[Advances in the diagnosis, treatment, and prognosis of acute decompensatory cirrhosis]

Acute decompensatory cirrhosis is a common cause of hospital admission, readmission, and death, causing a heavy burden on patients, their families, and society. This article reviews the research advancement from the perspectives of concept evolution, pathogenesis, treatment, outcome, and prognosis models, providing new ideas for preventing and treating acute decompensatory cirrhosis.

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Spatially resolved transcriptomic technologies are promising tools to study complex biological processes such as mammalian embryogenesis. However, the imbalance between resolution, gene capture, and field of view of current methodologies precludes their systematic application to analyze relatively large and three-dimensional mid- and late-gestation embryos. Here, we combined DNA nanoball (DNB)-patterned arrays and in situ RNA capture to create spatial enhanced resolution omics-sequencing (Stereo-seq). We applied Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas (MOSTA), which maps with single-cell resolution and high sensitivity the kinetics and directionality of transcriptional variation during mouse organogenesis. We used this information to gain insight into the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues such as the dorsal midbrain. Our panoramic atlas will facilitate in-depth investigation of longstanding questions concerning normal and abnormal mammalian development.

Rolling back human pluripotent stem cells to an eight-cell embryo-like stage

After fertilization, the quiescent zygote experiences a burst of genome activation that initiates a short-lived totipotent state. Understanding the process of totipotency in human cells would have broad applications. However, in contrast to in mice1,2, demonstration of the time of zygotic genome activation or the eight-cell (8C) stage in in vitro cultured human cells has not yet been reported, and the study of embryos is limited by ethical and practical considerations. Here we describe a transgene-free, rapid and controllable method for producing 8C-like cells (8CLCs) from human pluripotent stem cells. Single-cell analysis identified key molecular events and gene networks associated with this conversion. Loss-of-function experiments identified fundamental roles for DPPA3, a master regulator of DNA methylation in oocytes3, and TPRX1, a eutherian totipotent cell homeobox (ETCHbox) family transcription factor that is absent in mice4. DPPA3 induces DNA demethylation throughout the 8CLC conversion process, whereas TPRX1 is a key executor of 8CLC gene networks. We further demonstrate that 8CLCs can produce embryonic and extraembryonic lineages in vitro or in vivo in the form of blastoids5 and complex teratomas. Our approach provides a resource to uncover the molecular process of early human embryogenesis.

Cell transcriptomic atlas of the non-human primate Macaca fascicularis

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.

The mTORC1-eIF4F axis controls paused pluripotency

Mouse embryonic stem cells (mESCs) can self-renew indefinitely and maintain pluripotency. Inhibition of mechanistic target of rapamycin (mTOR) by the kinase inhibitor INK128 is known to induce paused pluripotency in mESCs cultured with traditional serum/LIF medium (SL), but the underlying mechanisms remain unclear. In this study, we demonstrate that mTOR complex 1 (mTORC1) but not complex 2 (mTORC2) mediates mTOR inhibition-induced paused pluripotency in cells grown in both SL and 2iL medium (GSK3 and MEK inhibitors and LIF). We also show that mTORC1 regulates self-renewal in both conditions mainly through eIF4F-mediated translation initiation that targets mRNAs of both cytosolic and mitochondrial ribosome subunits. Moreover, inhibition of mitochondrial translation is sufficient to induce paused pluripotency. Interestingly, eIF4F also regulates maintenance of pluripotency in an mTORC1-independent but MEK/ERK-dependent manner in SL, indicating that translation of pluripotency genes is controlled differently in SL and 2iL. Our study reveals a detailed picture of how mTOR governs self-renewal in mESCs and uncovers a context-dependent function of eIF4F in pluripotency regulation.

Translational and post-translational control of human naïve versus primed pluripotency

Deciphering the regulatory network for human naive and primed pluripotency is of fundamental theoretical and applicable significance. Here, by combining quantitative proteomics, phosphoproteomics, and acetylproteomics analyses, we revealed RNA processing and translation as the most differentially regulated processes between naive and primed human embryonic stem cells (hESCs). Although glycolytic primed hESCs rely predominantly on the eukaryotic initiation factor 4E (eIF4E)-mediated cap-dependent pathway for protein translation, naive hESCs with reduced mammalian target of rapamycin complex (mTORC1) activity are more tolerant to eIF4E inhibition, and their bivalent metabolism allows for translating selective mRNAs via both eIF4E-dependent and eIF4E-independent/eIF4A2-dependent pathways to form a more compact naive proteome. Globally up-regulated proteostasis and down-regulated post-translational modifications help to further refine the naive proteome that is compatible with the more rapid cycling of naive hESCs, where CDK1 plays an indispensable coordinative role. These findings may assist in better understanding the unrestricted lineage potential of naive hESCs and in further optimizing conditions for future clinical applications

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RNA processing and translation are most different between naive and primed hESCs

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Glycolytic primed hESCs mainly rely on eIF4E-dependent translation

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Bivalent metabolism in naive hESCs promotes eIF4E-independent translation

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CDK1 is required for naive pluripotency partially by activating E-cadherin signaling

[Research progress of sodium butyrate in metabolic-associated fatty liver disease]

Metabolic-associated fatty liver disease (MAFLD) has become the most common chronic liver disease affecting global public health, and its incidence rate is increasing year by year. The molecular mechanism of its pathogenesis is not yet fully understood, and there is a shortage of effective clinical prevention and treatment methods. Studies have found that sodium butyrate can participate in gene regulation, immune regulation, intestinal barrier function regulation, oxidative stress and other in-vivo physiological activities. Furthermore, it also plays an important role in preventing and alleviating the MAFLD occurrence and development. This article reviews the related studies of sodium butyrate on gene expression regulation, fat metabolism improvement, intestinal flora regulation, and steatohepatitis improvement with MAFLD.

