A systematic evaluation of computational methods for cell segmentation.

Cell segmentation is a fundamental task in analyzing biomedical images. Many computational methods have been developed for cell segmentation and instance segmentation, but their performances are not well understood in various scenarios. We systematically evaluated the performance of 18 segmentation methods to perform cell nuclei and whole cell segmentation using light microscopy and fluorescence staining images. We found that general-purpose methods incorporating the attention mechanism exhibit the best overall performance. We identified various factors influencing segmentation performances, including image channels, choice of training data, and cell morphology, and evaluated the generalizability of methods across image modalities. We also provide guidelines for choosing the optimal segmentation methods in various real application scenarios. We developed Seggal, an online resource for downloading segmentation models already pre-trained with various tissue and cell types, substantially reducing the time and effort for training cell segmentation models.

TNFAIP3 Derived from Skeletal Stem Cells Alleviated Rat Osteoarthritis by Inhibiting the Necroptosis of Subchondral Osteoblasts.

Recent investigations have shown that the necroptosis of tissue cells in joints is important in the development of osteoarthritis (OA). This study aimed to investigate the potential effects of exogenous skeletal stem cells (SSCs) on the necroptosis of subchondral osteoblasts in OA. Human SSCs and subchondral osteoblasts isolated from human tibia plateaus were used for Western blotting, real-time PCR, RNA sequencing, gene editing, and necroptosis detection assays. In addition, the rat anterior cruciate ligament transection OA model was used to evaluate the effects of SSCs on osteoblast necroptosis in vivo. The micro-CT and pathological data showed that intra-articular injections of SSCs significantly improved the microarchitecture of subchondral trabecular bones in OA rats. Additionally, SSCs inhibited the necroptosis of subchondral osteoblasts in OA rats and necroptotic cell models. The results of bulk RNA sequencing of SSCs stimulated or not by tumor necrosis factor α suggested a correlation of SSCs-derived tumor necrosis factor α-induced protein 3 (TNFAIP3) and cell necroptosis. Furthermore, TNFAIP3-derived from SSCs contributed to the inhibition of the subchondral osteoblast necroptosis in vivo and in vitro. Moreover, the intra-articular injections of TNFAIP3-overexpressing SSCs further improved the subchondral trabecular bone remodeling of OA rats. Thus, we report that TNFAIP3 from SSCs contributed to the suppression of the subchondral osteoblast necroptosis, which suggests that necroptotic subchondral osteoblasts in joints may be possible targets to treat OA by stem cell therapy.

FGF4 ameliorates the liver inflammation by reducing M1 macrophage polarization in experimental autoimmune hepatitis.

BACKGROUND: The global prevalence of autoimmune hepatitis (AIH) is increasing due in part to the lack of effective pharmacotherapies. Growing evidence suggests that fibroblast growth factor 4 (FGF4) is crucial for diverse aspects of liver pathophysiology. However, its role in AIH remains unknown. Therefore, we investigated whether FGF4 can regulate M1 macrophage and thereby help treat liver inflammation in AIH. METHODS: We obtained transcriptome-sequencing and clinical data for patients with AIH. Mice were injected with concanavalin A to induce experimental autoimmune hepatitis (EAH). The mechanism of action of FGF4 was examined using macrophage cell lines and bone marrow-derived macrophages. RESULTS: We observed higher expression of markers associated with M1 and M2 macrophages in patients with AIH than that in individuals without AIH. EAH mice showed greater M1-macrophage polarization than control mice. The expression of M1-macrophage markers correlated positively with FGF4 expression. The loss of hepatic Fgf4 aggravated hepatic inflammation by increasing the abundance of M1 macrophages. In contrast, the pharmacological administration of FGF4 mitigated hepatic inflammation by reducing M1-macrophage levels. The efficacy of FGF4 treatment was compromised following the in vivo clearance of macrophage populations. Mechanistically, FGF4 treatment activated the phosphatidylinositol 3-kinase (PI3K)-protein kinase B (AKT)-signal pathway in macrophages, which led to reduced M1 macrophages and hepatic inflammation. CONCLUSION: We identified FGF4 as a novel M1/M2 macrophage-phenotype regulator that acts through the PI3K-AKT-signaling pathway, suggesting that FGF4 may represent a novel target for treating inflammation in patients with AIH.

Unraveling the rapid progression of non-target lesions: risk factors and the therapeutic potential of PCSK9 inhibitors in post-PCI patients.

