that response inhibition deficits were positively associated with trait rumination, and this association was mediated by increases in aggressive behaviors and interpersonal stressors. The associations between these variables remained significant even after controlling for depression level. There were no significant direct or indirect associations between attentional inhibition deficits and rumination. These results suggest that response inhibition deficits, among the subcomponents of inhibition, have an indirect positive association with rumination through interpersonal processes. Results also showed nonsignificant differences between rumination and worry in the magnitude of correlation coefficients with the two subcomponents of inhibition. Therefore, it remains unclear whether the positive association with response inhibition is unique to rumination.

Causes and consequences of stress generation: Longitudinal associations of negative events, aggressive behaviors, rumination, and depressive symptoms.

The present study examined the causes and consequences of stress generation in university students in Japan. A two-wave longitudinal study with an 8- or 9-week interval was conducted in the fall of 2020. Undergraduate and graduate students at four universities in Japan (N = 201) completed self-report measures assessing experiences of negative interpersonal dependent events, negative non-interpersonal events, and negative independent events at two times. At the same time, they also responded to measures of aggressive behaviors, trait rumination, and depressive symptoms. Path analyses revealed that baseline aggressive behaviors were positively associated with an increase in subsequent negative interpersonal dependent events, even after controlling for the influences of negative interpersonal dependent events, rumination, and depressive symptoms at baseline. However, aggressive behaviors were not significantly associated with subsequent negative non-interpersonal dependent events or negative independent events. These findings suggest that aggressive behaviors may have been a factor leading to interpersonal stress generation. Furthermore, all categories of negative event experiences predicted an increase in subsequent depressive symptoms, but not subsequent rumination, and rumination was not significantly associated with subsequent depressive symptoms. This research extends previous studies on the causes and consequences of stress generation conducted in the US by using specific measures of aggressive behaviors and including a non-restricted sample of university students in Japan. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12144-022-02859-9.

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases.

The FANTOM web resource (http://fantom.gsc.riken.jp/) was developed to provide easy access to the data produced by the FANTOM project. It contains the most complete and comprehensive sets of actively transcribed enhancers and promoters in the human and mouse genomes. We determined the transcription activities of these regulatory elements by CAGE (Cap Analysis of Gene Expression) for both steady and dynamic cellular states in all major and some rare cell types, consecutive stages of differentiation and responses to stimuli. We have expanded the resource by employing different assays, such as RNA-seq, short RNA-seq and a paired-end protocol for CAGE (CAGEscan), to provide new angles to study the transcriptome. That yielded additional atlases of long noncoding RNAs, miRNAs and their promoters. We have also expanded the CAGE analysis to cover rat, dog, chicken, and macaque species for a limited number of cell types. The CAGE data obtained from human and mouse were reprocessed to make them available on the latest genome assemblies. Here, we report the recent updates of both data and interfaces in the FANTOM web resource.

Do shorter inter-stimulus intervals in the go/no-go task enable better assessment of response inhibition?

Young, Sutherland, and McCoy indicated that a Go/No-Go Task (GNG) becomes more difficult as the inter-stimulus intervals (ISIs) becomes shorter. However, is the number of commission errors under extremely short ISIs a useful metric for assessing response inhibition? This study challenges the assumption that a shorter ISI in the GNG enables better assessment of response inhibition. University students (N = 213) completed the GNG, the Conners Continuous Performance Test 3rd Edition (CCPT), and the Modified Stroop Task. The GNG comprised four blocks of 400, 600, 800, and 1000 ms ISIs, whereas the stimulus presentation was fixed at 250 ms. Consistent with Young et al., shorter ISIs in the GNG resulted in more commission errors. In the block with the shortest ISI, participants also failed more frequently in responses in go trials than in the other blocks, which appears to increase in error variance of commission errors. Consistent with this interpretation, the association between the number of commission errors in the block with 400 ms ISI and CCPT performance was weaker than those between the number of commission errors in other blocks and CCPT performance. It is concluded that using the number of commission errors in the condition with extremely short ISIs in the GNG might be inappropriate for assessing response inhibition.

Systematic analysis of transcription start sites in avian development.