Capture of the newly transcribed RNA interactome using click chemistry

Application of synthetic nucleoside analogues to capture newly transcribed RNAs has unveiled key features of RNA metabolism. Whether this approach could be adapted to isolate the RNA-bound proteome (RNA interactome) was, however, unexplored. We have developed a new method (capture of the newly transcribed RNA interactome using click chemistry, or RICK) for the systematic identification of RNA-binding proteins based on the incorporation of 5-ethynyluridine into newly transcribed RNAs followed by UV cross-linking and click chemistry-mediated biotinylation. The RNA-protein adducts are then isolated by affinity capture using streptavidin-coated beads. Through high-throughput RNA sequencing and mass spectrometry, the RNAs and proteins can be elucidated globally. A typical RICK experimental procedure takes only 1 d, excluding the steps of cell preparation, 5-ethynyluridine labeling, validation (silver staining, western blotting, quantitative reverse-transcription PCR (qRT-PCR) or RNA sequencing (RNA-seq)) and proteomics. Major advantages of RICK are the capture of RNA-binding proteins interacting with any type of RNA and, particularly, the ability to discern between newly transcribed and steady-state RNAs through controlled labeling. Thanks to its versatility, RICK will facilitate the characterization of the total and newly transcribed RNA interactome in different cell types and conditions.

Chromatin lncRNA Platr10 controls stem cell pluripotency by coordinating an intrachromosomal regulatory network

Background

A specific 3-dimensional intrachromosomal architecture of core stem cell factor genes is required to reprogram a somatic cell into pluripotency. As little is known about the epigenetic readers that orchestrate this architectural remodeling, we used a novel chromatin RNA in situ reverse transcription sequencing (CRIST-seq) approach to profile long noncoding RNAs (lncRNAs) in the Oct4 promoter.

Results

We identify Platr10 as an Oct4 - Sox2 binding lncRNA that is activated in somatic cell reprogramming. Platr10 is essential for the maintenance of pluripotency, and lack of this lncRNA causes stem cells to exit from pluripotency. In fibroblasts, ectopically expressed Platr10 functions in trans to activate core stem cell factor genes and enhance pluripotent reprogramming. Using RNA reverse transcription-associated trap sequencing (RAT-seq), we show that Platr10 interacts with multiple pluripotency-associated genes, including Oct4, Sox2, Klf4, and c-Myc, which have been extensively used to reprogram somatic cells. Mechanistically, we demonstrate that Platr10 helps orchestrate intrachromosomal promoter-enhancer looping and recruits TET1, the enzyme that actively induces DNA demethylation for the initiation of pluripotency. We further show that Platr10 contains an Oct4 binding element that interacts with the Oct4 promoter and a TET1-binding element that recruits TET1. Mutation of either of these two elements abolishes Platr10 activity.

Conclusion

These data suggest that Platr10 functions as a novel chromatin RNA molecule to control pluripotency in trans by modulating chromatin architecture and regulating DNA methylation in the core stem cell factor network.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13059-021-02444-6.

Growth differentiation factor 11 relieves acute lung injury in mice by inhibiting inflammation and apoptosis

OBJECTIVE

Acute lung injury (ALI) is the most common organ damage in sepsis and sepsis-induced ALI is a clinically extremely dangerous disease. Therefore, it is essential to find an effective way to treat ALI. We hope to provide a new target for the treatment of clinical ALI by studying the effect of GDF11 on LPS-induced ALI.

MATERIALS AND METHODS

C57BL/6 male mice and lipopolysaccharide (LPS) were used to induce mouse ALI. Recombinant GDF11 protein was used to treat mice to detect the effect of GDF11 on mouse ALI. In addition, BEAS-2B cells were used to further validate the effects of GDF11 on inflammation and apoptosis of alveolar epithelial cells.

RESULTS

Recombinant GDF11 protein significantly reduced the expression of inflammatory factors and apoptosis-related pathways in mouse lung tissues. Overexpression of GDF11 in BEAS-2B cells also significantly attenuated the levels of inflammation and apoptosis in the cells. In addition, GDF11 can reduce the activity of TLR2/HMGB1/NF-κB signaling pathway, which is an important mechanism for GDF11 to play a role in lung protection.

CONCLUSIONS

GDF11 can exert lung protection effects by inhibiting the TLR2/HMGB1/NF-κB signaling pathway and reduce the level of inflammation and apoptosis of the lung.

Multilevel Risk Factors for Weight Change after Breast Cancer Diagnosis Among Black Women

Background: Weight gain after breast cancer diagnosis increases the risk of mortality. African American/Black breast cancer survivors are more likely to have excess body weight than their White counterparts, which may contribute to their higher mortality rate. Emerging evidence suggests that post-diagnosis weight gain may result from multilevel determinants. However, no study has investigated the multilevel characteristics among Black breast cancer survivors. Objective: To evaluate associations between individual-level factors and neighborhood social and built environment factors with weight change after breast cancer diagnosis among Black women. Methods: We evaluated associations of interest among 785 women enrolled in the Women's Circle of Health Follow-Up Study (WCHFS), a longitudinal study of Black breast cancer survivors in New Jersey. Weight change was primarily based on measurements at baseline and follow-up visits (Median: 10.3 and 23.2 mo. since diagnosis, respectively). Participants were grouped into categories of stable weight (52.4%), ≥3% weight loss (20.0%), and ≥3% weight gain (27.6%). Using multivariate- adjusted multinomial logistic regression and multilevel multinomial logistic regression, we evaluated relative risk ratios (RRRs) for associations between multilevel factors and post-diagnosis weight change category. Results: Black breast cancer survivors who were older at diagnosis, had higher household income, post-menopausal status, and higher baseline BMI were less likely to gain weight compared to women with stable weight. Former smoking, higher tumor stage, and chemotherapy were associated with increased relative risk of weight gain (e.g. RRR-chemo: 1.45, 95% CI: 1.01, 2.08). Black women residing in neighborhoods in the highest tertile for density of walkable destinations had a decreased relative risk of post- diagnosis weight gain (e.g. RRR-T3 highest density vs. T1 lowest: 0.39, 95% CI: 0.20, 0.75), while those residing in neighborhoods with higher density of fast food restaurants had increased relative risk of weight gain (RRR-T3 highest density vs. T1 lowest: 1.94, 95% CI: 1.23, 3.05). Conclusion: Both individual and neighborhood factors may influence the risk of weight gain among Black women after breast cancer diagnosis.