BACKGROUND: Rapid progression of non-target lesions (NTLs) leads to a high incidence of NTL related cardiac events post-PCI, which accounting half of the recurrent cardiac events. It is important to identify the risk factors and establish an accurate clinical prediction model for the rapid progression of NTLs post-PCI. PCSK9 inhibitors lower LDL-c levels significantly, also show the anti-inflammation effect, and may have the potential to reduce the rapid progression of NTLs post-PCI. We tried to test this hypothesis and explore the potential mechanisms. METHODS: This retrospective study included 1250 patients who underwent the first PCI and underwent repeat coronary angiography for recurrence of chest pain within 24 months. General characteristics, laboratory tests and inflammatory factors(IL-10, IL-6, IL-8, IL-1ß, sIL-2R, and TNF-α) were collected. Machine learning (LASSO regression) was mainly employed to select the important characteristic risk factors for the rapid progression of NTLs post-PCI and build prediction models. Finally, mediator analysis was employed to explore the potential mechanisms by which PCSK9 inhibitors reduce the rapid progression of NTLs post-PCI. RESULTS: There were more diabetes, less beta-blockers and PCSK9 inhibitors application, higher HbA1c, LDL-c, ApoB, TG, TC, uric acid, hs-CRP, TNF-α, IL-6, IL-8, and sIL-2R in NTL progressed group. LDL-c, hs-CRP, IL-8, and sIL-2R were characteristic risk factors for the rapid progression of NTLs post-PCI, combining LDL-c, hs-CRP, IL-8, and sIL-2R builds the optimal model for predicting the rapid progression of NTLs post-PCI (AUC = 0.632). LDL-c had a clear and incomplete mediating effect (95% CI, mediating effect: 51.56%) in the reduction of the progression of NTLs by PCSK9 inhibitors, and there was a possible mediating effect of IL-8 (90% CI), and sIL-2R (90% CI). CONCLUSIONS: LDL-c, hs-CRP, IL-8, and sIL-2R may be the key characteristic risk factors for the rapid progression of NTLs post-PCI, and combining these parameters might predict the rapid progression of NTLs post-PCI. The application of PCSK9 inhibitors had a negative correlation with the rapid progression of NTLs. In addition to the significant LDL-c-lowering, PCSK9 inhibitors may reduce the rapid progression of NTLs by reducing local inflammation of plaque. TRIAL REGISTRATION: ChiCTR2200058529; Date of registration: 2022-04-10.

Associations of lipids and lipid-modifying drug target genes with atrial fibrillation risk based on genomic data.

BACKGROUND: The causal associations of lipids and the drug target genes with atrial fibrillation (AF) risk remain obscure. We aimed to investigate the causal associations using genetic evidence. METHODS: Mendelian randomization (MR) analyses were conducted using summary-level genome-wide association studies (GWASs) in European and East Asian populations. Lipid profiles (low-density lipoprotein cholesterol, triglyceride, and lipoprotein[a]) and lipid-modifying drug target genes (3-hydroxy-3-methylglutaryl-CoA reductase, proprotein convertase subtilisin/kexin type 9, NPC1-like intracellular cholesterol transporter 1, apolipoprotein C3, angiopoietin-like 3, and lipoprotein[a]) were used as exposures. AF was used as an outcome. The inverse variance weighted method was applied as the primary method. Summary-data-based Mendelian randomization analyses were performed for further validation using expression quantitative trait loci data. Mediation analyses were conducted to explore the indirect effect of coronary heart disease. RESULTS: In the European population, MR analyses demonstrated that elevated levels of lipoprotein(a) increased AF risk. Moreover, analyses focusing on drug targets revealed that the genetically proxied target gene LPA, which simulates the effects of drug intervention by reducing lipoprotein(a), exhibited an association with AF risk. This association was validated in independent datasets. There were no consistent and significant associations observed for other traits when analyzed in different datasets. This finding was also corroborated by Summary-data-based Mendelian randomization analyses between LPA and AF. Mediation analyses revealed that coronary heart disease plays a mediating role in this association. However, in the East Asian population, no statistically significant evidence was observed to support these associations. CONCLUSIONS: This study provided genetic evidence that Lp(a) may be a causal factor for AF and that LPA may represent a promising pharmacological target for preventing AF in the European population.

The association between chronic sinonasal inflammation and nasopharyngeal carcinoma - A systematic review and meta-analysis.

