The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.

Understanding how genetic variants impact molecular phenotypes is a key goal of functional genomics, currently hindered by reliance on a single haploid reference genome. Here, we present the EN-TEx resource of 1,635 open-access datasets from four donors (∼30 tissues × âˆ¼15 assays). The datasets are mapped to matched, diploid genomes with long-read phasing and structural variants, instantiating a catalog of >1 million allele-specific loci. These loci exhibit coordinated activity along haplotypes and are less conserved than corresponding, non-allele-specific ones. Surprisingly, a deep-learning transformer model can predict the allele-specific activity based only on local nucleotide-sequence context, highlighting the importance of transcription-factor-binding motifs particularly sensitive to variants. Furthermore, combining EN-TEx with existing genome annotations reveals strong associations between allele-specific and GWAS loci. It also enables models for transferring known eQTLs to difficult-to-profile tissues (e.g., from skin to heart). Overall, EN-TEx provides rich data and generalizable models for more accurate personal functional genomics.

STAB2: an updated spatio-temporal cell atlas of the human and mouse brain.

The brain is constituted of heterogeneous types of neuronal and non-neuronal cells, which are organized into distinct anatomical regions, and show precise regulation of gene expression during development, aging and function. In the current database release, STAB2 provides a systematic cellular map of the human and mouse brain by integrating recently published large-scale single-cell and single-nucleus RNA-sequencing datasets from diverse regions and across lifespan. We applied a hierarchical strategy of unsupervised clustering on the integrated single-cell transcriptomic datasets to precisely annotate the cell types and subtypes in the human and mouse brain. Currently, STAB2 includes 71 and 61 different cell subtypes defined in the human and mouse brain, respectively. It covers 63 subregions and 15 developmental stages of human brain, and 38 subregions and 30 developmental stages of mouse brain, generating a comprehensive atlas for exploring spatiotemporal transcriptomic dynamics in the mammalian brain. We also augmented web interfaces for querying and visualizing the gene expression in specific cell types. STAB2 is freely available at https://mai.fudan.edu.cn/stab2.

An augmented Mendelian randomization approach provides causality of brain imaging features on complex traits in a single biobank-scale dataset.

Mendelian randomization (MR) is an effective approach for revealing causal risk factors that underpin complex traits and diseases. While MR has been more widely applied under two-sample settings, it is more promising to be used in one single large cohort given the rise of biobank-scale datasets that simultaneously contain genotype data, brain imaging data, and matched complex traits from the same individual. However, most existing multivariable MR methods have been developed for two-sample setting or a small number of exposures. In this study, we introduce a one-sample multivariable MR method based on partial least squares and Lasso regression (MR-PL). MR-PL is capable of considering the correlation among exposures (e.g., brain imaging features) when the number of exposures is extremely upscaled, while also correcting for winner's curse bias. We performed extensive and systematic simulations, and demonstrated the robustness and reliability of our method. Comprehensive simulations confirmed that MR-PL can generate more precise causal estimates with lower false positive rates than alternative approaches. Finally, we applied MR-PL to the datasets from UK Biobank to reveal the causal effects of 36 white matter tracts on 180 complex traits, and showed putative white matter tracts that are implicated in smoking, blood vascular function-related traits, and eating behaviors.

TMEM2 inhibits the development of Graves' orbitopathy through the JAK-STAT signaling pathway.