Cap Analysis of Gene Expression (CAGE) in combination with single-molecule sequencing technology allows precision mapping of transcription start sites (TSSs) and genome-wide capture of promoter activities in differentiated and steady state cell populations. Much less is known about whether TSS profiling can characterize diverse and non-steady state cell populations, such as the approximately 400 transitory and heterogeneous cell types that arise during ontogeny of vertebrate animals. To gain such insight, we used the chick model and performed CAGE-based TSS analysis on embryonic samples covering the full 3-week developmental period. In total, 31,863 robust TSS peaks (>1 tag per million [TPM]) were mapped to the latest chicken genome assembly, of which 34% to 46% were active in any given developmental stage. ZENBU, a web-based, open-source platform, was used for interactive data exploration. TSSs of genes critical for lineage differentiation could be precisely mapped and their activities tracked throughout development, suggesting that non-steady state and heterogeneous cell populations are amenable to CAGE-based transcriptional analysis. Our study also uncovered a large set of extremely stable housekeeping TSSs and many novel stage-specific ones. We furthermore demonstrated that TSS mapping could expedite motif-based promoter analysis for regulatory modules associated with stage-specific and housekeeping genes. Finally, using Brachyury as an example, we provide evidence that precise TSS mapping in combination with Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-on technology enables us, for the first time, to efficiently target endogenous avian genes for transcriptional activation. Taken together, our results represent the first report of genome-wide TSS mapping in birds and the first systematic developmental TSS analysis in any amniote species (birds and mammals). By facilitating promoter-based molecular analysis and genetic manipulation, our work also underscores the value of avian models in unravelling the complex regulatory mechanism of cell lineage specification during amniote development.

SCPortalen: human and mouse single-cell centric database.

Published single-cell datasets are rich resources for investigators who want to address questions not originally asked by the creators of the datasets. The single-cell datasets might be obtained by different protocols and diverse analysis strategies. The main challenge in utilizing such single-cell data is how we can make the various large-scale datasets to be comparable and reusable in a different context. To challenge this issue, we developed the single-cell centric database 'SCPortalen' (http://single-cell.clst.riken.jp/). The current version of the database covers human and mouse single-cell transcriptomics datasets that are publicly available from the INSDC sites. The original metadata was manually curated and single-cell samples were annotated with standard ontology terms. Following that, common quality assessment procedures were conducted to check the quality of the raw sequence. Furthermore, primary data processing of the raw data followed by advanced analyses and interpretation have been performed from scratch using our pipeline. In addition to the transcriptomics data, SCPortalen provides access to single-cell image files whenever available. The target users of SCPortalen are all researchers interested in specific cell types or population heterogeneity. Through the web interface of SCPortalen users are easily able to search, explore and download the single-cell datasets of their interests.

Uric Acid-Induced Enhancements of Kv1.5 Protein Expression and Channel Activity via the Akt-HSF1-Hsp70 Pathway in HL-1 Atrial Myocytes.

BACKGROUND: Intracellular uric acid is known to increase the protein level and channel current of atrial Kv1.5; however, mechanisms of the uric acid-induced enhancement of Kv1.5 expression remain unclear. Methods and Results: The effects of uric acid on mRNA and protein levels of Kv1.5, as well as those of Akt, HSF1 and Hsp70, in HL-1 cardiomyocytes were studied by using qRT-PCR and Western blotting. The uptake of uric acid was measured using radio-labeled uric acid. The Kv1.5-mediated channel current was also measured by using patch clamp techniques. Uric acid up-taken by HL-1 cells significantly increased the level of Kv1.5 proteins in a concentration-dependent manner, with this increase abolished by an uric acid transporter inhibitor. Uric acid slowed degradation of Kv1.5 proteins without altering its mRNA level. Uric acid enhanced phosphorylation of Akt and HSF1, and thereby increased both transcription and translation of Hsp70; these effects were abolished by a PI3K inhibitor. Hsp70 knockdown abolished the uric acid-induced increases of Kv1.5 proteins and channel currents. CONCLUSIONS: Intracellular uric acid could stabilize Kv1.5 proteins through phosphorylation of Akt and HSF1 leading to enhanced expression of Hsp70.