PURPOSE: There has been mounting evidence that inflammation is a key risk factor towards the development of certain cancers. Past studies have shown associations between nasopharyngeal carcinoma (NPC) and sinonasal tract inflammation. We aim to conduct a review and meta-analysis on the association between NPC and chronic sinus inflammation. MATERIALS AND METHODS: We conducted a meta-analysis, searching 4 international databases from 1 January 1973 to 28 March 2022 for studies reporting on sinonasal inflammation and NPC in adult patients (>18 years old). We included cohort, case-control or cross-sectional studies. These studies must examine the association between a prior history of sinonasal inflammation and the risk of developing NPC. The outcome is the incidence of NPC in patients who had prior sinonasal inflammation. RESULTS: 8 studies (8245 NPC; 1,036,087 non-NPC) were included. The overall odds ratio (OR) of patients having NPC after reporting sinonasal inflammation was 1.81 (95 % CI 1.73-1.89). Of note, chronic rhinosinusitis (CRS) (OR of 1.78 (95 %-CI: 1.68-1.90)) was more closely associated with an increased risk of NPC, as compared to allergic rhinitis (AR) (OR of 1.60 (95 %-CI: 1.52-1.68)). CONCLUSION: Chronic sinonasal inflammation is significantly associated with NPC in this systemic review and meta-analysis. The true cause-effect relationship and the potential effects of targeted screening need to be explored thoroughly with large scale prospective studies.

Thienyltriazine Triamides: Thickness Insensitive Interlayer Materials Featuring Fine-tuned Optoelectronic and Aggregation Characters for Efficient Organic Solar Cells.

A novel class of thienyltriazine triamides (TTTAs) was facile synthesized and firstly used as cathode interlayers (CILs) for organic solar cells (OSCs). By utilizing different aromatic arms and pendant polar groups, their optoelectronic properties and aggregation behaviors were effectively modulated. The combination of thienyltriazine (TT) core, naphthylamide arm and imidazole pendant group endows TT-N-M with suitable energy levels, intensified work function tunability, higher conductivity, and well-balanced crystallinity and film-forming ability, boosting both the performance and stability of OSCs significantly. Remarkably, the solar cell efficiency remains stable at around 90% of the optimal efficiency even as the interlayer thickness varied from 5 to 95 nm, demonstrating its insensitivity to thickness. Moreover, TT-N-M exhibits compatibility with various active layer systems, achieving a maximum efficiency of 19.60% for single-junction solar cell. Its exceptional tolerance to thickness fluctuations and performance establishes a new benchmark for multi-armed CIL-based OSCs, also positioning them among the most high-performing CIL materials documented thus far. This work not only broadens the scope of CIL materials for OSCs but also offers deep insights into design strategies and structure-properties relationships, being beneficial for the future development of more efficient CIL materials for organic optoelectronic applications.

Configurational Isomerization-Induced Orientation Switching: Non-Fused Ring Dipodal Phosphonic Acids as Hole-Extraction Layers for Efficient Organic Solar Cells.

Phosphonic acid (PA) self-assembled molecules have recently emerged as efficient hole-extraction layers (HELs) for organic solar cells (OSCs). However, the structural effects of PAs on their self-assembly behaviors on indium tin oxide (ITO) and thus photovoltaic performance remain obscure. Herein, we present a novel class of PAs, namely "non-fused ring dipodal phosphonic acids" (NFR-DPAs), featuring simple and malleable non-fused ring backbones and dipodal phosphonic acid anchoring groups. The efficacy of configurational isomerism in modulating the photoelectronic properties and switching molecular orientation of PAs atop electrodes results in distinct substrate surface energy and electronic characteristics. The NFR-DPA with linear (C2h symmetry) and brominated backbone exhibits favorable face-on orientation and enhanced work function modification capability compared to its angular (C2v symmetry) and non-brominated counterparts. This makes it versatile HELs in mitigating interfacial resistance for energy barrier-free hole collection, and affording optimal active layer morphology, which results in an impressive efficiency of 19.11% with a low voltage loss of 0.52 V for binary OSC devices and an excellent efficiency of 19.66% for ternary OSC devices. This study presents a new dimension to design PA-based HELs for high-performance OSCs.

Marker-Free Isoelectric Focusing Patterns for Identification of Meat Samples via Deep Learning.

Isoelectric focusing (IEF) is a powerful tool for resolving complex protein samples, which generates IEF patterns consisting of multiplex analyte bands. However, the interpretation of IEF patterns requires the careful selection of isoelectric point (pI) markers for profiling the pH gradient and a trivial process of pI labeling, resulting in low IEF efficiency. Here, we for the first time proposed a marker-free IEF method for the efficient and accurate classification of IEF patterns by using a convolutional neural network (CNN) model. To verify our method, we identified 21 meat samples whose IEF patterns comprised different bands of meat hemoglobin, myoglobin, and their oxygen-binding variants but no pI marker. Thanks to the high throughput and short assay time of the microstrip IEF, we efficiently collected 1449 IEF patterns to construct the data set for model training. Despite the absence of pI markers, we experimentally introduced the severe pH gradient drift into 189 IEF patterns in the data set, thereby omitting the need for profiling the pH gradient. To enhance the model robustness, we further employed data augmentation during the model training to mimic pH gradient drift. With the advantages of simple preprocessing, a rapid inference of 50 ms, and a high accuracy of 97.1%, the CNN model outperformed the traditional algorithm for simultaneously identifying meat species and cuts of meat of 105 IEF patterns, suggesting its great potential of being combined with microstrip IEF for large-scale IEF analyses of complicated protein samples.