JMJD3 acts in tandem with KLF4 to facilitate reprogramming to pluripotency

The interplay between the Yamanaka factors (OCT4, SOX2, KLF4 and c-MYC) and transcriptional/epigenetic co-regulators in somatic cell reprogramming is incompletely understood. Here, we demonstrate that the histone H3 lysine 27 trimethylation (H3K27me3) demethylase JMJD3 plays conflicting roles in mouse reprogramming. On one side, JMJD3 induces the pro-senescence factor Ink4a and degrades the pluripotency regulator PHF20 in a reprogramming factor-independent manner. On the other side, JMJD3 is specifically recruited by KLF4 to reduce H3K27me3 at both enhancers and promoters of epithelial and pluripotency genes. JMJD3 also promotes enhancer-promoter looping through the cohesin loading factor NIPBL and ultimately transcriptional elongation. This competition of forces can be shifted towards improved reprogramming by using early passage fibroblasts or boosting JMJD3’s catalytic activity with vitamin C. Our work, thus, establishes a multifaceted role for JMJD3, placing it as a key partner of KLF4 and a scaffold that assists chromatin interactions and activates gene transcription.

Previous work suggested that histone demethylase JMJD3 is detrimental to somatic cell reprogramming. Here, the authors show that while JMJD3 has a context-independent detrimental effect on early stages of reprogramming, during late stages it activates epithelial and pluripotency genes together with Klf4.

Exonuclease combinations reduce noises in 3D genomics technologies

Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source, which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased the valid-pairs ratio from ∼40% to ∼80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.

β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus

Mouse embryonic stem cells cultured with MEK (mitogen-activated protein kinase kinase) and GSK3 (glycogen synthase kinase 3) inhibitors (2i) more closely resemble the inner cell mass of preimplantation blastocysts than those cultured with SL [serum/leukemia inhibitory factor (LIF)]. The transcriptional mechanisms governing this pluripotent ground state are unresolved. Release of promoter-proximal paused RNA polymerase II (Pol2) is a multistep process necessary for pluripotency and cell cycle gene transcription in SL. We show that β-catenin, stabilized by GSK3 inhibition in medium with 2i, supplies transcriptional coregulators at pluripotency loci. This selectively strengthens pluripotency loci and renders them addicted to transcription initiation for productive gene body elongation in detriment to Pol2 pause release. By contrast, cell cycle genes are not bound by β-catenin, and proliferation/self-renewal remains tightly controlled by Pol2 pause release under 2i conditions. Our findings explain how pluripotency is reinforced in the ground state and also provide a general model for transcriptional resilience/adaptation upon network perturbation in other contexts.

PML2-mediated thread-like nuclear bodies mark late senescence in Hutchinson-Gilford progeria syndrome

Progerin accumulation disrupts nuclear lamina integrity and causes nuclear structure abnormalities, leading to premature aging, that is, Hutchinson–Gilford progeria syndrome (HGPS). The roles of nuclear subcompartments, such as PML nuclear bodies (PML NBs), in HGPS pathogenesis, are unclear. Here, we show that classical dot‐like PML NBs are reorganized into thread‐like structures in HGPS patient fibroblasts and their presence is associated with late stage of senescence. By co‐immunoprecipitation analysis, we show that farnesylated Progerin interacts with human PML2, which accounts for the formation of thread‐like PML NBs. Specifically, human PML2 but not PML1 overexpression in HGPS cells promotes PML thread development and accelerates senescence. Further immunofluorescence microscopy, immuno‐TRAP, and deep sequencing data suggest that these irregular PML NBs might promote senescence by perturbing NB‐associated DNA repair and gene expression in HGPS cells. These data identify irregular structures of PML NBs in senescent HGPS cells and support that the thread‐like PML NBs might be a novel, morphological, and functional biomarker of late senescence.

Role of Long Non-coding RNAs in Reprogramming to Induced Pluripotency

The generation of induced pluripotent stem cells through somatic cell reprogramming requires a global reorganization of cellular functions. This reorganization occurs in a multi-phased manner and involves a gradual revision of both the epigenome and transcriptome. Recent studies have shown that the large-scale transcriptional changes observed during reprogramming also apply to long non-coding RNAs (lncRNAs), a type of traditionally neglected RNA species that are increasingly viewed as critical regulators of cellular function. Deeper understanding of lncRNAs in reprogramming may not only help to improve this process but also have implications for studying cell plasticity in other contexts, such as development, aging, and cancer. In this review, we summarize the current progress made in profiling and analyzing the role of lncRNAs in various phases of somatic cell reprogramming, with emphasis on the re-establishment of the pluripotency gene network and X chromosome reactivation.

