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Female-specific subpopulation of myelinated Ah-type baroreceptor neurons (BRNs) in nodose ganglia is the neuroanatomical base of sexual-dimorphic autonomic control of blood pressure regulation, and KCa1.1 is a key player in modulating the neuroexcitation in nodose ganglia. In this study we investigated the exact mechanisms underlying KCa1.1-mediated neuroexcitation of myelinated Ah-type BRNs in the presence or absence of estrogen. BRNs were isolated from adult ovary intact (OVI) or ovariectomized (OVX) female rats, and identified electrophysiologically and fluorescently. Action potential (AP) and potassium currents were recorded using whole-cell recording. Consistently, myelinated Ah-type BRNs displayed a characteristic discharge pattern and significantly reduced excitability after OVX with narrowed AP duration and faster repolarization largely due to an upregulated iberiotoxin (IbTX)-sensitive component; the changes in AP waveform and repetitive discharge of Ah-types from OVX female rats were reversed by G1 (a selective agonist for estrogen membrane receptor GPR30, 100 nM) and/or IbTX (100 nM). In addition, the effect of G1 on repetitive discharge could be completely blocked by G15 (a selective antagonist for estrogen membrane receptor GPR30, 3 μM). These data suggest that estrogen deficiency by removing ovaries upregulates KCa1.1 channel protein in Ah-type BRNs, and subsequently increases AP repolarization and blunts neuroexcitation through estrogen membrane receptor signaling. Intriguingly, this upregulated KCa1.1 predicted electrophysiologically was confirmed by increased mean fluorescent intensity that was abolished by estrogen treatment. These electrophysiological findings combined with immunostaining and pharmacological manipulations reveal the crucial role of KCa1.1 in modulation of neuroexcitation especially in female-specific subpopulation of myelinated Ah-type BRNs and extend our current understanding of sexual dimorphism of neurocontrol of BP regulation., (© 2021. The Author(s), under exclusive licence to CPS and SIMM.)

Purpose: To describe the spectral-domain optical coherence tomography (SD-OCT) features of typical cystoid degeneration. Methods: This was a retrospective study of 11 eyes with typical cystoid degeneration (TCD). All patients had a complete ocular examination, ultra-widefield (UWF) pseudocolor fundus photography and SD-OCT with a 55° wide-field lens. We analyzed the cross-sectional structural information of SD-OCT imaging with TCD. Results: On SD-OCT, the TCD regions exhibited rolling hills patterns with irregularly elevated retinal surface, and multiple intraretinal hyporeflective cavities separated by irregular septums were seen in the neurosensory retina. Destructive changes were seen in the ellipsoid zone and the pigment epithelium. Consolidated vitreous with moderate to high reflectivity was seen over the lesion and there might be vitreoretinal adhesions and tractions. Results: SD-OCT shows exquisite structural features of the anatomy in vivo detail of the TCD. This imaging technique may deepen our structural understanding of TCD and may influence decision-making in clinical practice.

In single-cell RNA-seq (scRNA-seq) data analysis, a fundamental problem is to determine the number of cell clusters based on the gene expression profiles. However, the performance of current methods is still far from satisfactory, presumably due to their limitations in capturing the expression variability among cell clusters. Batch effects represent the undesired variability between data measured in different batches. When data are obtained from different labs or protocols batch effects occur. Motivated by the practice of batch effect removal, we considered cell clusters as batches. We hypothesized that the number of cell clusters (i.e. batches) could be correctly determined if the variances among clusters (i.e. batch effects) were removed. We developed a new method, namely, removal of batch effect and testing (REBET), for determining the number of cell clusters. In this method, cells are first partitioned into k clusters. Second, the batch effects among these k clusters are then removed. Third, the quality of batch effect removal is evaluated with the average range of normalized mutual information (ARNMI), which measures how uniformly the cells with batch-effects-removal are mixed. By testing a range of k values, the k value that corresponds to the lowest ARNMI is determined to be the optimal number of clusters. We compared REBET with state-of-the-art methods on 32 simulated datasets and 14 published scRNA-seq datasets. The results show that REBET can accurately and robustly estimate the number of cell clusters and outperform existing methods. Contact: H.D.L. (hongdong@csu.edu.cn) or Q.S.X. (qsxu@csu.edu.cn)., (© The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Objective: Cardiovascular dysfunction has been reported as an important mechanism of weaning failure, and recent data suggest that elevated brain natriuretic peptide (BNP) levels is associated with an increased risk of weaning failure. Therefore, we performed this meta-analysis to evaluate the correlation between elevated BNP levels and weaning failure in critically ill patients subject to mechanical ventilation., Methods: A systematic search in Cochrane Library, Embase, PubMed and Web of Science was performed up to September 25, 2019. Standard mean differences (SMD) and corresponding 95% confidence intervals (CIs) of the BNP levels were calculated for each study., Results: Nine studies with a total number of 589 were included in the final meta-analysis. The results showed that elevated BNP levels were significantly associated with the risk of weaning failure (SMD: 0.76, 95% CI: 0.47 to 1.05, P < .00001). The finding was consistent with the BNP measured before (SMD: 0.68, 95% CI: 0.26 to 1.11, P = .002) or at the end of spontaneous breathing trial (SBT) (SMD: 0.85, 95% CI: 0.52 to 1.18, P < .00001)., Conclusions: This meta-analysis showed that increased plasma BNP concentration was associated with weaning failure in ICU patients., (© 2021 John Wiley & Sons Ltd.)

Neuromyelitis optica spectrum disorder (NMOSD) is a severe central nervous system (CNS) autoimmune disease that primarily damages the optic nerves and spinal cord. Group 2 innate lymphoid cells (ILC2) are potent producers of type 2 cytokines that orchestrate immune and inflammatory responses. However, the role of ILC2 in CNS autoimmune diseases remains unknown. In patients with NMOSD, we identified a significant reduction of ILC2 in peripheral blood, which was correlated with disease severity. Using a mouse model of NMOSD induced by intracerebral injection of NMOSD-IgG with complement, we found CNS infiltration of ILC2 mainly expressing interleukin (IL)-5 and IL-13. The depletion of ILC2 led to increased CNS lesion volume, reduced CNS glucose metabolism, and augmented astrocyte injury and demyelination. The exacerbated NMOSD pathology was accompanied by increased accumulation of Iba1 + cells and complement activity in CNS lesions. In addition, the expansion of ILC2 using IL-33 attenuated NMO pathology. Collectively, these findings suggest a beneficial role of ILC2 in NMOSD, which deserves further investigation for future design of immune therapies to treat patients with NMOSD., (© 2021 Federation of American Societies for Experimental Biology.)

T-cell reduction is an important characteristic of coronavirus disease 2019 (COVID-19), and its immunopathology is a subject of debate. It may be due to the direct effect of the virus on T-cell exhaustion or indirectly due to T cells redistributing to the lungs. HIV/AIDS naturally served as a T-cell exhaustion disease model for recognizing how the immune system works in the course of COVID-19. In this study, we collected the clinical charts, T-lymphocyte analysis, and chest CT of HIV patients with laboratory-confirmed COVID-19 infection who were admitted to Jin Yin-tan Hospital (Wuhan, China). The median age of the 21 patients was 47 years [interquartile range (IQR) = 40-50 years] and the median CD4 T-cell count was 183 cells/μl (IQR = 96-289 cells/μl). Eleven HIV patients were in the non-AIDS stage and 10 were in the AIDS stage. Nine patients received antiretroviral treatment (ART) and 12 patients did not receive any treatment. Compared to the reported mortality rate (nearly 4%-10%) and severity rate (up to 20%-40%) among COVID-19 patients in hospital, a benign duration with 0% severity and mortality rates was shown by 21 HIV/AIDS patients. The severity rates of COVID-19 were comparable between non-AIDS (median CD4 = 287 cells/μl) and AIDS (median CD4 = 97 cells/μl) patients, despite some of the AIDS patients having baseline lung injury stimulated by HIV: 7 patients (33%) were mild (five in the non-AIDS group and two in the AIDS group) and 14 patients (67%) were moderate (six in the non-AIDS group and eight in the AIDS group). More importantly, we found that a reduction in T-cell number positively correlates with the serum levels of interleukin 6 (IL-6) and C-reactive protein (CRP), which is contrary to the reported findings on the immune response of COVID-19 patients (lower CD4 T-cell counts with higher levels of IL-6 and CRP). In HIV/AIDS, a compromised immune system with lower CD4 T-cell counts might waive the clinical symptoms and inflammatory responses, which suggests lymphocyte redistribution as an immunopathology leading to lymphopenia in COVID-19., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Lin, Lin, Wang, Wen, Xiang, Fan, Li, Wu, Lin, Lin, Sun, Chen, Chen, Lian, Xie, Lin, Xie, Li, Peng, Wang, Lin, Chen, Huang and Fu.)

