Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition

Epithelial-to-mesenchymal transition (EMT), a fundamental transdifferentiation process in development, produces diverse phenotypes in different physiological or pathological conditions. Many genes involved in EMT have been identified to date, but mechanisms contributing to the phenotypic diversity and those governing the coupling between the dynamics of epithelial (E) genes and that of the mesenchymal (M) genes are unclear. In this study, we employed combinatorial perturbations to mammary epithelial cells to induce a series of EMT phenotypes by manipulating two essential EMT-inducing elements, namely TGF-β and ZEB1. By measuring transcriptional changes in more than 700 E-genes and M-genes, we discovered that the M-genes exhibit a significant diversity in their dependency to these regulatory elements and identified three groups of M-genes that are controlled by different regulatory circuits. Notably, functional differences were detected among the M-gene clusters in motility regulation and in survival of breast cancer patients. We computationally predicted and experimentally confirmed that the reciprocity and reversibility of EMT are jointly regulated by ZEB1. Our integrative analysis reveals the key roles of ZEB1 in coordinating the dynamics of a large number of genes during EMT, and it provides new insights into the mechanisms for the diversity of EMT phenotypes

How do cardiovascular diseases harm labor force participation? Evidence of nationally representative survey data from Japan, a super-aged society

ObjectiveTo evaluate how cardiovascular diseases harm labor force participation (LFP) among the Japanese population and verify the validity of plasma biomarkers as instrumental variables of cardiovascular diseases after adjusting for a broad set of confounders including dietary intake.DesignUsing nationally representative repeated cross-sectional surveys in Japan, the Comprehensive Survey of Living Conditions and National Health and Nutrition Survey, with plasma biomarkers as instrumental variables for quasi-randomization.SettingOnset of cardiovascular diseases in those receiving regular treatment for hypertension, intracerebral hemorrhage, intracerebral infarction, angina pectoris, myocardial infarction, or other types of cardiovascular diseases.ParticipantsA total of 65,615 persons aged ≥ 20 years (35,037 women and 30,578 men) who completed a survey conducted every three years from 1995 through 2013.Main outcome measuresRespondent employment and weekly working hours during each survey year.ResultsCardiovascular diseases significantly and remarkably reduced the probability of working by 15.4% (95% CI: -30.6% to -0.2%). The reduction in working probability was detected for women only. Respondents aged ≥ 40 years were less likely to work once diagnosed and the reduction was enlarged for those aged ≥ 65 years, while those aged < 40 years appeared to be unaffected. Probability of engaging in manual labor significantly decreased once diagnosed; however, no impact was found for cognitive occupations. Among employed respondents, the adverse effects of cardiovascular diseases decreased working hours by five hours per week. Validity of the biomarker instrumental variables was generally verified.ConclusionsA vicious circle is suggested between LFP and unfavorable health. However, the effects vary across age, sex, and occupation type, even after adjusting for causal effects, which could cause a downward bias in LFP impact

SkewC : Identifying cells with skewed gene body coverage in single-cell RNA sequencing data

The analysis and interpretation of single-cell RNA sequencing (scRNA-seq) experiments are compromised by the presence of poor-quality cells. For meaningful analyses, such poor-quality cells should be excluded as they introduce noise in the data. We introduce SkewC, a quality-assessment tool, to identify skewed cells in scRNA-seq experiments. The tool's methodology is based on the assessment of gene coverage for each cell, and its skewness as a quality measure; the gene body coverage is a unique characteristic for each protocol, and different protocols yield highly different coverage profiles. This tool is designed to avoid misclustering or false clusters by identifying, isolating, and removing cells with skewed gene body coverage profiles. SkewC is capable of processing any type of scRNA-seq dataset, regardless of the protocol. We envision SkewC as a distinctive QC method to be incorporated into scRNA-seq QC processing to preclude the possibility of scRNA-seq data misinterpretation.Peer reviewe

FANTOM5 CAGE profiles of human and mouse samples

In the FANTOM5 project, transcription initiation events across the human and mouse genomes were mapped at a single base-pair resolution and their frequencies were monitored by CAGE (Cap Analysis of Gene Expression) coupled with single-molecule sequencing. Approximately three thousands of samples, consisting of a variety of primary cells, tissues, cell lines, and time series samples during cell activation and development, were subjected to a uniform pipeline of CAGE data production. The analysis pipeline started by measuring RNA extracts to assess their quality, and continued to CAGE library production by using a robotic or a manual workflow, single molecule sequencing, and computational processing to generate frequencies of transcription initiation. Resulting data represents the consequence of transcriptional regulation in each analyzed state of mammalian cells. Non-overlapping peaks over the CAGE profiles, approximately 200,000 and 150,000 peaks for the human and mouse genomes, were identified and annotated to provide precise location of known promoters as well as novel ones, and to quantify their activities