Voxel-wise meta-analysis of structural changes in gray matter of Parkinson's disease patients with mild cognitive impairment

Evidence from previous voxel-based morphometry (VBM) studies indicates that widespread brain regions are involved in Parkinson’s disease with mild cognitive impairment (PD-MCI). However, the spatial localization reported for gray matter (GM) abnormalities is heterogeneous. The aim of the present study was to quantitatively integrate studies on GM abnormalities observed in PD-MCI in order to determine whether a pattern exists. Eligible whole-brain VBM studies were identified by a systematic search of articles in PubMed and EMBASE databases spanning from 1995 to January 1, 2019. A meta-analysis was performed to investigate regional GM abnormalities in PD-MCI. The anisotropic effect size version of seed-based d mapping (AES-SDM) meta-analysis was conducted to explore the GMV differences of PD-MCI compared with PD patients with normal cognitive function (PD-NC). A total of 12 studies comprising 243 PD-MCI patients and 326 PD-NC were included in the meta-analysis. PD-MCI patients showed a robust GM decrease in the left insula and left superior temporal gyrus. Moreover, meta-regression analysis demonstrated that age, PD duration and stage, and Unified Parkinson’s Disease Rating Scale III and Mini-Mental State Examination scores might be partly correlated with the GM abnormalities observed in PD-MCI patients. The convergent findings of this quantitative meta-analysis revealed a characteristic neuroanatomical pattern in PD-MCI. The findings provide some evidence that MCI in PD may result in the breakdown of the insula and temporal gyrus, which may serve as specific regions of interest for further investigations.

Generation of two LRRK2 homozygous knockout human induced pluripotent stem cell lines using CRISPR/Cas9

Mutations in the Leucine rich repeat kinase 2 (LRRK2) gene are found in both familial and sporadic Parkinson's disease (PD), and are also associated with immune-related disorders including Crohn's disease (CD) and leprosy. We have generated two homozygous LRRK2 knockout human induced pluripotent stem cell (iPSC) lines using CRISPR-Cas9 in a well-characterized human iPSC clone. The LRRK2 knockout cell lines retained normal morphology, gene expression, and the capacity to differentiate into cell types of the three germ layers. These cell lines are valuable for elucidating the role of LRRK2 in innate immunity and PD.

Generation of Rybp homozygous knockout murine ES cell line GIBHe001-A-1 by using CRISPR/Cas9 technology

RYBP (Ring1 and YY1 Binding Protein) is critical for pluripotency and differentiation of embryonic stem cells (ESCs). RYBP depletion disturbs both neural and myocardial differentiation of ESCs. Moreover, low level of RYBP is correlated with diseases such as glioblastoma. To study the biological function of RYBP in neural differentiation of ESCs, here we generated Rybp homozygous knockout murine ESC line based on Sox1-GFP reporter using CRISPR/Cas9 genome editing technology. The last two exons of Rybp gene in which contain 115 amino acids have been replaced with PGK-Pruo by homologous recombination.

Overexpression of miR-638 attenuated the effects of hypoxia/reoxygenation treatment on cell viability, cell apoptosis and autophagy by targeting ATG5 in the human cardiomyocytes

OBJECTIVE

Myocardial ischemia/reperfusion (I/R) injury largely contributed to the damage of myocardial tissues in patients with coronary disease, which may subsequently lead to heart failure. MicroRNAs (miRNAs) are considered to be involved in the process of myocardial I/R injury. The present study aimed to investigate the in vitro functional role of miR-638 in the myocardial I/R injury in the human cardiomyocytes (HCMs).

PATIENTS AND METHODS

MTT assay and flow cytometry assay were performed to determine cell viability and apoptosis of HCMs. Real Time-quantitative Polymerase Chain Reaction was used to determine miRNA and mRNA expression levels. The protein levels were determined by Western blot assay.

RESULTS

Hypoxia/reoxygenation (H/R) treatment suppressed cell viability, increased cell apoptotic rate and suppressed miR-638 expression in the HCMs. The downregulation of miR-638 suppressed cell viability and induced cell apoptosis in the HCMs. The overexpression of miR-638 attenuated the effects of H/R treatment on the cell viability and cell apoptosis in the HCMs. In addition, miR-638 suppressed the expression of autophagy-related 5 (ATG5) by targeting the 3'untranslated region of ATG5. Enforced expression of ATG5 reversed the effects of miR-638 overexpression on cell viability and cell apoptosis in H/R-treated HCMs. More importantly, H/R treatment promoted autophagy in the HCMs, and this effect was significantly reversed by miR-638 mimic transfection.

CONCLUSIONS

Our results suggested that the overexpression of miR-638 attenuated the effects of H/R treatment on cell viability, cell apoptosis and autophagy, at least partly by regulating the ATG5 expression in the HCMs.

Generation of a PARK2 homozygous knockout induced pluripotent stem cell line (GIBHi002-A-1) with two common isoforms abolished

Loss of function mutations in PARK2 (encoding PARKIN) cause autosomal recessive Parkinson's disease (PD), which often manifests at a juvenile age. Molecular and biochemical studies show that PARKIN functions as an E3 ubiquitin ligase controlling mitochondrial homeostasis. Yet, the exact mechanisms are unclear due to the use of sub-optimal models including cancer cells and fibroblasts. We have generated a PARK2 knockout (KO) isogenic cell line using a well-characterized induced pluripotent stem cell (iPSC) clone with good differentiation potential. This cell line lacks the expression of all PARKIN isoforms and is valuable for elucidating the role of PARK2 mutations in PD.