Introduction and Aims: Elevated plasma levels of C-reactive protein (CRP) are closely associated with progressive renal injury in patients with chronic kidney disease (CKD). Here, we tested a hypothesis that CRP may promote renal fibrosis and inflammation via a TGF-β/Smad3-dependent mechanism. Methods: Role and mechanisms of TGF-β/Smad3 in CRP-induced renal fibrosis and inflammation were examined in a mouse model of unilateral ureteral obstruction (UUO) induced in CRP Tg/Smad3 KO mice and in a rat tubular epithelial cell line in which Smad3 gene is stably knocked down (S3KD-NRK52E). Results: We found that mice overexpressing the human CRP gene were largely promoted renal inflammation and fibrosis as evidenced by increasing IL-1β, TNF-α, MCP-1 expression, F4/80 + macrophages infiltration, and marked accumulation of α-smooth muscle actin (α-SMA), collagen I and fibronectin in the UUO kidney, which were blunted when Smad3 gene was deleted in CRPtg-Smad3KO. Mechanistically, we found that the protection of renal inflammation and fibrosis in the UUO kidney of CRPtg-Smad3KO mice was associated with the inactivation of CD32-NF-κB and TGF-β/Smad3 signaling. Conclusion: In conclusion, Smad3 deficiency protects against CRP-mediated renal inflammation and fibrosis in the UUO kidney by inactivating CD32-NF-κB and TGF-β/Smad3 signaling., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Fear learning and memory are crucial for animal survival. Abnormal fear memory is a hallmark of many neuropsychiatric disorders. Appropriate neuronal activation and excitability in the basolateral amygdala (BLA) are necessary for the formation of fear memory. The gene cylindromatosis ( Cyld ), which encodes a lysine-63 deubiquitinase, is expressed in several brain regions including the amygdala. The functions of the cylindromatosis protein (CYLD) in the regulation of the neuronal activity, neural circuits and fear memory, remain largely unknown, however. Here, we report that Cyld knockout impairs amygdala-dependent tone-cued fear memory. The number of c-Fos + neurons responding to the tone-cued fear test was reduced in the BLA of Cyld -/- mice, suggesting that the absence of CYLD causes aberrant neuronal activation. We found that this aberrant neuronal activation in the BLA of Cyld -/- mice may relate to the decreased excitability of principal neurons. Another possibility of aberrant neuronal activation could be the impaired excitatory synaptic transmission in the BLA of Cyld -/- mice. Specifically, both the frequency of spontaneous excitatory postsynaptic currents and the amplitude of miniature excitatory postsynaptic currents in BLA principal neurons were decreased. In addition, Cyld mutation caused an increase in both the frequency of miniature inhibitory postsynaptic currents in principal neurons and the number of parvalbumin + interneurons, consistent with excessive local circuit inhibition in the BLA of Cyld -/- mice. Taken together, these results suggest that CYLD deficiency disrupts the neuronal activity and synaptic transmission in the BLA of mice which may contribute to the impaired fear memory observed in Cyld -/- mice., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Li, Li, Yang and Long.)

Recent studies have indicated the use of recombinant human bone morphogenetic protein-2 (rhBMP-2) to be a viable adjunctive to alveolar cleft reconstruction owing to its osteoinductive capacity. This study aimed to evaluate the efficacy of rhBMP-2 in the treatment of alveolar cleft with autologous bone grafts by precise volumetric analysis. Twenty-six patients (aged 8-14) with unilateral alveolar clefts were enrolled in this comparative study. Patients were divided into two groups: the iliac crest bone graft (ICBG) was placed at the side of the cleft in the control group (ICBG group), and rhBMP-2 was mixed with the ICBG in the rhBMP-2 group (BMP group). Helical computed tomographic images were obtained preoperatively and 12 months postoperatively. The datasets were reconstructed as three-dimensional (3D) images using Mimics software and processed using Geomagic Wrap. The newly formed bone of the alveolar cleft was segmented by identifying the differences between preoperative and postoperative 3D images. In the ICBG group, the volume of newly formed bone ranged from 0.25 to 0.88 cm 3 , and the mean (SD) bone formation percentage was 42.01% (15.57%). In the BMP group, the volume of newly formed bone ranged from 0.34 to 1.09 cm 3 , and the bone formation mean (SD) percentage was 55.79% (11.84%). There was a statistically significant difference between the two groups in terms of the postoperative percentage of bone formation (p = 0.022). Thus, rhBMP-2 combined with an autologous bone graft is a promising technique to improve the results of secondary alveolar bone grafting., (Copyright © 2020 The British Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.)

In recent years, the application of single cell RNA-seq (scRNA-seq) has become more and more popular in fields such as biology and medical research. Analyzing scRNA-seq data can discover complex cell populations and infer single-cell trajectories in cell development. Clustering is one of the most important methods to analyze scRNA-seq data. In this paper, we focus on improving scRNA-seq clustering through gene selection, which also reduces the dimensionality of scRNA-seq data. Studies have shown that gene selection for scRNA-seq data can improve clustering accuracy. Therefore, it is important to select genes with cell type specificity. Gene selection not only helps to reduce the dimensionality of scRNA-seq data, but also can improve cell type identification in combination with clustering methods. Here, we proposed RFCell, a supervised gene selection method, which is based on permutation and random forest classification. We first use RFCell and three existing gene selection methods to select gene sets on 10 scRNA-seq data sets. Then, three classical clustering algorithms are used to cluster the cells obtained by these gene selection methods. We found that the gene selection performance of RFCell was better than other gene selection methods., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Zhao, Fang, Lin, Deng, Xu and Li.)

Background: Inflammatory bowel disease (IBD) is an autoimmune disease. The pathogenesis of IBD is complicated and intestinal mucosal barrier damage is considered as the trigger factor for the initiation and recurrence of IBD. Total Glucosides of Paeony (TGP) has shown good inhibitory effects on immune-inflammation in clinic studies. However, its effect and mechanism on IBD are largely unknown., Purpose: The purpose of this study is to evaluate the effect and mechanism of TGP on IBD., Study Design: DSS-induced colitis mouse model was used. TGP was given by gavage. Caco-2 cells were stimulated by outer membrane vesicles (OMV) to establish an in vitro model., Methods: C57BL/6 mice were divided into normal control group, model group, mesalazine group, paeoniflorin (PA) group, high-dose group of TGP, and low-dose group of TGP. The model was induced with 2.5% DSS for 7 days, and TGP was intragastrically administered for 10 days. The therapeutic effect of TGP was evaluated by symptoms, histochemical analysis, RT-qPCR and ELISA. The mechanism was explored by intestinal permeability, Western blot and immunofluorescence in vivo and in vitro., Results: Our results showed that TGP could significantly improve the symptoms and pathological changes, with reduced levels of TNF-α, IL-17A, IL-23 and IFN-γ in the colon tissues and serum under a dose-dependent manner. TGP also reduced the intestinal permeability and restored the protein expression of tight junction and adherens junction proteins of intestinal epithelial cells in vivo and in vitro. Furthermore, TGP could inhibit the expression of p-Lyn and Snail and prevent Snail nuclear localization, thereby maintaining tight and adherens junctions., Conclusion: TGP effectively improves the symptoms of DSS-induced colitis in mice, protects the intestinal epithelial barrier by inhibiting the Lyn/Snail signaling pathway, and maybe a promise therapeutic agent for IBD treatment., (Copyright © 2021. Published by Elsevier GmbH.)