Seismic imaging of mantle wedge corner flow and arc magmatism.

I reviewed studies on the inhomogeneous seismic structure of the mantle wedge in subduction zones, in relation to corner flow and its implications for arc magmatism. Seismic studies in Tohoku clearly imaged the descending flow portion of the corner flow as a thin seismic low-velocity layer right above the slab. Slab-derived H2O is fixed to the layer as hydrous minerals, which are brought down by the slab and eventually decompose. The released H2O rises and encounters the ascending flow, formed to fill the gap caused by the descending flow. The combination of H2O addition and adiabatic decompression causes partial melting within the ascending flow. For many subduction zones, seismic tomography has distinctly imaged the ascending flow of the corner flow as a seismic low-velocity and/or high-attenuation layer in the mantle wedge inclined nearly parallel to the slab. These observations indicate that the volcanic front in subduction zones is formed both by the ascending flow and the addition of slab-derived H2O.

[Automated Classification of Calcification and Stent on Computed Tomography Coronary Angiography Using Deep Learning].

In computed tomography coronary angiography (CTCA), calcification and stent make it difficult to evaluate intravascular lumen. This is a cause of low positive-predictive value of coronary stenosis. Therefore, it is expected to develop a computer-aided diagnosis (CAD) system that can automatically detect stenosis in coronary arteries. The purpose of this study is to automatically recognize calcifications or stents in coronary arteries and classify them from the normal coronary artery in CTCA. We used 4960 coronary-cross-sectional images, which consisted of 1113 images with calcification, 1353 images with a stent, and 2494 normal artery images. These images were automatically classified using the deep convolutional neural network (LeNet, AlexNet, and GoogLeNet). The classification accuracy of LeNet, AlexNet, and GoogLeNet were 58.4%, 75.9%, and 81.3%, respectively. The proposed method would be a fundamental technique of CAD in CTCA.

PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease.

Next-generation sequencing experiments have shown that microRNAs (miRNAs) are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched miRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by 1 nt at their 3' end, and moreover that the 3' end of miR-21 is posttranscriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small-RNA sequencing suggested that PARN degrades miR-21 in the 3'-to-5' direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a down-regulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the noncancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncogenic miRNA miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases.

Beneficial effects of Galectin-9 on allergen-specific sublingual immunotherapy in a Dermatophagoides farinae-induced mouse model of chronic asthma.

BACKGROUND: Allergen-specific sublingual immunotherapy is a potential disease-modifying treatment for allergic asthma. Galectin-9 (Gal-9), a ß-galactoside-binding protein with various biologic effects, acts as an immunomodulator in excessive immunologic reactions by expanding regulatory T cells (Treg) and enhancing transforming growth factor (TGF)-ß signaling. We investigated the efficacy of sublingually administered Gal-9 as an adjuvant to a specific allergen in a Dermatophagoides farinae (Df)-induced mouse model of chronic asthma. METHODS: BALB/c mice were intranasally sensitized with Df extract 5 days/week for 5 weeks, and then sublingual Df-allergen extract for 2 weeks (5 days/week). Three days after the final sublingual treatment, mice were intranasally challenged with Df extract. The early asthmatic response (EAR) was evaluated 5 min after the last Df challenge. Airway hyperresponsiveness (AHR) was assayed and bronchoalveolar lavage (BAL) was performed 24 h after the last allergen challenge. Serum IgE and cytokine levels, and number of inflammatory cells in the BAL fluid (BALF) were analyzed. RESULTS: Sublingual Df treatment in the presence of Gal-9, but not alone, significantly reduced AHR; EAR; number of eosinophils and interleukin-13 in the BALF; and serum IgE levels. BALF TGF-ß1 levels were significantly increased in the presence of Gal-9 compared with Df alone. Treg depletion blocked the inhibitory effects of Gal-9 on the EAR, AHR, eosinophilic airway inflammation, and Df-specific serum IgE levels, and suppressed BALF TGF-ß1 levels. CONCLUSIONS: Gal-9 exhibited beneficial effects of sublingual Df allergen-specific immunotherapy in a Df-induced mouse model of chronic asthma, possibly by Gal-9-induced TGF-ß1 production in the lung.