Generation of an induced pluripotent stem cell line (GIBHi003-A) from a Parkinson's disease patient with mutant PINK1 (p. I368N)

Familial Parkinson's disease (PD) can be caused by deleterious mutations in PINK1 (encoding PINK1) in an autosomal recessive manner. Functional studies suggest that PINK1 works as a regulator of mitochondrial homeostasis. However, how loss of PINK1 induces dopaminergic neuron degeneration is still unclear. Here, we have generated a patient-derived induced pluripotent stem cell (iPSC) line with mutant PINK1 (p. I368N). This cell line will facilitate PD disease modeling in vitro and can be used for generating isogenic cell lines through gene correction.

mTORC1-PGC1 axis regulates mitochondrial remodeling during reprogramming

Metabolic reprogramming, hallmarked by enhanced glycolysis and reduced mitochondrial activity, is a key event in the early phase of somatic cell reprogramming. Although extensive work has been conducted to identify the mechanisms of mitochondrial remodeling in reprogramming, many questions remain. In this regard, different laboratories have proposed a role in this process for either canonical (ATG5-dependent) autophagy-mediated mitochondrial degradation (mitophagy), noncanonical (ULK1-dependent, ATG5-independent) mitophagy, mitochondrial fission or reduced biogenesis due to mTORC1 suppression. Clarifying these discrepancies is important for providing a comprehensive picture of metabolic changes in reprogramming. Yet, the comparison among these studies is difficult because they use different reprogramming conditions and mitophagy detection/quantification methods. Here, we have systematically explored mitochondrial remodeling in reprogramming using different culture media and reprogramming factor cocktails, together with appropriate quantification methods and thorough statistical analysis. Our experiments show lack of evidence for mitophagy in mitochondrial remodeling in reprogramming, and further confirm that the suppression of the mTORC1-PGC1 pathway drives this process. Our work helps to clarify the complex interplay between metabolic changes and nutrient sensing pathways in reprogramming, which may also shed light on other contexts such as development, aging and cancer.

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

Long noncoding RNAs (lncRNAs) can regulate the activity of target genes by participating in the organization of chromatin architecture. We have devised a “chromatin-RNA in situ reverse transcription sequencing” (CRIST-seq) approach to profile the lncRNA interaction network in gene regulatory elements by combining the simplicity of RNA biotin labeling with the specificity of the CRISPR/Cas9 system. Using gene-specific gRNAs, we describe a pluripotency-specific lncRNA interacting network in the promoters of Sox2 and Pou5f1, two critical stem cell factors that are required for the maintenance of pluripotency. The promoter-interacting lncRNAs were specifically activated during reprogramming into pluripotency. Knockdown of these lncRNAs caused the stem cells to exit from pluripotency. In contrast, overexpression of the pluripotency-associated lncRNA activated the promoters of core stem cell factor genes and enhanced fibroblast reprogramming into pluripotency. These CRIST-seq data suggest that the Sox2 and Pou5f1 promoters are organized within a unique lncRNA interaction network that determines the fate of pluripotency during reprogramming. This CRIST approach may be broadly used to map lncRNA interaction networks at target loci across the genome.

The relationship between plasma homocysteine levels and MTHFR gene variation, age, and sex in Northeast China

Background

Hyperhomocysteinemia (HHcy) is the risk factor for cardiovascular disease and stroke. However, the impacts on the genetic variation of methylene tetrahydrofolate reductase (MTHFR) on plasma homocysteine levels in the Northeast Chinese population have not been studied. Therefore, this study was carried out to determine the relationship between HHcy and MTHFR gene variation, and whether it was influenced by age and sex of the population in Northeast China.

Materials and Methods

A total of 466 subjects were randomly enrolled in this study. According to the homocysteine levels (Hcy ≥ 15 μmol/L) of the subjects, they were divided into hyperhomocysteine (HHcy = 206) and normal homocysteine (Hcy = 260). Polymerase chain reaction/high-resolution dissolution curve and homocysteine determination kit methods were used for genotype testing and homocysteine detection, respectively.

Results

High plasma homocysteine levels are associated with MTHFR 677T and 1298A [P < 0.00, odds ratio (confidence interval) = 1.842 (1.418-2.394) >1], which is related to increasing age (P_range = 0.0005-0.0161), with the homocysteine levels of males higher than females (P < 0.0001).

Conclusion

High plasma homocysteine levels were linked to the MTHFR gene mutation. In addition, plasma homocysteine levels increased significantly with age with male's homocysteine levels higher than that of females.

[Analysis of correlation between serum fatty acid profile and cognitive impairment in the elderly]

Objective: To explore the relationship between cognitive impairment and serum fatty acid profile. Methods: Participants aged ≥60 years were selected from 3 communities in Shijiazhuang in 2015. The questionnaire was performed to collect basic information. And Montreal Cognitive Assessment was applied for the evaluation of cognitive impairment. Blood lipid parameters and serum fatty acid profiles were analyzed for all the subjects. A total of 529 subjects were finally included in this research. Multivariate ordinal logistic model was used to analyze the relationship between serum fatty acid profile and cognitive impairment. Results: Normal, mild and moderate cognitive impairment accounted for 41.2% (n=218), 51.4% (n=272) and 7.4% (n=39) of all the subjects respectively. With control of age, gender, education, total cholesterol (TC), total triglyceride (TG), low density lipoprotein cholesterol (LDL-C), and high density lipoprotein cholesterol (HDL-C), the OR (95%CI) of eicosenoic acid, nervonic acid and ratio of n-3 and n-6 polyunsaturated fatty acid (n-3/n-6) was 1.06 (1.01-1.10), 0.93 (0.91-0.96), and 0.17 (0.04-0.73). Conclusion: The risk of cognitive impairment decreased with the raise of serum nervonic acid concentration and n-3/n-6, and increased with the raise of serum eicosenoic acid concentration.