Proline-serine-threonine-phosphatase-interacting protein 2 (PSTPIP2) belongs to the Fes/CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domain family. It exhibits lipid-binding, membrane deformation, and F-actin binding activity, suggesting broader roles at the membrane-cytoskeleton interface. PSTPIP2 is known to participate in macrophage activation, neutrophil migration, cytokine production, and osteoclast differentiation. In recent years, it has been observed to play important roles in innate immune diseases and autoinflammatory diseases (AIDs). Current research indicates that the protein tyrosine phosphatase PTP-PEST, Src homology domain-containing inositol 5'-phosphatase 1 (SHIP1), and C-terminal Src kinase (CSK) can bind to PSTPIP2 and inhibit the development of AIDs. However, the mechanisms underlying the function of PSTPIP2 have not been fully elucidated. This article reviews the research progress and mechanisms of PSTPIP2 in AIDs. PSTPIP2 also provides a new therapeutic target for the treatment of AIDs., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Xu, Li, Du, Li, Meng, Huang and Li.)

Aim: To observe whether silicone oil (SO) tamponade could decrease macular perfusion after retinal detachment repair., Methods: A prospective observational case-control study. Patients diagnosed with primary macular off rhegmatogenous retinal detachment undergoing successful retinal repair surgery with vitrectomy were strictly selected. Optical coherence tomography angiography findings were compared between SO and air tamponade groups. Two postoperative visiting points were set (1 and 3mo)., Results: Totally 29 patients (29 eyes) were enrolled. Twenty cases had SO tamponade while 9 cases were with air tamponade. At the first visiting point, superficial parafoveal vessel density (PFSVD) significantly decreased in the SO group ( P =0.0403), especially in the superior quadrant or superior-hemi area ( P =0.0089, 0.0426, respectively). Parafoveal deep vessel density (PFDVD) had no difference between the two groups. At the second visiting point, all quadrants of PFSVD reduced significantly in the SO group ( P =0.0256, 0.0001, 0.0031, <0.0001 in temporal, superior, nasal, and inferior area, respectively), but PFDVD remained no different. In the air group, all areas of PFSVD showed significantly improving from the first visit to the second one ( P =0.0324, 0.0001, 0.0371, 0.0026, in temporal, superior, nasal, and inferior area, respectively); however, almost all quadrants of PFDVD showed no changes during this period. In the SO group, both PFSVD and PFDVD showed no obvious changes between the two visiting points. Besides, parafoveal full retinal thickness in the SO group reduced significantly at both visiting points over the air tamponade, while the foveal avascular zone area showed no difference in the two groups., Conclusion: After retinal detachment surgery with vitrectomy and SO tamponade, superficial macular perfusion and full retinal thickness could decrease obviously when compared to air tamponade. This reduction process could persist throughout the tamponade period., (International Journal of Ophthalmology Press.)

Alcoholic liver disease (ALD) is the most common chronic liver disease worldwide. Currently, there is no definitive treatment for alcohol-induced liver injury (ALI). Inflammatory response and oxidative stress play a crucial role in ALI. Cyclooxygenase 2 (COX-2) can be induced by inflammation and it has been reported that the enhanced expression of COX-2 in alcoholic liver injury. Rutaecarpine (RUT) was extracted from evodia rutaecarpa. RUT has a wide range of pharmacological activities. In order to increase its anti-inflammatory activity, our group introduced sulfonyl group to synthesized the 3-[2-(trifluoromethoxy)benzenesulfonamide]-rutaecarpine (3-B-RUT). In this study, we explored the protective effect of 3-B-RUT on alcoholic liver injury in vivo and in vitro and preliminarily explore its mechanism. Mice ALI model was established according to the chronic-plus-binge ethanol model. Results showed that 3-B-RUT (20 μg/kg) attenuated alcohol-induced liver injury and suppressed liver inflammation and oxidative stress, and the effect was comparable to RUT (20 mg/kg). In vitro results are consistent with in vivo results. Mechanistically, the 3-B-RUT might suppress inflammatory response and oxidative stress by regulating activation of NF-κB/COX-2 pathway. In summary, 3-B-RUT, a derivative of RUT, may be a promising clinical candidate for ALI treatment., (Copyright © 2021. Published by Elsevier B.V.)

Intron retention (IR) has been implicated in the pathogenesis of complex diseases such as cancers; its association with Alzheimer's disease (AD) remains unexplored. We performed genome-wide analysis of IR through integrating genetic, transcriptomic, and proteomic data of AD subjects and mouse models from the Accelerating Medicines Partnership-Alzheimer's Disease project. We identified 4535 and 4086 IR events in 2173 human and 1736 mouse genes, respectively. Quantitation of IR enabled the identification of differentially expressed genes that conventional exon-level approaches did not reveal. There were significant correlations of intron expression within innate immune genes, like HMBOX1, with AD in humans. Peptides with a high probability of translation from intron-retained mRNAs were identified using mass spectrometry. Further, we established AD-specific intron expression Quantitative Trait Loci, and identified splicing-related genes that may regulate IR. Our analysis provides a novel resource for the search for new AD biomarkers and pathological mechanisms., (© 2021 The Authors. Alzheimer's & Dementia published by Wiley Periodicals LLC on behalf of Alzheimer's Association.)

Background and Aims: Alcoholic fatty liver (AFL) is an early form of alcoholic liver disease (ALD) that usually manifests as lipid synthesis abnormalities in hepatocytes. β-arrestin2 (Arrb2) is involved in multiple biological processes. The present study aimed to explore the role of Arrb2 in the regulation of lipid metabolism in AFL and the underlying mechanism and identify potential targets for the treatment of AFL., Methods: The expression of Arrb2 was detected in liver tissues obtained from AFL patients and Gao-binge AFL model mice. In addition, we specifically knocked down Arrb2 in AFL mouse liver in vivo and used Arrb2-siRNA or pEX3-Arrb2 to silence or overexpress Arrb2 in AML-12 cells in vitro to explore the functional role and underlying regulatory mechanism of Arrb2 in AFL. Finally, we investigated whether Arrb2 could cause changes in hepatic lipid metabolites, thereby leading to dysregulation of lipid metabolism based on liquid chromatography-mass spectrometry (LC-MS) analysis., Results: Arrb2 was up-regulated in the livers of AFL patients and AFL mice. The in vivo and in vitro results confirmed that Arrb2 could induce lipid accumulation and metabolism disorders. Mechanistically, Arrb2 induced hepatic metabolism disorder via AMP-activated protein kinase (AMPK) pathway. The results of LC-MS analysis revealed that hepatic lipid metabolites with the most significant differences were primary bile acids., Conclusions: Arrb2 induces hepatic lipid metabolism disorders via AMPK pathway in AFL. On one hand, Arrb2 increases fatty acid synthesis. On the other hand, Arrb2 could increase the cholesterol synthesis, thereby leading to the up-regulation of primary bile acid levels., (© 2021 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