A mouse model was used to investigate the role of the hyaluronidase, transmembrane protein 2 (TMEM2), on the progression of Graves' orbital (GO) disease. We established a GO mouse model through immunization with a plasmid expressing the thyroid stimulating hormone receptor. Orbital fibroblasts (OFs) were subsequently isolated from both GO and non-GO mice for comprehensive in vitro analyses. The expression of TMEM2 was assessed using qRT-PCR, Western blot and immunohistochemistry in vivo. Disease pathology was evaluated by H&E staining and Masson's trichrome staining in GO mouse tissues. Our investigation revealed a notable reduction in TMEM2 expression in GO mouse orbital tissues. Through overexpression and knockdown assays, we demonstrated that TMEM2 suppresses inflammatory cytokines and reactive oxygen species production. TMEM2 also inhibits the formation of lipid droplets in OFs and the expression of adipogenic factors. Further incorporating Gene Set Enrichment Analysis of relevant GEO datasets and subsequent in vitro cell experiments, robustly confirmed that TMEM2 overexpression was associated with a pronounced upregulation of the JAK/STAT signaling pathway. In vivo, TMEM2 overexpression reduced inflammatory cell infiltration, adipogenesis, and fibrosis in orbital tissues. These findings highlight the varied regulatory role of TMEM2 in GO pathogenesis. Our study reveals that TMEM2 plays a crucial role in mitigating inflammation, suppressing adipogenesis, and reducing fibrosis in GO. TMEM2 has potential as a therapeutic target and biomarker for treating or alleviating GO. These findings advance our understanding of GO pathophysiology and provide opportunities for targeted interventions to modulate TMEM2 for therapeutic purposes.

Deciphering the genetic architecture of human brain structure and function: a brief survey on recent advances of neuroimaging genomics.

Brain imaging genomics is an emerging interdisciplinary field, where integrated analysis of multimodal medical image-derived phenotypes (IDPs) and multi-omics data, bridging the gap between macroscopic brain phenotypes and their cellular and molecular characteristics. This approach aims to better interpret the genetic architecture and molecular mechanisms associated with brain structure, function and clinical outcomes. More recently, the availability of large-scale imaging and multi-omics datasets from the human brain has afforded the opportunity to the discovering of common genetic variants contributing to the structural and functional IDPs of the human brain. By integrative analyses with functional multi-omics data from the human brain, a set of critical genes, functional genomic regions and neuronal cell types have been identified as significantly associated with brain IDPs. Here, we review the recent advances in the methods and applications of multi-omics integration in brain imaging analysis. We highlight the importance of functional genomic datasets in understanding the biological functions of the identified genes and cell types that are associated with brain IDPs. Moreover, we summarize well-known neuroimaging genetics datasets and discuss challenges and future directions in this field.

Sarcopenic obesity is part of obesity paradox in dementia development: evidence from a population-based cohort study.

BACKGROUND: Sarcopenic obesity, a clinical and functional condition characterized by the coexistence of obesity and sarcopenia, has not been investigated in relation to dementia risk and its onset. METHODS: We included 208,867 participants from UK biobank, who aged 60 to 69 years at baseline. Dementia diagnoses were identified using hospital records and death register data. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox proportional hazards models to evaluate the associations of obesity, sarcopenia, and sarcopenic obesity with dementia risk, stratified by sex. Stratified analyses were performed across dementia-related polygenic risk score (PRS). Restricted mean survival time models were established to estimate the difference and 95%CIs of dementia onset across different status. Additionally, linear regression models were employed to estimate associations of different status with brain imaging parameters. The mediation effects of chronic diseases were also examined. RESULTS: Obese women with high PRS had a decreased risk (HR = 0.855 [0.761-0.961]), but obese men with low PRS had an increased risk (HR = 1.223 [1.045-1.431]). Additionally, sarcopenia was associated with elevated dementia risk (HRwomen = 1.323 [1.064-1.644]; HRmen = 2.144 [1.753-2.621]) in those with low PRS. Among those with high PRS, however, the association was only significant in early-life (HRwomen = 1.679 [1.355-2.081]; HRmen = 2.069 [1.656-2.585]). Of note, sarcopenic obesity was associated with higher dementia risk (HRwomen = 1.424 [1.227-1.653]; HRmen = 1.989 [1.702-2.323]), and results remained similar stratified by PRS. Considering dementia onset, obesity was associated with dementia by 1.114 years delayed in women, however, 0.170 years advanced in men. Sarcopenia (women: 0.080 years; men: 0.192 years) and sarcopenic obesity (women: 0.109 years; men: 0.511 years) respectively advanced dementia onset. Obesity, sarcopenia, and sarcopenic obesity were respectively related to alterations in different brain regions. Association between sarcopenic obesity and dementia was mediated by chronic diseases. CONCLUSIONS: Sarcopenic obesity and sarcopenia were respectively associated with increased dementia risk and advanced dementia onset to vary degree. The role of obesity in dementia may differ by sex and genetic background.

Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes.

The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in millions of deaths worldwide. The disease presents with various manifestations that can vary in severity and long-term outcomes. Previous efforts have contributed to the development of effective strategies for treatment and prevention by uncovering the mechanism of viral infection. We now know all the direct protein-protein interactions that occur during the lifecycle of SARS-CoV-2 infection, but it is critical to move beyond these known interactions to a comprehensive understanding of the "full interactome" of SARS-CoV-2 infection, which incorporates human microRNAs (miRNAs), additional human protein-coding genes, and exogenous microbes. Potentially, this will help in developing new drugs to treat COVID-19, differentiating the nuances of long COVID, and identifying histopathological signatures in SARS-CoV-2-infected organs. To construct the full interactome, we developed a statistical modeling approach called MLCrosstalk (multiple-layer crosstalk) based on latent Dirichlet allocation. MLCrosstalk integrates data from multiple sources, including microbes, human protein-coding genes, miRNAs, and human protein-protein interactions. It constructs "topics" that group SARS-CoV-2 with genes and microbes based on similar patterns of co-occurrence across patient samples. We use these topics to infer linkages between SARS-CoV-2 and protein-coding genes, miRNAs, and microbes. We then refine these initial linkages using network propagation to contextualize them within a larger framework of network and pathway structures. Using MLCrosstalk, we identified genes in the IL1-processing and VEGFA-VEGFR2 pathways that are linked to SARS-CoV-2. We also found that Rothia mucilaginosa and Prevotella melaninogenica are positively and negatively correlated with SARS-CoV-2 abundance, a finding corroborated by analysis of single-cell sequencing data.

Impact of a dual glucose-dependent insulinotropic peptide/glucagon-like peptide-1 receptor agonist tirzepatide on heart rate among patients with type 2 diabetes: A systematic review and pairwise and network meta-analysis.

AIMS: To evaluate the impact of a dual glucose-dependent insulinotropic peptide (GIP) and glucagon-like peptide-1 (GLP-1) receptor agonist tirzepatide (TZP), and its potential dose-response effect, on heart rate. METHODS: Articles were searched from PubMed, Web of Science, Embase, Cochrane Library, and clinical trials registries (ClinicalTrials.gov) databases. Randomized controlled trials (RCTs) comparing TZP at doses of 5, 10 and 15 mg in adults with type 2 diabetes were included. Six study arms were summarized from original research (TZP 5, 10 and 15 mg, GLP-1 receptor agonists [GLP-1RAs], insulin, placebo). The GLP-1RA and non-GLP-1RA groups were combined to form a control group. Two reviewers independently extracted data and assessed the quality of each study. Mean differences (MDs) were calculated as effect estimates for continuous outcomes. Pairwise meta-analyses and network meta-analyses were conducted. The study protocol was prospectively registered (PROSPERO ID: CRD42023418551). RESULTS: Eight articles were included in this systematic review and meta-analysis. The mean baseline heart rate ranged from 65.2 to 75.7 beats per minute. Pairwise meta-analysis showed that, compared with combined the control group, there were significantly greater increases in heart rates in the TZP group (MD 1.82, 95% confidence interval [CI] 0.75, 2.89). Similar significant rises were identified when comparing TZP with GLP-1RAs and non-GLP-1RAs (GLP-1 RAs: MD 2.29, 95% CI 1.00, 3.59; non-GLP-1RAs: MD 1.58, 95% CI 0.26, 2.91). TZP 5 mg was associated with smaller increases in heart rates compared to TZP 10 mg and TZP 15 mg (TZP 10 mg: MD -0.97, 95% CI -1.79, -0.14; TZP 15 mg: MD -2.57, 95% CI -3.79, -1.35). TZP 10 mg increased heart rate less than TZP 15 mg (MD -1.5, 95% CI -2.38, -0.82). Network meta-analysis indicated that TZP 15 mg was associated with significant increases in heart rate compared with TZP 5 mg (MD 2.53, 95% CI 1.43, 3.62), TZP 10 mg (MD 1.44, 95% CI 0.35, 2.53), GLP-1RAs (MD 3.46, 95% CI 1.67, 5.25), insulin (MD 2.86, 95% CI 1.32, 4.41) and placebo (MD 2.96, 95% CI 1.36, 4.57). CONCLUSIONS: Our study showed not only that there was a greater increase in heart rate in the TZP group than in the control, GLP-1RA and non-GLP-1RA groups, but also that the 15-mg dose of TZP had the strongest impact on increasing heart rates compared with the other five inventions, with a TZP dose-response impact on heart rate. Further research on the effects of TZP treatment-related increases in heart rate is required.

POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins.

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation. Accurate identification of RBP binding sites in multiple cell lines and tissue types from diverse species is a fundamental endeavor towards understanding the regulatory mechanisms of RBPs under both physiological and pathological conditions. Our POSTAR annotation processes make use of publicly available large-scale CLIP-seq datasets and external functional genomic annotations to generate a comprehensive map of RBP binding sites and their association with other regulatory events as well as functional variants. Here, we present POSTAR3, an updated database with improvements in data collection, annotation infrastructure, and analysis that support the annotation of post-transcriptional regulation in multiple species including: we made a comprehensive update on the CLIP-seq and Ribo-seq datasets which cover more biological conditions, technologies, and species; we added RNA secondary structure profiling for RBP binding sites; we provided miRNA-mediated degradation events validated by degradome-seq; we included RBP binding sites at circRNA junction regions; we expanded the annotation of RBP binding sites, particularly using updated genomic variants and mutations associated with diseases. POSTAR3 is freely available at http://postar.ncrnalab.org.

HER2-positive breast cancer progresses rapidly after pyrotinib resistance: acquired RET gene fusion and TP53 gene mutation are potential reasons.

Approximately 15-20% of the patients with breast cancer overexpress human epidermal growth factor receptor 2 ( HER2 ). HER2 -positive breast cancer is highly aggressive and has a high relapse rate, suggesting that it is prone to and progresses rapidly after drug resistance. Pyrotinib resistance and changes in patients' conditions after drug resistance are challenging clinical issues and require medical attention. Recently, there are few clinical reports on changes in patients' conditions after pyrotinib resistance. We report a case of a 46-year-old patient with HER2 -positive breast cancer who developed resistance to pyrotinib and rapidly progressed to uncontrolled liver failure in less than a week. To elucidate the cause of the rapid progression, we collected samples of the patient's ascites and performed next-generation sequencing (NGS). On the basis of the NGS results, we speculated that the rapid progression after pyrotinib resistance might be due to RET gene fusion and TP53 gene mutations. Therefore, this case report aims to alert oncologists that patients with HER2 -positive breast cancer, who are resistant to pyrotinib or other targeted drugs, could experience rapid or even flare-up progression and that RET gene fusion and TP53 gene mutations might be potential causes.

GENCODE 2021.

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.

Chinese Expert Consensus on the Use of Biologics in Patients with Chronic Rhinosinusitis (2022, Zhuhai).

BACKGROUND: Chronic rhinosinusitis (CRS) is a common inflammatory disease in otolaryngology, mainly manifested as nasal congestion, nasal discharge, facial pain/pressure, and smell disorder. CRS with nasal polyps (CRSwNP), an important phenotype of CRS, has a high recurrence rate even after receiving corticosteroids and/or functional endoscopic sinus surgery. In recent years, clinicians have focused on the application of biological agents in CRSwNP. However, it has not reached a consensus on the timing and selection of biologics for the treatment of CRS so far. SUMMARY: We reviewed the previous studies of biologics in CRS and summarized the indications, contraindications, efficacy assessment, prognosis, and adverse effects of biologics. Also, we evaluated the treatment response and adverse reactions of dupilumab, omalizumab, and mepolizumab in the management of CRS and made recommendations. KEY MESSAGES: Dupilumab, omalizumab, and mepolizumab have been approved for the treatment of CRSwNP by the US Food and Drug Administration. Type 2 and eosinophilic inflammation, need for systemic steroids or contraindication to systemic steroids, significantly impaired quality of life, anosmia, and comorbid asthma are required for the use of biologics. Based on current evidence, dupilumab has the prominent advantage in improving quality of life and reducing the risk of comorbid asthma in CRSwNP among the approved monoclonal antibodies. Most patients tolerate biological agents well in general with few major or severe adverse effects. Biologics have provided more options for severe uncontrolled CRSwNP patients or patients who refuse to have surgery. In the future, more novel biologics will be assessed in high-quality clinical trials and applied clinically.