[The diagnostic framework for screening Alzheimer's disease in the Chinese population]

Criteria for diagnosis of Alzheimer's disease (AD) is not available in China. The international criteria is not a proper choice due to issues such as translation and lead to low diagnostic rate and high rate of missed diagnosis. The research group of Alzheimer's Disease Chinese (ADC) reviewed knowledge and techniques in neuropsychology, neuroimaging, molecular biology, and clinical neurology, and systematically studied the detection techniques such as memory, language, visuospatial, executive function, and medial temporal lobe visual scores on MRI, and their optimal threshold and diagnostic value for the diagnosis of AD. Through a systematic review and consensus meeting, a diagnostic framework for screening AD in the Chinese population was established. Among these methods, an operational standard for clinical pathology models increased the diagnostic sensitivity by 15%. The sensitivity and specificity of screening memory impairment increased by 18.1% and 11.6%, respectively. The sensitivity of screening medial temporal lobe atrophy increased by 24.5% and missed diagnosis was decreased by 34.5%. An operational standard for clinical biology models, incorporating the latest molecular imaging and molecular biology techniques, has enabled the early diagnosis of AD in China. The framework combines a principled diagnostic guideline with an operational screening protocol, which is applicable to all clinical settings and of great significance for the early detection, early diagnosis and early treatment of AD.

[Dementia screening and diagnostic framework in Chinese population]

There are no standard diagnostic criteria for Alzheimer's disease (AD) in China. The copied international criteria has led to a high rate of missed diagnosis due to issues such as translation and cultural discrepancy. Under the principles of semantic equivalence, content equivalence and performance equivalence, the research group of Alzheimer's Disease Chinese (ADC) adopted several effective methods, such as two-way translation, content conversion, performance evaluation, etc. to systematically study the cognitive, behavioral, functional, and general assessment techniques in dementia screening and diagnosis, as well as their screening thresholds and diagnostic values. We also established a dementia screening and assessment framework in clinical practice through systematic reviews and group consensus. It has improved the early diagnosis rate of dementia in China, been accepted by home and abroad academic institutions, which is of great significance for early diagnosis and treatment of dementia.

A Familial Hypercholesterolemia Human Liver Chimeric Mouse Model Using Induced Pluripotent Stem Cell-derived Hepatocytes

Familial hypercholesterolemia (FH) is mostly caused by low-density lipoprotein receptor (LDLR) mutations and results in an increased risk of early-onset cardiovascular disease due to marked elevation of LDL cholesterol (LDL-C) in blood. Statins are the first line of lipid-lowering drugs for treating FH and other types of hypercholesterolemia, but new approaches are emerging, in particular PCSK9 antibodies, which are now being tested in clinical trials. To explore novel therapeutic approaches for FH, either new drugs or new formulations, we need appropriate in vivo models. However, differences in the lipid metabolic profiles compared to humans are a key problem of the available animal models of FH. To address this issue, we have generated a human liver chimeric mouse model using FH induced pluripotent stem cell (iPSC)-derived hepatocytes (iHeps). We used Ldlr^-/-/Rag2^-/-/Il2rg^-/- (LRG) mice to avoid immune rejection of transplanted human cells and to assess the effect of LDLR-deficient iHeps in an LDLR null background. Transplanted FH iHeps could repopulate 5-10% of the LRG mouse liver based on human albumin staining. Moreover, the engrafted iHeps responded to lipid-lowering drugs and recapitulated clinical observations of increased efficacy of PCSK9 antibodies compared to statins. Our human liver chimeric model could thus be useful for preclinical testing of new therapies to FH. Using the same protocol, similar human liver chimeric mice for other FH genetic variants, or mutations corresponding to other inherited liver diseases, may also be generated.

Publisher Correction: NCoR/SMRT co-repressors cooperate with c-MYC to create an epigenetic barrier to somatic cell reprogramming

In the version of this Article originally published, in Fig. 2c, the '+' sign and 'OSKM' were superimposed in the label '+OSKM'. In Fig. 4e, in the labels, all instances of 'Ant' should have been 'Anti-'. And, in Fig. 7a, the label '0.0' was misplaced; it should have been on the colour scale bar. These figures have now been corrected in the online versions.

Efficacy, acceptability, and tolerability of antidepressant treatments for patients with post-stroke depression: a network meta-analysis

The aim of this study was to investigate the efficacy, acceptability, and tolerability of antidepressants in treating post-stroke depression (PSD) by performing a network meta-analysis of randomized controlled trials of the current literature. Eligible studies were retrieved from online databases, and relevant data were extracted. The primary outcome was efficacy as measured by the mean change in overall depressive symptoms. Secondary outcomes included discontinued treatment for any reason and specifically due to adverse events. Fourteen trials were eligible, which included 949 participants and 9 antidepressant treatments. Few significant differences were found for all outcomes. For the primary outcome, doxepin, paroxetine, and nortriptyline were significantly more effective than a placebo [standardized mean differences: −1.93 (95%CI=−3.56 to −0.29), −1.39 (95%CI=−2.59 to −0.21), and −1.25 (95%CI=−2.46 to −0.04), respectively]. Insufficient evidence exists to select a preferred antidepressant for treating patients with post-stroke depression, and our study provides little evidence that paroxetine may be the potential choice when starting treatment for PSD. Future studies with paroxetine and larger sample sizes, multiple medical centers, and sufficient intervention durations is needed for improving the current evidence.

Boosting ATM activity alleviates aging and extends lifespan in a mouse model of progeria

DNA damage accumulates with age (Lombard et al., 2005). However, whether and how robust DNA repair machinery promotes longevity is elusive. Here, we demonstrate that ATM-centered DNA damage response (DDR) progressively declines with senescence and age, while low dose of chloroquine (CQ) activates ATM, promotes DNA damage clearance, rescues age-related metabolic shift, and prolongs replicative lifespan. Molecularly, ATM phosphorylates SIRT6 deacetylase and thus prevents MDM2-mediated ubiquitination and proteasomal degradation. Extra copies of Sirt6 extend lifespan in Atm-/- mice, with restored metabolic homeostasis. Moreover, the treatment with CQ remarkably extends lifespan of Caenorhabditis elegans, but not the ATM-1 mutants. In a progeria mouse model with low DNA repair capacity, long-term administration of CQ ameliorates premature aging features and extends lifespan. Thus, our data highlights a pro-longevity role of ATM, for the first time establishing direct causal links between robust DNA repair machinery and longevity, and providing therapeutic strategy for progeria and age-related metabolic diseases.