Advances in sequencing technologies facilitate personalized disease-risk profiling and clinical diagnosis. In recent years, some great progress has been made in noninvasive diagnoses based on cell-free DNAs (cfDNAs). It exploits the fact that dead cells release DNA fragments into the circulation, and some DNA fragments carry information that indicates their tissues-of-origin (TOOs). Based on the signals used for identifying the TOOs of cfDNAs, the existing methods can be classified into three categories: cfDNA mutation-based methods, methylation pattern-based methods and cfDNA fragmentation pattern-based methods. In cfDNA mutation-based methods, the SNP information or the detected mutations in driven genes of certain diseases are employed to identify the TOOs of cfDNAs. Methylation pattern-based methods are developed to identify the TOOs of cfDNAs based on the tissue-specific methylation patterns. In cfDNA fragmentation pattern-based methods, cfDNA fragmentation patterns, such as nucleosome positioning or preferred end coordinates of cfDNAs, are used to predict the TOOs of cfDNAs. In this paper, the strategies and challenges in each category are reviewed. Furthermore, the representative applications based on the TOOs of cfDNAs, including noninvasive prenatal testing, noninvasive cancer screening, transplantation rejection monitoring and parasitic infection detection, are also reviewed. Moreover, the challenges and future work in identifying the TOOs of cfDNAs are discussed. Our research provides a comprehensive picture of the development and challenges in identifying the TOOs of cfDNAs, which may benefit bioinformatics researchers to develop new methods to improve the identification of the TOOs of cfDNAs., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Introduction: Passive immunotherapies targeting Aβ continue to be evaluated as Alzheimer's disease (AD) therapeutics, but there remains debate over the mechanisms by which these immunotherapies work. Besides the amount of preexisting Aβ deposition and the type of deposit (compact or diffuse), there is little data concerning what factors, independent of those intrinsic to the antibody, might influence efficacy. Here we (i) explored how constitutive priming of the underlying innate activation states by Il10 and Il6 might influence passive Aβ immunotherapy and (ii) evaluated transcriptomic data generated in the AMP-AD initiative to inform how these two cytokines and their receptors' mRNA levels are altered in human AD and an APP mouse model., Methods: rAAV2/1 encoding EGFP, Il6 or Il10 were delivered by somatic brain transgenesis to neonatal (P0) TgCRND8 APP mice. Then, at 2 months of age, the mice were treated bi-weekly with a high-affinity anti-Aβ1-16 mAb5 monoclonal antibody or control mouse IgG until 6 months of age. rAAV mediated transgene expression, amyloid accumulation, Aβ levels and gliosis were assessed. Extensive transcriptomic data was used to evaluate the mRNA expression levels of IL10 and IL6 and their receptors in the postmortem human AD temporal cortex and in the brains of TgCRND8 mice, the later at multiple ages., Results: Priming TgCRND8 mice with Il10 increases Aβ loads and blocks efficacy of subsequent mAb5 passive immunotherapy, whereas priming with Il6 priming reduces Aβ loads by itself and subsequent Aβ immunotherapy shows only a slightly additive effect. Transcriptomic data shows that (i) there are significant increases in the mRNA levels of Il6 and Il10 receptors in the TgCRND8 mouse model and temporal cortex of humans with AD and (ii) there is a great deal of variance in individual mouse brain and the human temporal cortex of these interleukins and their receptors., Conclusions: The underlying immune activation state can markedly affect the efficacy of passive Aβ immunotherapy. These results have important implications for ongoing human AD immunotherapy trials, as they indicate that underlying immune activation states within the brain, which may be highly variable, may influence the ability for passive immunotherapy to alter Aβ deposition.

Background: Subclavian vein stenosis or occlusion may be caused by a transvenous pacemaker, which makes the reimplantation of a new pacemaker lead difficult. Transvenous pacemaker lead implantation-related subclavian vein occlusion may present difficulty with regard to cardiac resynchronization therapy (CRT) upgrade., Case Summary: We report the case of a 46-year-old man who was admitted with total subclavian vein occlusion caused by a permanent pacemaker that had been implanted 2 years previously. We successfully treated this patient with an upgrade to a CRT pacemaker by utilizing transferable interventional coronary and radiological techniques. The patient recovered uneventfully during the follow-up period., Conclusion: CRT upgrade is still a viable technique for the treatment of subclavian vein obstruction caused by previous pacemaker implantation., Competing Interests: Conflict-of-interest statement: The authors declare that they have no competing interests., (©The Author(s) 2021. Published by Baishideng Publishing Group Inc. All rights reserved.)

Diabetic nephropathy (DN) leads to high morbidity and disability. Inflammation plays a critical role in the pathogenesis of DN, which involves renal cells and immune cells, the microenvironment, as well as extrinsic factors, such as hyperglycemia, chemokines, cytokines, and growth factors. Epigenetic modifications usually regulate gene expression via DNA methylation, histone modification, and non-coding RNAs without altering the DNA sequence. During the past years, numerous studies have been published to reveal the mechanisms of epigenetic modifications that regulate inflammation in DN. This review aimed to summarize the latest evidence on the interplay of epigenetics and inflammation in DN, and highlight the potential targets for treatment and diagnosis of DN., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Shao, Zhang, Li, Meng and Chen.)

Breast cancer (BC) affects the breast tissue and is the second most common cause of mortalities among women. Ferroptosis is an iron-dependent cell death mode that is characterized by intracellular accumulation of reactive oxygen species (ROS). We constructed a prognostic multigene signature based on ferroptosis-associated differentially expressed genes (DEGs). Moreover, we comprehensively analyzed the role of ferroptosis-associated miRNAs, lncRNAs, and immune responses. A total of 259 ferroptosis-related genes were extracted. KEGG function analysis of these genes revealed that they were mainly enriched in the HIF-1 signaling pathway, NOD-like receptor signaling pathway, central carbon metabolism in cancer, and PPAR signaling pathway. Fifteen differentially expressed genes (ALOX15, ALOX15B, ANO6, BRD4, CISD1, DRD5, FLT3, G6PD, IFNG, NGB, NOS2, PROM2, SLC1A4, SLC38A1, and TP63) were selected as independent prognostic factors for BC patients. Moreover, T cell functions, including the CCR score, immune checkpoint, cytolytic activity, HLA, inflammation promotion, para-inflammation, T cell co-stimulation, T cell co-inhibition, and type II INF responses were significantly different between the low-risk and high-risk groups of the TCGA cohort. Immune checkpoints between the two groups revealed that the expressions of PDCD-1 (PD-1), CTLA4, LAG3, TNFSF4/14, TNFRSF4/8/9/14/18/25, and IDO1/2 among others were significantly different. A total of 1185 ferroptosis-related lncRNAs and 219 ferroptosis-related miRNAs were also included in this study. From the online database, we identified novel ferroptosis-related biomarkers for breast cancer prognosis. The findings of this study provide new insights into the development of new reliable and accurate cancer treatment options.

The endometrium is unique as an accessible anatomic location that can be repeatedly biopsied and where diagnostic biopsies do not extirpate neoplastic lesions. We exploited these features to retrospectively characterize serial genomic alterations along the precancer/cancer continuum in individual women. Cases were selected based on (1) endometrial cancer diagnosis/hysterectomy and (2) preceding serial endometrial biopsies including for some patients an early biopsy before a precancer histologic diagnosis. A comprehensive panel was designed for endometrial cancer genes. Formalin-fixed, paraffin-embedded specimens for each cancer, preceding biopsies, and matched germline samples were subjected to barcoded high-throughput sequencing to identify mutations and track their origin and allelic frequency progression. In total, 92 samples from 21 patients were analyzed, providing an opportunity for new insights into early endometrial cancer progression. Definitive invasive endometrial cancers exhibited expected mutational spectra, and canonical driver mutations were detectable in preceding biopsies. Notably, ≥1 cancer mutations were detected prior to the histopathologic diagnosis of an endometrial precancer in the majority of patients. In 18/21 cases, ≥1 mutations were confirmed by abnormal protein levels or subcellular localization by immunohistochemistry, confirming genomic data and providing unique views of histologic correlates. In 19 control endometria, mutation counts were lower, with a lack of canonical endometrial cancer hotspot mutations. Our study documents the existence of endometrial lesions that are histologically indistinct but are bona fide endometrial cancer precursors. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland., (© 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.)

Motivation: High resolution annotation of gene functions is a central goal in functional genomics. A single gene may produce multiple isoforms with different functions through alternative splicing. Conventional approaches, however, consider a gene as a single entity without differentiating these functionally different isoforms. Towards understanding gene functions at higher resolution, recent efforts have focused on predicting the functions of isoforms. However, the performance of existing methods is far from satisfactory mainly because of the lack of isoform-level functional annotation., Results: We present IsoResolve, a novel approach for isoform function prediction, which leverages the information from gene function prediction models with domain adaptation (DA). IsoResolve treats gene-level and isoform-level features as source and target domains, respectively. It uses DA to project the two domains into a latent variable space in such a way that the latent variables from the two domains have similar distribution, which enables the gene domain information to be leveraged for isoform function prediction. We systematically evaluated the performance of IsoResolve in predicting functions. Compared with five state-of-the-art methods, IsoResolve achieved significantly better performance. IsoResolve was further validated by case studies of genes with isoform-level functional annotation., Availability and Implementation: IsoResolve is freely available at https://github.com/genemine/IsoResolve., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Single-cell RNA sequencing (scRNA-seq) technology provides quantitative gene expression profiles at single-cell resolution. As a result, researchers have established new ways to explore cell population heterogeneity and genetic variability of cells. One of the current research directions for scRNA-seq data is to identify different cell types accurately through unsupervised clustering methods. However, scRNA-seq data analysis is challenging because of their high noise level, high dimensionality and sparsity. Moreover, the impact of multiple latent factors on gene expression heterogeneity and on the ability to accurately identify cell types remains unclear. How to overcome these challenges to reveal the biological difference between cell types has become the key to analyze scRNA-seq data. For these reasons, the unsupervised learning for cell population discovery based on scRNA-seq data analysis has become an important research area. A cell similarity assessment method plays a significant role in cell clustering. Here, we present BioRank, a new cell similarity assessment method based on annotated gene sets and gene ranks. To evaluate the performances, we cluster cells by two classical clustering algorithms based on the similarity between cells obtained by BioRank. In addition, BioRank can be used by any clustering algorithm that requires a similarity matrix. Applying BioRank to 12 public scRNA-seq datasets, we show that it is better than or at least as well as several popular similarity assessment methods for single cell clustering.