Cellular transcriptional alterations of peripheral blood in Alzheimer's disease.

BACKGROUND: Alzheimer's disease (AD), a progressive neurodegenerative disease, is the most common cause of dementia worldwide. Accumulating data support the contributions of the peripheral immune system in AD pathogenesis. However, there is a lack of comprehensive understanding about the molecular characteristics of peripheral immune cells in AD. METHODS: To explore the alterations of cellular composition and the alterations of intrinsic expression of individual cell types in peripheral blood, we performed cellular deconvolution in a large-scale bulk blood expression cohort and identified cell-intrinsic differentially expressed genes in individual cell types with adjusting for cellular proportion. RESULTS: We detected a significant increase and decrease in the proportion of neutrophils and B lymphocytes in AD blood, respectively, which had a robust replicability across other three AD cohorts, as well as using alternative algorithms. The differentially expressed genes in AD neutrophils were enriched for some AD-associated pathways, such as ATP metabolic process and mitochondrion organization. We also found a significant enrichment of protein-protein interaction network modules of leukocyte cell-cell activation, mitochondrion organization, and cytokine-mediated signaling pathway in neutrophils for AD risk genes including CD33 and IL1B. Both changes in cellular composition and expression levels of specific genes were significantly associated with the clinical and pathological alterations. A similar pattern of perturbations on the cellular proportion and gene expression levels of neutrophils could be also observed in mild cognitive impairment (MCI). Moreover, we noticed an elevation of neutrophil abundance in the AD brains. CONCLUSIONS: We revealed the landscape of molecular perturbations at the cellular level for AD. These alterations highlight the putative roles of neutrophils in AD pathobiology.

Serum amyloid protein (SAA) as a healthy marker for immune function in Tridacna crocea.

Serum amyloid protein (SAA) is known as an acute reactive protein of innate immunity in mammals. However, in invertebrates, the role of SAA in innate immunity is still unclear. In this study, a full-length cDNA of the SAA gene (named TcSAA) was cloned from Tridacna crocea, mollusca. The gene includes a 193 bp 5' untranslated region (UTR) and a 129 bp 3' UTR sequence, and the open reading frame (ORF) with 393 bp nucleotides encodes a polypeptide of 130 amino acids. TcSAA contains a typical signal peptide and an SAA functional domain. The mRNA expression of TcSAA was detected in all 12 selected tissues and 7 different developmental stages. Furthermore, the expression of TcSAA was increased quickly in hemocytes after challenge with V. coralliilyticus or LPS. Furthermore, rTcSAA could bind V. coralliilyticus and V. alginolyticus, and the protein could reduce the lethality rate of the clams from 80% to 55% which caused by V. coralliilyticus about 48 h after injection. In summary, these results indicate that TcSAA may act as a marker for monitoring health and protecting T. crocea.

Short report: nasal obstruction recovery after septoplasty in patients with nasal septal deviation affected by anxiety and depression.

This research was aimed to explore whether the recovery of subjective symptoms and objective examination in nasal septum deviation (NSD) patients after septoplasty were related to the degree of preoperative anxiety or depression, in the hope of providing new ideas for clinical treatment. A total of 150 NSD patients were included in this prospective research. Visual analogue scale (VAS) scores, Nasal Obstruction Symptom Evaluation (NOSE) scores, self-rating anxiety scale (SAS) scores, self-rating depression scale (SDS) scores, total inspiratory and expiratory nasal resistance were recorded before and 6 months after operation. The results showed preoperative anxiety or depression was not statistically different between groups in terms of age, gender and course, but positively correlated with nasal obstruction (VAS and NOSE). The recovery of nasal obstruction in patients with anxiety or depression was worse than that in normal NSD patients 6 months after surgery, and was decreased with the increase of anxiety or depression degree. And no significant difference showed in the reduction of total inspiratory and expiratory nasal resistance between groups. In conclusion, anxiety and depression affected the improvement of nasal obstruction feeling in NSD patients after septoplasty, and the improvement was negatively correlated with the degree of anxiety and depression. It is necessary to evaluate the anxiety and depression of NSD patients before septoplasty.