As cells live and divide, their genetic material gets damaged. The DNA damage response is a network of proteins that monitor, recognize and fix the damage, which is also called DNA lesions. For example, an enzyme called ATM senses when DNA is broken and then begins a process that will get it repaired, while another enzyme known as SIRT6 participates in the actual mending process.

When organisms get older, the repair machinery becomes less efficient, and the number of DNA lesions and errors increases. The accumulation of DNA damage may cause the ‘symptoms’ of old age – from cancer, to wrinkles and the slowing down of the body’s chemical processes. In fact, individuals with defective ATMs (who thus struggle to repair their DNA) age abnormally fast; conversely, SIRT6 promotes longevity. If declining repair mechanisms cause aging, would boosting the DNA damage response slow down this process?

Chloroquine is a drug used to combat malaria, but it can also enhance the activity of ATM without damaging DNA. Qian, Liu et al. show that chloroquine helps cells remove broken DNA and keep dividing for longer. In animals, the drug increases the lifespan of worms and prolongs the lives of mice who have mutations that make them age quicker.

Qian, Liu et al. also demonstrate that ATM works by chemically altering the pro-longevity enzyme SIRT6. These changes make SIRT6 more stable, and keep it safe from cellular processes that destroy it. In addition, mice that are genetically engineered to lack ATM can survive for longer if they also produce extra SIRT6. These experiments show that enhancing the DNA damage response can slow down aging, thus linking the DNA repair machinery to longevity.

Progeria is a group of rare genetic conditions with inefficient DNA repair; people with progeria age fast and die young. The results by Qian, Liu et al., if confirmed in humans, could provide a new way of treating these diseases.

Non-alcoholic fatty liver disease is associated with stroke severity and progression of brainstem infarctions

BACKGROUND AND PURPOSE

Non-alcoholic fatty liver disease (NAFLD) is closely correlated to visceral obesity, dyslipidaemia, insulin resistance and type 2 diabetes mellitus. We sought to assess the association between a specific stroke subgroup, brainstem infarctions (BSIs) and NAFLD. Furthermore, we evaluated whether NAFLD is an independent risk factor in patients with BSIs.

METHODS

Non-alcoholic fatty liver disease was assessed in 306 patients with radiologically confirmed BSIs via liver ultrasound. Differences between patients with and without NAFLD were compared. Data associated with stroke severity and progression after admission were collected.

RESULTS

Non-alcoholic fatty liver disease was found in 130 (42.5%) patients with acute BSIs; 58 (19.0%) had National Institutes of Health Stroke Scale scores >7 and 57 (18.6%) had progression after admission. Initial National Institutes of Health Stroke Scale scores, incidence of progression and stroke severity, and modified Rankin Scale scores at discharge were significantly higher in patients with NAFLD than in those without NAFLD. NAFLD was associated with stroke severity [Cox regression: hazard ratio (HR), 2.243; 95% confidence interval (CI), 1.254-4.013, P < 0.01]. This risk remained statistically significant after controlling for age, gender, diabetes mellitus and C-reactive protein (HR, 2.327; 95% CI, 1.252-4.324, P < 0.01). In addition, NAFLD was associated with progression (HR, 2.155; 95% CI, 1.201-3.865, P < 0.05) and remained significant after controlling for age, gender, diabetes mellitus, fibrinogen and C-reactive protein (HR, 2.378; 95% CI, 1.260-4.486, P < 0.01).

CONCLUSIONS

These results suggest that NAFLD is a potential risk factor when evaluating the severity and progression of acute BSIs. This relationship is independent of classic risk factors and metabolic syndrome features.

[Epidemiological survey of visual impairment in Funing County, Jiangsu]

Objective: To investigate the prevalence of visual impairment and factors associated with visual impairment among people aged 50 years and above in Funing County, Jiangsu Province. Methods: Cross-sectional study. Random cluster sampling was used in selecting individuals aged ≥50 years in 30 clusters, and 5 947 individuals received visual acuity testing and eye examination. Stata 13.0 software was used to analyze the data. Multivariate logistic regression was used to detect possible factors of visual impairment such as age, gender and education. Statistical significance was defined as P< 0.05. Results: A total of 6 145 persons aged 50 years and above were enumerated, and 5 947 (96.8%) participants were examined. Based on the criteria of World Health Organization (WHO) visual impairment classification and presenting visual acuity, 138 persons were diagnosed as blindness, and 1 405 persons were diagnosed as low vision. The prevalence of blindness and low vision was 2.32% and 23.63%, respectively. And the prevalence of visual impairment was 25.95%. Based on the criteria of WHO visual impairment classification and best-corrected visual acuity, 92 persons were diagnosed as blindness, and 383 persons were diagnosed as low vision. The prevalence of blindness and low vision was 1.55% and 6.44%, respectively. And the prevalence of visual impairment was 7.99%. Concerning presenting visual acuity and best-corrected visual acuity, the prevalence of blindness and low vision was higher in old people, females and less educated persons. Cataract (46.63%) was the leading cause of blindness. Uncorrected refractive error (36.51%) was also a main cause of visual impairment. Conclusion: The prevalence of visual impairment is higher in old people, females and less educated persons in Funing County, Jiangsu Province. Cataract is still the leading cause of visual impairment. (Chin J Ophthalmol, 2017, 53: 502-508).