Abstract: Precise volumetric evaluation of the alveolar cleft facilitates accurate preparation of bone substitutes and reduces donor site morbidity. This study investigates 2 advanced presurgical volumetric assessment methods that use computer-aided engineering (CAE) software. Preoperative computed tomography (CT) scans from 20 unilateral alveolar cleft patients undergoing secondary alveolar bone grafting (SABG) were analyzed by CAE software. Cleft defect volumes were calculated using the mirror-reversed technique and the subtraction method. The mirror-reversed technique determines defect volume by reversing the noncleft side to the cleft side. The subtraction method determines defect volume by subtracting a mask of the preoperative cleft from a mask generated after simulated cleft filling. The mean defect volumes and calculation times of the mirror-reversed technique (1.27 ± 0.35 cm3; 11.80 ± 1.79 seconds) and the subtractive method (1.23 ± 0.32 cm3; 9.43 ± 1.35 seconds) did not differ significantly. In Bland-Altman analysis the 2 methods were equivalent for alveolar cleft defect assessment. Both methods exhibited acceptable interobserver reliability, high precision, clinical convenience, time efficiency, and high reproducibility, and can serve as valuable tools for the planning and execution of SABG. The subtraction method has broader potential applicability and can simulate intraoperative bone grafting more effectively., Competing Interests: The authors report no conflicts of interest., (Copyright © 2020 by Mutaz B. Habal, MD.)

Hydrogels are known to be soft and wet smart materials that respond to external stimuli. Numerous hydrogel actuators have been developed that perform volume and shape changes, and reversible motions. Heterogeneity, periodicity, and integration of hydrogels with different properties are needed to realize biomimetic motions. In order to achieve specific actuations with predictable pathways, it is critical to fabricate hydrogel structures in a well-controlled manner. This review article summarizes recent progress in representative methods to fabricate hydrogel actuators by different methods, ranging from sequential synthesis, macroscopic supramolecular assembling, field-induced alignment, photolithography, ionoprinting, 3D printing, and gradient structuring. The advantages and limits of these methods are compared and analyzed. Finally, a brief perspective and conclusion are presented to point out some important issues for further studies.

Prostate cancer (PC) is the most common carcinoma among men worldwide which results in 26% of leading causes of cancer-related death. However, the ideal and effective molecular marker remains elusive. CircRNA, initially observed in plant-infected viruses and Sendai virus in 1979, is generated from pre-mRNA back-splicing and comes in to play by adequate expression. The differential expression in prostate tissues compared with the control reveals the promising capacity in modulating processes including carcinogenesis and metastasis. However, the biological mechanisms of regulatory network in PC needs to systemically concluded. In this review, we enlightened the comprehensive studies on the definite mechanisms of circRNAs affecting tumor progression and metastasis. What's more, we validated the potential clinical application of circRNAs serving as diagnostic and prognostic biomarker. The discussion and analysis in circRNAs will broaden our knowledge of the pathogenesis of PC and further optimize the current therapies against different condition., Competing Interests: Competing Interests: Hong Zhou, Xu-dong Zheng, Chang-ming Lin, Jie Mine, Shuang Hu, Liang-yun Li, Jia-si Chen, Yu-min Liu, Hao-dong Li, Xiao-ming Meng, Jun Li, Ya-ru Yang and Tao Xu declare that they have no conflict of interest., (© The author(s).)

Alternative splicing (AS) leads to transcriptome diversity in eukaryotic cells and is one of the key regulators driving cellular differentiation. Although AS is of crucial importance for normal hematopoiesis and hematopoietic malignancies, its role in early hematopoietic development is still largely unknown. Here, by using high-throughput transcriptomic analyses, we show that pervasive and dynamic AS takes place during hematopoietic development of human pluripotent stem cells (hPSCs). We identify a splicing factor switch that occurs during the differentiation of mesodermal cells to endothelial progenitor cells (EPCs). Perturbation of this switch selectively impairs the emergence of EPCs and hemogenic endothelial progenitor cells (HEPs). Mechanistically, an EPC-induced alternative spliced isoform of NUMB dictates EPC specification by controlling NOTCH signaling. Furthermore, we demonstrate that the splicing factor SRSF2 regulates splicing of the EPC-induced NUMB isoform, and the SRSF2-NUMB-NOTCH splicing axis regulates EPC generation. The identification of this splicing factor switch provides a new molecular mechanism to control cell fate and lineage specification., (© 2020 The Authors. Published under the terms of the CC BY NC ND 4.0 license.)

MicroRNA-3175 (miR-3175) expression is upregulated in prostate cancer, but its roles and the underlying mechanisms in prostate cancer cell growth and invasion need to be elucidated. This study aimed to uncover the roles of miR-3175 in regulating cell growth and migration, as well as the expression of its predicted target gene cardiac sodium channel β4-subunit gene (SCN4B). Real-time quantitative PCR (RT-qPCR) and/or western blotting techniques were used to measure miR-3175 and SCN4B expression levels in prostate cancer cells. Inhibitor or mimics transfections were used to overexpress or silence miR-3175 in prostate cancer cells. MTT and Edu assays were applied to assess cell viability. Scratch assay and transwell chambers were used to examine cell migration and invasion abilities. The interaction between miR-3175 and SCN4B was determined by means of luciferase gene reporter, RT-qPCR, and western blotting assays. The results showed that miR-3175 expression was increased and SCN4B expression was decreased in prostate cancer cell lines as compared with normal human prostatic epithelial cells. Compared with the control group, knockdown of miR-3175 resulted in strong inhibitions of cell growth, migration, invasion, and N-cadherin expression, together with an increase in E-cadherin expression. In addition, knockdown of miR-3175 dramatically increased the luciferase activity of the luciferase vector of SCN4B, and increased SCN4B expression. Together, this study illustrated that downregulation of miR-3175 repressed the proliferation and invasion of prostate cancer cells, which might be induced by SCN4B downregulation., (© 2020 The Authors. The Kaohsiung Journal of Medical Sciences published by John Wiley & Sons Australia on behalf of Kaohsiung Medical University.)

Alcohol consumption is one of the risk factors for kidney injury. The underlying mechanism of alcohol-induced kidney injury remains largely unknown. We previously found that the kidney in a mouse model of alcoholic kidney injury had severe inflammation. In this study, we found that the administration of alcohol was associated with the activation of NLRP3 inflammasomes and NF-κB signaling, and the production of pro-inflammatory cytokines. Whole-genome methylation sequencing (WGBS) showed that the DNA encoding fat mass and obesity-associated protein (FTO) was significantly methylated in the alcoholic kidney. This finding was confirmed with the bisulfite sequencing (BSP), which showed that alcohol increased DNA methylation of FTO in the kidney. Furthermore, inhibition of DNA methyltransferases (DNMTs) by 5-azacytidine (5-aza) reversed alcohol-induced kidney injury and decreased the mRNA and protein levels of FTO. Importantly, we found that FTO, the m 6 A demethylase, epigenetically modified peroxisome proliferator activated receptor-α (PPAR-α) in a YTH domain family 2 (YTHDF2)-dependent manner, which resulted in inflammation in alcoholic kidney injury models. In conclusion, our findings indicate that alcohol increases the methylation of PPAR-α m 6 A by FTO-mediated YTHDF2 epigenetic modification, which ultimately leads to the activation of NLRP3 inflammasomes and NF-κB-driven renal inflammation in the kidney. These findings may provide novel strategies for preventing and treating alcoholic kidney diseases., (Copyright © 2020. Published by Elsevier Ltd.)