E3 ligase CHIP and Hsc70 regulate Kv1.5 protein expression and function in mammalian cells.

Kv1.5 confers ultra-rapid delayed-rectifier potassium channel current (IKur) which contributes to repolarization of the atrial action potential. Kv1.5 proteins, degraded via the ubiquitin-proteasome pathway, decreased in some atrial fibrillation patients. Carboxyl-terminus heat shock cognate 70-interacting protein (CHIP), an E3 ubiquitin ligase, is known to ubiquitinate short-lived proteins. Here, we investigated the roles of CHIP in Kv1.5 degradation to provide insights into the mechanisms of Kv1.5 decreases and treatments targeting Kv1.5 for atrial fibrillation. Coexpression of CHIP with Kv1.5 in HEK293 cells increased Kv1.5 protein ubiquitination and decreased the protein level. Immunofluorescence revealed decreases of Kv1.5 proteins in the endoplasmic reticulum and on the cell membrane. A siRNA against CHIP suppressed Kv1.5 protein ubiquitination and increased its protein level. CHIP mutants, lacking either the N-terminal tetratricopeptide region domain or the C-terminal U-box domain, failed to exert these effects on Kv1.5 proteins. Immunoprecipitation showed that CHIP formed complexes with Kv1.5 proteins and heat shock cognate protein 70 (Hsc70). Effects of Hsc70 on Kv1.5 were similar to CHIP by altering interaction of CHIP with Kv1.5 protein. Coexpression of CHIP and Hsc70 with Kv1.5 additionally enhanced Kv1.5 ubiquitination. Kv1.5 currents were decreased by overexpression of CHIP or Hsc70 but were increased by knockdown of CHIP or Hsc70 in HEK 293 cells stably expressing Kv1.5. These effects of CHIP and Hsc70 were also observed on endogenous Kv1.5 in HL-1 mouse cardiomyocytes, decreasing IKur and prolonging action potential duration. These results indicate that CHIP decreases the Kv1.5 protein level and functional channel by facilitating its degradation in concert with chaperone Hsc70.

Molecular Mechanisms Underlying Urate-Induced Enhancement of Kv1.5 Channel Expression in HL-1 Atrial Myocytes.

BACKGROUND: Hyperuricemia induces endothelial dysfunction, oxidative stress and inflammation, increasing cardiovascular morbidities. It also raises the incidence of atrial fibrillation; however, underlying mechanisms are unknown. METHODS AND RESULTS: The effects of urate on expression of Kv1.5 in cultured mouse atrial myocytes (HL-1 cells) using reverse transcriptase-PCR, immunoblots, flow cytometry and patch-clamp experiments were studied. Treatment with urate at 7 mg/dl for 24 h increased the Kv1.5 protein level, enhanced ultra-rapid delayed-rectifier K(+)channel currents and shortened action potential duration in HL-1 cells. HL-1 cells expressed the influx uric acid transporter (UAT), URATv1, and the efflux UATs, ABCG2 and MRP4. An inhibitor against URATv1, benzbromarone, abolished the urate effects, whereas an inhibitor against ABCG2, KO143, augmented them. Flow cytometry showed that urate induced an increase in reactive oxygen species, which was abolished by the antioxidant, N-acetylcysteine (NAC), and the NADPH-oxidase inhibitor, apocynin. Both NAC and apocynin abolished the enhancing effects of urate on Kv1.5 expression. A urate-induced increase in the Kv1.5 proteins was accompanied by phosphorylation of extracellular signal-regulated kinase (ERK), and was abolished by an ERK inhibitor, PD98059. NAC abolished phosphorylation of ERK by urate. CONCLUSIONS: Intracellular urate taken up by UATs enhanced Kv1.5 protein expression and function in HL-1 atrial myocytes, which could be attributable to ERK phosphorylation and oxidative stress derived from nicotinamide adenine dinucleotide phosphate (NADPH)-oxidase.