Long-term recurrence-free survival and complications of percutaneous balloon compression and radiofrequency thermocoagulation of Gasserian ganglion for trigeminal neuralgia: A retrospective study of 1313 cases.

OBJECTIVE: To estimate long-term recurrence, complications after percutaneous balloon compression (PBC) and radiofrequency thermocoagulation (RFT) of gasserian ganglion among a large sample of patients with trigeminal neuralgia (TN) during a long-term follow-up. METHODS: A retrospective analysis of 1313 patients undergoing PBC or RFT for the treatment of TN was conducted from 2006 to 2020. Recurrence-free survival (RFS) was assessed by the Kaplan-Meier method. Complications including facial numbness, corneal reflex decrease and masseter weakness were also estimated. RESULTS: For patients who received first initial PBC and RFT, the median RFS was 130.1 months (95% CI: 124.4, 135.9) and 123.3 months (95% CI: 117.6, 128.9) in PBC and RFT group with log-rank p = 0.108. The RFS rate was, respectively, 90.6% (95% CI: 88.1%-93.3%) and 91.4% (95% CI: 89.1%-93.7%) at 1 year, 84.6% (95% CI: 81.4%-87.8%) and 83.3% (95% CI: 80.3%-86.3%) at 3 years, 81.5% (95% CI: 78.1%-85.0%), and 78.6% (95% CI: 75.2%-81.9%) at 5 years, 71.5% (95% CI: 67.5%-75.5%), and 64.8% (95% CI: 61.0%-68.7%) at 10 years in two groups. No significant difference was observed in facial numbness degree between two groups after procedure. Compared with PBC group, ophthalmic complication prevalence was higher in RFT group (9.6%) (p = 0.001). However, masseter weakness incidence was lower (10.7%) than that in PBC group (24.0%) with p < 0.001. CONCLUSIONS: Patients with TN seemed to attain similar long-term benefit from PBC and RFT, especially in elderly. However, in order to reduce postoperative complications, PBC provided a safer and alternative for treating TN involving ophthalmic division, whereas RFT could be employed as a preferred regimen for maxillary and mandibular TN.

Neferine suppresses autophagy-induced inflammation, oxidative stress and adipocyte differentiation in Graves' orbitopathy.

Previous studies in Graves' orbitopathy (GO) patient-derived fibroblasts showed that inhibition of autophagy suppresses adipogenic differentiation. Autophagy activation is associated with inflammation, production of reactive oxygen species and fibrosis. Neferine is an alkaloid extracted from Nelumbo nucifera, which induces Nrf2 expression and inhibits autophagy. Here, we have elucidated the role of neferine on interleukin (IL)-13-induced autophagy using patient-derived orbital fibroblasts as an in vitro model of GO. GO patient-derived orbital fibroblasts were isolated and cultured to generate an in vitro model of GO. Autophagy was determined by Western blot detection of the markers such as Beclin-1, Atg-5 and LC3 and by immunofluorescence detection of autophagosome formation. Analysis of differentiation towards an adipogenic lineage was performed by Oil red O staining. The expression of inflammatory factors was detected by ELISA and semiquantitative RT-PCR. Neferine inhibited autophagy in GO orbital fibroblasts, as indicated by the suppression of IL-13-induced autophagosome formation, overexpression of autophagy markers, increased LC3-II/LC3-I levels and finally down-regulation of p62. Neferine suppressed IL-13-induced inflammation, ROS generation, fibrosis and adipogenic differentiation in GO patient-derived orbital fibroblasts. The anti-inflammatory, antioxidant and antiadipogenic effects of neferine were accompanied by the up-regulation of Nrf2. These results indicated that orbital tissue remodelling and inflammation in GO may be mediated by autophagy, and neferine suppressed autophagy-related inflammation and adipogenesis through a mechanism involving Nrf2.