Clustering is an efficient way to analyze single-cell RNA sequencing data. It is commonly used to identify cell types, which can help in understanding cell differentiation processes. However, different clustering results can be obtained from different single-cell clustering methods, sometimes including conflicting conclusions, and biologists will often fail to get the right clustering results and interpret the biological significance. The cluster ensemble strategy can be an effective solution for the problem. As the graph partitioning-based clustering methods are good at clustering single-cell, we developed Sc-GPE, a novel cluster ensemble method combining five single-cell graph partitioning-based clustering methods. The five methods are SNN-cliq, PhenoGraph, SC3, SSNN-Louvain, and MPGS-Louvain. In Sc-GPE, a consensus matrix is constructed based on the five clustering solutions by calculating the probability that the cell pairs are divided into the same cluster. It solved the problem in the hypergraph-based ensemble approach, including the different cluster labels that were assigned in the individual clustering method, and it was difficult to find the corresponding cluster labels across all methods. Then, to distinguish the different importance of each method in a clustering ensemble, a weighted consensus matrix was constructed by designing an importance score strategy. Finally, hierarchical clustering was performed on the weighted consensus matrix to cluster cells. To evaluate the performance, we compared Sc-GPE with the individual clustering methods and the state-of-the-art SAME-clustering on 12 single-cell RNA-seq datasets. The results show that Sc-GPE obtained the best average performance, and achieved the highest NMI and ARI value in five datasets., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2020 Zhu, Li, Li, Xie and Wang.)

Background: We investigate the safety of the application of the Rigidfix cross-pin system via different tibial tunnels in the tibial fixation during anterior cruciate ligament (ACL) reconstruction., Methods: Five adult fresh cadaver knees were fixed with the Rigidfix cross-pins in the tibial fixation site during ACL reconstruction. Two different tibial tunnel groups were established: in group A, the tunnel external aperture was placed at the 25° angle of coronal section; in group B, the tunnel external aperture was placed at the 45° angle of coronal section. The guide was placed at the plane 0.5 mm below articular facet through the tibial tunnel, with three rotation positions set at 0°, 30°, and 60° slopes. The incidences of iatrogenic injuries at tibial plateau cartilage (TPC), medial collateral ligament (MCL), and patellar tendon in three different slope angles were calculated in groups A and B and the results were analyzed by using chi square test., Results: The iatrogenic injuries at MCL, TPC, and patellar tendon could occur after the Rigidfix cross-pin system was placed 5 mm below tibial plateau cartilage for ACL reconstruction. The incidences of TPC injury (χ 2  = 5.662, P = 0.017) and MCL injury (P = 0.048, Fisher exact probability method) were significantly lower in group A than in group B. However, the incidence of patellar tendon injury showed no significant difference between these two groups (χ 2  = 0.120, P = 0.729)., Conclusions: When the Rigidfix cross-pin system is used for ACL reconstruction at the tibial fixation site, the external aperture of tibial tunnel should not be placed at the excessively posterosuperior site, to avoid MCL and TPC injuries.

Introduction: This study evaluates the role of thromboprophylaxis in venous thromboembolism (VTE) incidence in colorectal cancer (CRC) surgical patients., Evidence Acquisition: Literature search was conducted in electronic databases and studies (randomized controlled trials, or prospective/retrospective cohorts) were selected if they reported the incidence of VTE in CRC patients who underwent any type of open or laparoscopic surgery. Random-effects meta-analyses were performed to obtain pooled incidence estimates; or odds ratios (OR) of incidence between prophylaxis and no-prophylaxis groups; or between VTE and non-VTE patients to identify risk factors., Evidence Synthesis: Twenty-four studies (804,003 patients) were included. Prophylaxis was performed mainly with low molecular weight heparins. Odds of VTE were significantly lower in prophylactic than in non-prophylactic patients (OR 0.42 [95% CI: 0.28, 0.63]; P<0.00001). Incidence of radiological and symptomatic VTE in patients with prophylaxis was 9.7% [95% CI: 8.6, 10.8] and 1.3% [95% CI: 0.7, 2.0] respectively. Odds of bleeding were higher in patients with prophylaxis (OR: 3.37 [95% CI: 1.05, 10.8]; P=0.04). Incidence of bleeding in patients with and without prophylaxis was 4.3% [95% CI: 3.2, 5.4] and 1.2% [95% CI: 0.02, 2.4] respectively. Operative time, anesthesia duration, and hospital stay were longer in patients with VTE. Obesity, disseminated cancer, chemotherapy, steroid use, emergency case status, advanced stage cancer, hypoalbuminemia, postoperative infection/sepsis, and history of VTE are identified as important risk factors for VTE incidence., Conclusions: Thromboprophylaxis reduces the incidence of VTE in CRC surgical patients but may increase the chances of bleeding. Several risk factors can influence VTE incidence.

Alcoholic liver disease (ALD) was a global liver disease which divided into liver inflammation, fatty liver, alcoholic hepatitis or cirrhosis. Abnormal expression levels of some microRNAs (miRNA) family members often lead to ALD and other liver diseases. MicroRNA-708 (miR-708) was known to suppress the proliferation and metastasis of hepatocellular carcinoma (HCC), but its role in the progression of ALD was not clear. In this study, the expression level of miR-708 was down-regulated in ethanol-induced L0-2 cells. ZEB1 could decrease the PPAR-α expression while increase the SREBP-1 expression. Meanwhile, the expression levels of TNF-α and IL-6 were up-regulated by ZEB1. Of note, ZEB1 aggravated the apoptotic rate of L0-2 cells induced by ethanol via inhibiting p-AKT and p-mTOR of AKT/mTOR signaling pathway. What's more, it was demonstrated that miR-708 family members particularly target ZEB1 3'-UTR regions and can down-regulate the expression level of ZEB1 in L0-2 cells. Sum up, these results indicated that miR-708 might inhibit the liver inflammation and lipid accumulation by targeting ZEB1 via regulating AKT/mTOR signaling pathway., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Objective: Infiltration of the inflammatory cells, such as macrophages and myocardial necrosis, are involved in myocarditis. Insulin-like growth factor (IGF-1) exerts a variety of biological effects. However, the role of IGF-1 in myocarditis remains unclear., Patients and Methods: LDL-R knockout mice were randomly divided into the control group, myocarditis group, and IGF-1 siRNA group. Real Time-Polymerase Chain Reaction (PCR) and Western blot were used to measure IGF-1 expression in myocardial tissue. The myocardial tissue changes were analyzed by HE staining. The total cholesterol (TC) and low-density lipoprotein cholesterol (LDL) in each group were detected. Flow cytometry was used to analyze the number of macrophages. The secretion of TNF-α and INF-γ and macrophage migration inhibitory factor (MIF) were detected by enzyme-linked immunosorbent assay (ELISA)., Results: Compared with the control group, IGF-1 expression, TC, and LDL in myocarditis group was significantly increased, along with decreased heart rate (HR), left ventricular end-systolic diameter (LVEDs), left ventricular end-diastolic diameter (LVEDd), and left ventricular mass index (LVMI). In addition, inflammatory cell infiltration, fibrosis, and macrophages number in the peritoneum were increased. Moreover, the secretion of TNF-α, INF-γ, and MIF was also significantly increased (p<0.05). However, IGF-1 siRNA treatment inhibited IGF-1 expression and reversed the changes in the myocarditis group with statistically significant differences compared with the myocarditis group (p<0.05)., Conclusions: IGF-1 expression is increased in myocarditis. The downregulation of IGF-1 expression inhibits macrophages infiltration, reduces the expression of MIF and inflammatory factors, and improves myocarditis injury.