Parasites, nutrition, immune responses and biology of metabolic tissues

Nutritional immunology, immunometabolism and identification of novel immunotherapeutic targets are areas of active investigation in parasitology. There is a well-documented crosstalk among immune cells and cells in metabolically active tissues that is important for homeostasis. The numbers and function of these cells are altered by obesity leading to inflammation. A variety of helminths spend some part of their life cycle in the gastrointestinal tract and even entirely enteral nematode infections exert beneficial effects on glucose and lipid metabolism. The foundation of this review is the ability of enteric nematode infections to improve obesity-induced type 2 diabetes and the metabolic syndrome, which are significant health issues in developed areas. It considers the impact of nutrition and specific nutritional deficiencies, which are occur in both undeveloped and developed areas, on the host's ability mount a protective immune response against parasitic nematodes. There are a number of proposed mechanisms by which parasitic nematodes can impact metabolism including effects gastrointestinal hormones, altering epithelial function and changing the number and/or phenotype of immune cells in metabolic tissues. Nematodes can also exert their beneficial effects through Th2 cytokines that activate the transcription factor STAT6, which upregulates genes that regulate glucose and lipid metabolism.

Parenting styles and body mass index: a systematic review of prospective studies among children

BACKGROUND

Parenting style may be an important determinant of an individual's future weight status. However, reviews that evaluate the relationship between parenting style and weight-related outcomes have not focused on prospective studies.

METHODS

We systematically searched PubMed, Embase and PsychInfo for studies published between 1995 and 2016 that evaluated the prospective relationship between parenting style experienced in childhood and subsequent weight outcomes.

RESULTS

We identified 11 prospective cohort studies. Among the eight studies that categorized parenting style into distinct groups (i.e. authoritative, authoritarian, permissive and neglectful), five provided evidence that authoritative parenting was associated with lower body mass index gains. Among the six highest quality studies, four suggested a protective role of authoritative parenting style against adverse weight-related outcomes. However, only one study controlled for a comprehensive set of confounders, and the small number of studies conducted within certain age groups precluded our ability to ascertain critical periods when parenting style is most strongly related to child weight.

CONCLUSIONS

The present literature supports the idea that authoritative parenting may be protective against later overweight and obesity, although findings are mixed. More prospective cohort studies of longer durations, with more sophisticated methods that examine age-varying relationships, and that control for a comprehensive set of confounders, are needed.

Randomized controlled trials of serotonin-norepinephrine reuptake inhibitor in treating major depressive disorder in children and adolescents: a meta-analysis of efficacy and acceptability

New generation antidepressant therapies, including serotonin-norepinephrine reuptake inhibitor (SNRIs), were introduced in the late 1980s; however, few comprehensive studies have compared the benefits and risks of various contemporary treatments for major depressive disorder (MDD) in young patients. A comprehensive literature search of PubMed, Cochrane, Embase, Web of Science, and PsycINFO databases was conducted from 1970 to January 2015. Only clinical trials that randomly assigned one SNRI or placebo to patients aged 7 to 18 years who met the diagnostic criteria for major depressive disorder were included. Treatment success, dropout rate, and suicidal ideation/attempt outcomes were measured. Primary efficacy was determined by pooling the risk ratios (RRs) of treatment response and remission. Acceptability was determined by pooling the RRs of dropouts for all reasons and for adverse effects as well as suicide-risk outcomes. Five trials with a total of 973 patients were included. SNRIs were not significantly more effective than placebo for treatment response but were for remission. The comparison of patients taking SNRIs that dropped out for all reasons and those taking placebo did not reach statistical significance. Significantly more patients taking SNRIs dropped out for adverse effects than those taking placebo. No significant difference was found in suicide-related risk outcomes. SNRI therapy does not display a superior efficacy and is not better tolerated compared to placebo in these young patients. However, duloxetine has a potential beneficial effect for depression in young populations, showing a need for further research.

Fumarylacetoacetate Hydrolase Knock-out Rabbit Model for Hereditary Tyrosinemia Type 1

Hereditary tyrosinemia type 1 (HT1) is a severe human autosomal recessive disorder caused by the deficiency of fumarylacetoacetate hydroxylase (FAH), an enzyme catalyzing the last step in the tyrosine degradation pathway. Lack of FAH causes accumulation of toxic metabolites (fumarylacetoacetate and succinylacetone) in blood and tissues, ultimately resulting in severe liver and kidney damage with onset that ranges from infancy to adolescence. This tissue damage is lethal but can be controlled by administration of 2-(2-nitro-4-trifluoromethylbenzoyl)-1,3-cyclohexanedione (NTBC), which inhibits tyrosine catabolism upstream of the generation of fumarylacetoacetate and succinylacetone. Notably, in animals lacking FAH, transient withdrawal of NTBC can be used to induce liver damage and a concomitant regenerative response that stimulates the growth of healthy hepatocytes. Among other things, this model has raised tremendous interest for the in vivo expansion of human primary hepatocytes inside these animals and for exploring experimental gene therapy and cell-based therapies. Here, we report the generation of FAH knock-out rabbits via pronuclear stage embryo microinjection of transcription activator-like effector nucleases. FAH^-/- rabbits exhibit phenotypic features of HT1 including liver and kidney abnormalities but additionally develop frequent ocular manifestations likely caused by local accumulation of tyrosine upon NTBC administration. We also show that allogeneic transplantation of wild-type rabbit primary hepatocytes into FAH^-/- rabbits enables highly efficient liver repopulation and prevents liver insufficiency and death. Because of significant advantages over rodents and their ease of breeding, maintenance, and manipulation compared with larger animals including pigs, FAH^-/- rabbits are an attractive alternative for modeling the consequences of HT1.