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.

Predicting mutation-induced changes in protein thermodynamic stability (ΔΔG) is of great interest in protein engineering, variant interpretation, and protein biophysics. We introduce ThermoNet, a deep, 3D-convolutional neural network (3D-CNN) designed for structure-based prediction of ΔΔGs upon point mutation. To leverage the image-processing power inherent in CNNs, we treat protein structures as if they were multi-channel 3D images. In particular, the inputs to ThermoNet are uniformly constructed as multi-channel voxel grids based on biophysical properties derived from raw atom coordinates. We train and evaluate ThermoNet with a curated data set that accounts for protein homology and is balanced with direct and reverse mutations; this provides a framework for addressing biases that have likely influenced many previous ΔΔG prediction methods. ThermoNet demonstrates performance comparable to the best available methods on the widely used Ssym test set. In addition, ThermoNet accurately predicts the effects of both stabilizing and destabilizing mutations, while most other methods exhibit a strong bias towards predicting destabilization. We further show that homology between Ssym and widely used training sets like S2648 and VariBench has likely led to overestimated performance in previous studies. Finally, we demonstrate the practical utility of ThermoNet in predicting the ΔΔGs for two clinically relevant proteins, p53 and myoglobin, and for pathogenic and benign missense variants from ClinVar. Overall, our results suggest that 3D-CNNs can model the complex, non-linear interactions perturbed by mutations, directly from biophysical properties of atoms.

POSTAR2: deciphering the post-transcriptional regulatory logics.

Post-transcriptional regulation of RNAs is critical to the diverse range of cellular processes. The volume of functional genomic data focusing on post-transcriptional regulation logics continues to grow in recent years. In the current database version, POSTAR2 (http://lulab.life.tsinghua.edu.cn/postar), we included the following new features and data: updated ∼500 CLIP-seq datasets (∼1200 CLIP-seq datasets in total) from six species, including human, mouse, fly, worm, Arabidopsis and yeast; added a new module 'Translatome', which is derived from Ribo-seq datasets and contains ∼36 million open reading frames (ORFs) in the genomes from the six species; updated and unified post-transcriptional regulation and variation data. Finally, we improved web interfaces for searching and visualizing protein-RNA interactions with multi-layer information. Meanwhile, we also merged our CLIPdb database into POSTAR2. POSTAR2 will help researchers investigate the post-transcriptional regulatory logics coordinated by RNA-binding proteins and translational landscape of cellular RNAs.

Comparison of Retrograde Intrarenal Surgery and Micro-Percutaneous Nephrolithotomy for Kidney Stones: A Meta-Analysis.

BACKGROUND: Advances in micro-percutaneous nephrolithotomy (PCNL) for kidney stones have made it an alternative approach to the retrograde intrarenal surgery (RIRS) approach. Nevertheless, the superiority of micro-PCNL over RIRS is still under debate. The results are controversial. OBJECTIVES: The purpose of this study was to systematically evaluate the clinical results in patients presenting with kidney stones treated with micro-PCNL or RIRS. METHODS: A literature search was done for electronic databases to identify researches that compared micro-PCNL and RIRS till December 2019. The clinical outcome included complications, stone-free rates (SFRs), hemoglobin reduction, length of hospital stay, and operative time. RESULTS: Five articles were included in our study. The pooled results revealed no statistical difference in the rate of complications (OR = 0.99, 95% CI = 0.57-1.74, p = 0.99), length of hospital stay (MD = -0.29, 95% CI = -0.82 to 0.24, p = 0.28), and operative time (MD = -6.63, 95% CI = -27.34 to 14.08, p = 0.53) between the 2 groups. However, significant difference was present in hemoglobin reduction (MD = -0.43, 95% CI = -0.55 to 0.30, p < 0.001) and the SFRs (OR = 0.59, 95% CI = 0.36-0.98, p = 0.04) when comparing RIRS with micro-PCNL. CONCLUSIONS: Compared with micro-PCNL to treat kidney stones, RIRS is associated with better stone clearance and bearing higher hemoglobin loss. As the advantages of both technologies have been shown in some fields, the continuation of well-designed clinical trials may be necessary.