Objective: Transmembrane protein 88 (TMEM88), a new protein of increasing concern existed in cell membrane, inhibits the typical Wnt/β-catenin signaling pathway to play a regulatory role on cell proliferation by binding to Dishevelled-1. Until recently, the connection between TMEM88 and alcoholic liver disease is unknown. In this research, we explored the effect of TMEM88 on the secretion of inflammatory cytokines in ethanol (EtOH)-induced RAW264.7 cells, moreover, the function of YAP signaling pathway in EtOH-induced RAW264.7 cells were investigated., Methods: We administered TMEM88 adenovirus (ADV-TMEM88) by tail vein injection into C57BL/6J mice in vivo. In vitro, RAW264.7 murine macrophages were stimulated with EtOH and were transfected with pEGFP-C1-TMEM88 and TMEM88 siRNA, respectively, protein expression and mRNA expression of IL-6 and IL-1β were assessed by Western Blotting and RT-qPCR, respectively., Results: Our group found that the overexpression of TMEM88 led to an up-regulation of IL-6 and IL-1β secretion, hinting that it had the possibility of linking with the initiation, the development, and the end of inflammation. In addition to that, TMEM88 silencing reduced the secretion of IL-6 and IL-1β in RAW264.7 cells. Moreover, we demonstrated that the YAP signaling pathway under the action of EtOH was activated by TMEM88., Conclusions: All in all, these experimental outcomes indicated that TMEM88 had an indispensable impact on EtOH-induced secretion of inflammatory cytokines (IL-6 and IL-1β) in RAW264.7 cells through YAP signaling pathway.

The regulation of macrophages during inflammatory responses is a crucial process in alcoholic liver disease (ALD) and aberrant macrophage DNA methylation is associated with inflammation. Our preliminary screening results of macrophage methylation in the present study demonstrated the zinc finger SWI2/SNF2 and MuDR (SWIM)-domain containing 3 (ZSWIM3) were hypermethylated in the 5' untranslated region (5'-UTR) region. ZSWIM3, a novel zinc finger-chelate domain of SWIM, is predicted to function in DNA-binding and protein-binding interactions. Its expression was found to be consistently decreased in macrophages isolated from livers of ethyl alcohol (EtOH)-fed mice and in EtOH+lipopolysaccharide (LPS)-induced RAW264.7 cells. Over-expression of ZSWIM3 was found to attenuate chronic+binge ethanol feeding-induced liver injury and inhibit inflammatory responses in vivo. Enforced expression of ZSWIM3 in vitro was also found to have anti-inflammatory effects. Aberrant expression of ZSWIM3 in alcohol-induced liver injury (ALI) was found to be associated with hypermethylation. Analysis of CpG prediction indicated the presence of two methylated sites in the ZSWIM3 promoter region and methylation inhibitor and DNA methyltransferases (DNMTs)-siRNA transfection were found to restore down-regulated ZSWIM3. Chromatin immunoprecipitation (ChIP) assay and molecular docking affirmed the role of DNMT 3b (DNMT3b) as a principal regulator of ZSWIM3 expression. Mechanistically, ZSWIM3 might affect inflammation by binding with tumor necrosis factor receptor-associated factor 2 (TRAF2), which further mediates the activation of the nuclear transcription factor κB (NF-κB) pathway. The present study, therefore, provides detailed insights into the possible structure and function of ZSWIM3 and thus, contributes new substantial research in the elucidation of the pathogenesis of ALI., (© 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.)

Rationale: SNX10 (sorting nexin 10) has been reported to play a critical role in regulating macrophage function and lipid metabolism., Objective: To investigate the precise role of SNX10 in atherosclerotic diseases and the underlying mechanisms., Methods and Results: SNX10 expression was compared between human healthy vessels and carotid atherosclerotic plaques. Myeloid cell-specific SNX10 knockdown mice were crossed onto the APOE -/- (apolipoprotein E) background and atherogenesis (high-cholesterol diet-induced) was monitored for 16 weeks. We found that SNX10 expression was increased in atherosclerotic lesions of aortic specimens from humans and APOE -/- mice. Myeloid cell-specific SNX10 deficiency (Δ knockout [KO]) attenuated atherosclerosis progression in APOE -/- mice. The population of anti-inflammatory monocytes/macrophages was increased in the peripheral blood and atherosclerotic lesions of ΔKO mice. In vitro experiments showed that SNX10 deficiency-inhibited foam cell formation through interrupting the internalization of CD36, which requires the interaction of SNX10 and Lyn-AKT (protein kinase B). The reduced Lyn-AKT activation by SNX10 deficiency promoted the nuclear translocation of TFEB (transcription factor EB), thereby enhanced lysosomal biogenesis and LAL (lysosomal acid lipase) activity, resulting in an increase of free fatty acids to fuel mitochondrial fatty acid oxidation. This further promoted the reprogramming of macrophages and shifted toward the anti-inflammatory phenotype., Conclusions: Our data demonstrate for the first time that SNX10 plays a crucial role in diet-induced atherogenesis via the previously unknown link between the Lyn-Akt-TFEB signaling pathway and macrophage reprogramming, suggest that SNX10 may be a potentially promising therapeutic target for atherosclerosis treatment.

Cancer is instigated by mutator phenotypes, including deficient mismatch repair and p53-associated chromosomal instability. More recently, a distinct class of cancers was identified with unusually high mutational loads due to heterozygous amino acid substitutions (most commonly P286R) in the proofreading domain of DNA polymerase ε, the leading strand replicase encoded by POLE. Immunotherapy has revolutionized cancer treatment, but new model systems are needed to recapitulate high mutational burdens characterizing human cancers and permit study of mechanisms underlying clinical responses. Here, we show that activation of a conditional LSL-PoleP286R allele in endometrium is sufficient to elicit in all animals endometrial cancers closely resembling their human counterparts, including very high mutational burden. Diverse investigations uncovered potentially novel aspects of Pole-driven tumorigenesis, including secondary p53 mutations associated with tetraploidy, and cooperation with defective mismatch repair through inactivation of Msh2. Most significantly, there were robust antitumor immune responses with increased T cell infiltrates, accelerated tumor growth following T cell depletion, and unfailing clinical regression following immune checkpoint therapy. This model predicts that human POLE-driven cancers will prove consistently responsive to immune checkpoint blockade. Furthermore, this is a robust and efficient approach to recapitulate in mice the high mutational burdens and immune responses characterizing human cancers.

Intron retention (IR) is an alternative splicing mode whereby introns, rather than being spliced out as usual, are retained in mature mRNAs. It was previously considered a consequence of mis-splicing and received very limited attention. Only recently has IR become of interest for transcriptomic data analysis owing to its recognized roles in gene expression regulation and associations with complex diseases. In this article, we first review the function of IR in regulating gene expression in a number of biological processes, such as neuron differentiation and activation of CD4 + T cells. Next, we briefly review its association with diseases, such as Alzheimer's disease and cancers. Then, we describe state-of-the-art methods for IR detection, including RNA-seq analysis tools IRFinder and iREAD, highlighting their underlying principles and discussing their advantages and limitations. Finally, we discuss the challenges for IR detection and potential ways in which IR detection methods could be improved., (Copyright © 2020 Zheng, Lin, Fang and Li.)

Clustering of single-cell RNA sequencing (scRNA-seq) data enables discovering cell subtypes, which is helpful for understanding and analyzing the processes of diseases. Determining the weight of edges is an essential component in graph-based clustering methods. While several graph-based clustering algorithms for scRNA-seq data have been proposed, they are generally based on k-nearest neighbor (KNN) and shared nearest neighbor (SNN) without considering the structure information of graph. Here, to improve the clustering accuracy, we present a novel method for single-cell clustering, called structural shared nearest neighbor-Louvain (SSNN-Louvain), which integrates the structure information of graph and module detection. In SSNN-Louvain, based on the distance between a node and its shared nearest neighbors, the weight of edge is defined by introducing the ratio of the number of the shared nearest neighbors to that of nearest neighbors, thus integrating structure information of the graph. Then, a modified Louvain community detection algorithm is proposed and applied to identify modules in the graph. Essentially, each community represents a subtype of cells. It is worth mentioning that our proposed method integrates the advantages of both SNN graph and community detection without the need for tuning any additional parameter other than the number of neighbors. To test the performance of SSNN-Louvain, we compare it to five existing methods on 16 real datasets, including nonnegative matrix factorization, single-cell interpretation via multi-kernel learning, SNN-Cliq, Seurat and PhenoGraph. The experimental results show that our approach achieves the best average performance in these datasets.