Biotin levels in blood and follicular fluid

It has been shown that biotin, a water-soluble vitamin (B7), plays roles in reproductive functions, such as oocyte maturation and embryo development, in experimental animals. On the other hand, little is known about the clinical effects of biotin on human reproduction. In this study, serum and follicular fluid biotin levels were measured in patients who underwent in vitro fertilization / intracytoplasmic sperm injection (IVF / ICSI), and their associations with reproductive outcomes were evaluated. As a result, biotin was detected in follicular fluid, as well as serum, and the biotin levels of follicular fluid were found to be positively correlated with those of serum. The biotin levels of serum were higher than those of follicular fluid, suggesting that biotin may be taken up into the follicular fluid from the blood. Although serum and follicular fluid biotin levels tended to be higher in pregnant patients than in non-pregnant patients, these data did not show the significant statistical difference. These findings indicate that biotin does not contribute to the maintenance of oocyte quality, and hence, it does not increase fertilization and pregnancy rates

Androgen’s effects in female

The metabolic effects of androgens and their underlying mechanisms in females have been revealed by recent studies. An excess of androgens can have adverse effects on feeding behavior and metabolic functions and induce metabolic disorders / diseases, such as obesity, insulin resistance, and diabetes, in women and experimental animals of reproductive age. Interestingly, these effects of androgens are not observed in ovariectomized animals, indicating that their effects might be dependent on the estrogen milieu. Central and peripheral mechanisms, such as alterations in the activity of hypothalamic factors, reductions in energy expenditure, skeletal muscle insulin resistance, and β-cell dysfunction, might be related to these androgens’ effects

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

トウキョウノウギョウダイガクフジノウジョウ ニ オケル シヨウカンリホウシキ ノ ヘンセン ニ トモナウ クロゲワシュハンショクメウシ ノ ハンショクセイセキ

東京農業大学富士農場では,昭和62年以降,家畜の飼養管理方式の改善につとめてきた。本調査では,昭和62年から平成18年までの間に本農場において繋養してきた黒毛和種繁殖牛延べ400頭における分娩後初回人工授精日数,人工授精回数,受胎率および空胎日数について飼養管理方式の変遷と併せて解析した。その結果,受胎率は自然哺乳期の44.8%に対し早期母子分離開始以降では50.6%と高い傾向を示した。空胎日数は舎飼期に120.3±90.6日であったが,放牧開始以降は90.0±72.3日と約30日程度短縮し,有意な差(P<0.05)が認められた。また,早期母子分離との関係では,自然哺乳期の125.1±94.8日に対し,早期母子分離開始以降は88.1±62.0日と約37日短縮しており,有意な差(P<0.05)が認められた。このことから,昭和62年から平成13年までは舎飼主体で十分な運動は行えていないと考えられ,平成13年以降の母子分離時期の早期化と放牧地面積の拡大が,受胎率向上と空胎日数短縮に良好な影響を及ぼしたと考えられた。Research has been carried out on how to improve feeding methods for domestic animals since 1987 at Fuji farm, Tokyo University of Agriculture. In this investigation, the days consumed for the first postpartum artificial insemination, the number of artificial inseminations, the conception rate, and the relation of days of the non-pregnancy in a total of 400 Japanese Black cows fed between 1987 to 2006 were analyzed along with the transition of feeding method. Conception rates were 50.6% with the early cow separation and it was higher than that (44.8%) of natural nursing period. Days of non-pregnancy during raising time in the cattle shed were 120.3±90.6, though it was 90.0&plusmn;72.3 days after the start of pasturing, approximately 30 days shorter, with a significant difference (P<0.05). Natural nursing period was 125.1±94.8, and it was 88.1±62.0 days after the start of early cow separation, approximately 37 days shorter with a significant difference (P<0.05). As a result, we thought that feeding in the livestock barn between 1987 to 2001, in which cows were not able to move around adequately and that making the cow separation time earlier from 2001 and the expansion of the pasture area had exerted an excellent influence on conception rate improvement and the shortening of non-pregnancy days