Clustering analysis of gene expression data is essential for understanding complex biological data, and is widely used in important biological applications such as the identification of cell subpopulations and disease subtypes. In commonly used methods such as hierarchical clustering (HC) and consensus clustering (CC), holistic expression profiles of all genes are often used to assess the similarity between samples for clustering. While these methods have been proven successful in identifying sample clusters in many areas, they do not provide information about which gene sets (functions) contribute most to the clustering, thus limiting the interpretability of the resulting cluster. We hypothesize that integrating prior knowledge of annotated gene sets would not only achieve satisfactory clustering performance but also, more importantly, enable potential biological interpretation of clusters. Here we report ClusterMine, an approach that identifies clusters by assessing functional similarity between samples through integrating known annotated gene sets in functional annotation databases such as Gene Ontology. In addition to the cluster membership of each sample as provided by conventional approaches, it also outputs gene sets that most likely contribute to the clustering, thus facilitating biological interpretation. We compare ClusterMine with conventional approaches on nine real-world experimental datasets that represent different application scenarios in biology. We find that ClusterMine achieves better performances and that the gene sets prioritized by our method are biologically meaningful. ClusterMine is implemented as an R package and is freely available at: www.genemine.org/clustermine.php.

The aberrant expression levels of microRNAs (miRNAs) are tightly linked with the initiation and development of various diseases and genetic disorders. Here, we reported a catalytic-hairpin-assembly-assisted DNA tetrahedron nanoprobe for intracellular miRNA detection. The target miRNA initiated the catalytic-hairpin-assembly reaction between the tetrahedron nanoprobes to generate large tetrahedron clusters with an enhanced fluorescence resonance energy transfer between the Cy3 and Cy5 dyes. The proposed nanoprobes were capable of visualizing the expression levels and spatial distributions of miRNA in living cells, providing a feasible approach in designing versatile nanostructures for reliable bioanalysis and clinical diagnosis.

Background: 7-Hydroxycoumarin (7-HC), also known as umbelliferon, is commonly found in Chinese herbs (e.g. Eucommiae Cortex, Prunellae Spica, Radix Angelicae Biseratae). Previous laboratory studies have indicated that 7-HC has anti-inflammatory, anti-oxidative, and anti-tumor effects. Cisplatin is a widely used chemotherapeutic agent for cancer. Nephrotoxicity is one of the limiting side effects of cisplatin use., Purpose: This study aimed to evaluate the renoprotective effect of 7-HC in a cisplatin-induced acute kidney injury (AKI) mouse model., Methods: AKI was induced in male C57BL/6 mice (aged 6-8 weeks) by a single intraperitoneal injection of cisplatin at 20 mg/kg. The mice received 7-HC at 30, 60, and 90 mg/kg intraperitoneally before or after cisplatin administration. Renal function, necroptosis, and cell proliferation were measured. Mechanisms underlying the reno-protective effect of 7-HC were explored in renal tubular epithelial cells treated with or without cisplatin., Results: In-vivo experiments showed that 7-HC significantly improved the loss in kidney function induced by cisplatin, as indicated by lower levels of serum creatinine and blood urea nitrogen, in AKI mice. Consistent herewith, cisplatin-induced tubular damage was alleviated by 7-HC as shown by morphological (periodic acid-Schiff staining) and kidney injury marker (KIM-1) analyses. We found that 7-HC suppressed renal necroptosis via the RIPK1/RIPK3/MLKL pathway and accelerated renal repair as evidenced by the upregulation of cyclin D1 in cisplatin-induced nephropathy. In-vitro experiments showed that knockdown of Sox9 attenuated the suppressive effect of 7-HC on KIM-1 and reversed the stimulatory effect of 7-HC on cyclin D1 expression in cisplatin-treated HK-2 cells, indicating that 7-HC may protect against AKI via a Sox9-dependent mechanism., Conclusion: 7-HC inhibits cisplatin-induced AKI by suppressing RIPK1/RIPK3/MLKL-mediated necroptosis and promoting Sox9-mediated tubular epithelial cell proliferation. 7-HC may serve as a preventive and therapeutic agent for AKI., Competing Interests: Declaration of Competing Interest The authors declare no competing financial interest., (Copyright © 2020 The Author(s). Published by Elsevier GmbH.. All rights reserved.)

Rationale : Circular RNAs (circRNAs) are a new form of noncoding RNAs that play crucial roles in various pathological processes. However, the expression profile and function of circRNAs in hepatic fibrosis (HF) remain largely unknown. In this study, we show a novel circFBXW4 mediates HF via targeting the miR-18b-3p/FBXW7 axis. Methods : We investigated the expression profile of circRNAs, microRNAs and mRNAs in hepatic stellate cells (HSCs) from HF progression and regression mice by circRNAs-seq and microarray analysis. We found a significantly dysregulated circFBXW4 in HF. Loss-of-function and gain-of-function analysis of circFBXW4 were performed to assess the role of circFBXW4 in HF. Furthermore, we confirmed that circFBXW4 directly binds to miR-18b-3p by luciferase reporter assay, RNA pull down and fluorescence in situ hybridization analysis. Results : We found that circFBXW4 downregulated in liver fibrogenesis. Enforcing the expression of circFBXW4 inhibited HSCs activation, proliferation and induced apoptosis, attenuated mouse liver fibrogenesis injury and showed anti-inflammation effect. Mechanistically, circFBXW4 directly targeted to miR-18b-3p to regulate the expression of FBXW7 in HF. Conclusions : circFBXW4 may act as a suppressor of HSCs activation and HF through the circFBXW4/miR-18b-3p/FBXW7 axis. Our findings identify that circFBXW4 serves as a potential biomarker for HF therapy., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)

Biological organisms capable of controlling and performing a wide variety of functions have inspired attempts to mimic biological systems with designable intelligence. Here we develop a multimachine communication network (MMCN) to mimic the operation and function of adaptive immune response (AIR) via connecting three kinds of DNA machines built from module-functionalized gold nanoparticles. These machines simulate three critical immune cells, dendritic cells, T and B lymphocytes, and their differentiation and coordinated interaction upon exposure and response to an invading pathogen. MMCN is composed of standard modules with track, movement, and fuel components that allow for the (1) integration and adaptability of a single machine, (2) convenient spatiotemporal control of the sequential activation of a single machine, and (3) rapid reaction rate and high efficiency owing to an enhanced local concentration of interacting species. We show that the proposed network can sense and clear the corresponding pathogen via consecutive activation and connection of the machines, simultaneously forming a memory to respond more rapidly and effectively upon the second invasion of the pathogen. This system may be extended to construct powerful networks to execute more sophisticated tasks and accomplish diverse functions.

Background: Intron retention (IR) has been traditionally overlooked as 'noise' and received negligible attention in the field of gene expression analysis. In recent years, IR has become an emerging field for interrogating transcriptomes because it has been recognized to carry out important biological functions such as gene expression regulation and it has been found to be associated with complex diseases such as cancers. However, methods for detecting IR today are limited. Thus, there is a need to develop novel methods to improve IR detection., Results: Here we present iREAD (intron REtention Analysis and Detector), a tool to detect IR events genome-wide from high-throughput RNA-seq data. The command line interface for iREAD is implemented in Python. iREAD takes as input a BAM file, representing the transcriptome, and a text file containing the intron coordinates of a genome. It then 1) counts all reads that overlap intron regions, 2) detects IR events by analyzing the features of reads such as depth and distribution patterns, and 3) outputs a list of retained introns into a tab-delimited text file. iREAD provides significant added value in detecting IR compared with output from IRFinder with a higher AUC on all datasets tested. Both methods showed low false positive rates and high false negative rates in different regimes, indicating that use together is generally beneficial. The output from iREAD can be directly used for further exploratory analysis such as differential intron expression and functional enrichment. The software is freely available at https://github.com/genemine/iread., Conclusion: Being complementary to existing tools, iREAD provides a new and generic tool to interrogate poly-A enriched transcriptomic data of intron regions. Intron retention analysis provides a complementary approach for understanding transcriptome.