CUL4B enhances the malignant phenotype of esophageal squamous cell carcinoma by suppressing TGFBR3 expression.

Cullin 4B (CUL4B), which acts as a scaffold protein in CUL4B-RING ubiquitin ligase complexes (CRL4B), is frequently overexpressed in cancer and represses tumor suppressors through epigenetic mechanisms. However, the expression and function of CUL4B in esophageal squamous cell carcinoma (ESCC) have not been well illustrated. In this study, we show that upregulation of CUL4B in ESCC cells enhances proliferation, invasion and cisplatin (CDDP)-resistance, while knockdown of CUL4B significantly represses the malignant activities. Mechanistically, we demonstrate that CUL4B promotes proliferation and migration of ESCC cells through inhibiting expression of transforming growth factor beta receptor III (TGFBR3). CRL4B complex binds to the promoter of TGFBR3, and represses its transcription by catalyzing monoubiquitination at H2AK119 and coordinating with PRC2 and HDAC complexes. Taken together, our findings establish a critical role for the CUL4B/TGFBR3 axis in the regulation of ESCC malignancy.

Bridging heterogeneous mutation data to enhance disease gene discovery.

Bridging heterogeneous mutation data fills in the gap between various data categories and propels discovery of disease-related genes. It is known that genome-wide association study (GWAS) infers significant mutation associations that link genotype and phenotype. However, due to the differences of size and quality between GWAS studies, not all de facto vital variations are able to pass the multiple testing. In the meantime, mutation events widely reported in literature unveil typical functional biological process, including mutation types like gain of function and loss of function. To bring together the heterogeneous mutation data, we propose a 'Gene-Disease Association prediction by Mutation Data Bridging (GDAMDB)' pipeline with a statistic generative model. The model learns the distribution parameters of mutation associations and mutation types and recovers false-negative GWAS mutations that fail to pass significant test but represent supportive evidences of functional biological process in literature. Eventually, we applied GDAMDB in Alzheimer's disease (AD) and predicted 79 AD-associated genes. Besides, 12 of them from the original GWAS, 60 of them are supported to be AD-related by other GWAS or literature report, and rest of them are newly predicted genes. Our model is capable of enhancing the GWAS-based gene association discovery by well combining text mining results. The positive result indicates that bridging the heterogeneous mutation data is contributory for the novel disease-related gene discovery.

The neutrophil percentage-to-albumin ratio is associated with all-cause mortality in patients with chronic heart failure.

BACKGROUND: In this study, we evaluated the predictive utility of neutrophil percentage-to-albumin ratio (NPAR) for all-cause mortality in patients with chronic heart failure (CHF). METHODS: Patients diagnosed as CHF enrolled in this retrospective cohort study were from Beijing Chaoyang Hospital, capital medical university. Admission NPAR was calculated as neutrophil percentage divided by serum albumin. The endpoints of this study were defined as 90-day, 1-year and 2-year all-cause mortality. Multivariable Cox proportional hazard regression model was performed to confirm the association between NPAR and all-cause mortality. Receiver operating characteristics (ROC) curves were used to evaluate the ability for NPAR to predict all-cause mortality. RESULTS: The 90-day (P = 0.009), 1-year (P < 0.001) and 2-year (P < 0.001) all-cause mortality in 622 patients with CHF were increased as admission NPAR increased. Multivariable Cox regression analysis found the higher NPAR value was still independently associated with increased risk of 90-day (Group III versus Group I: HR, 95% CI: 2.21, 1.01-4.86, P trend = 0.038), 1-year (Group III versus Group I: HR, 95% CI:2.13, 1.30-3.49, P trend = 0.003), and 2-year all-cause mortality (Group III versus Group I: HR, 95% CI:2.06, 1.37-3.09, P trend = 0.001), after adjustments for several confounders. ROC curves revealed that NPAR had a better ability to predict all-cause mortality in patients with CHF, than either albumin or the neutrophil percentage alone. CONCLUSIONS: NPAR was independently correlated with 90-day, 1-year, and 2-year all-cause mortality in patients with CHF.

Intracardiac echocardiography is a safe and effective alternative to transesophageal echocardiography for left atrial appendage thrombus evaluation at the time of atrial fibrillation ablation: The ICE-TEE study.

BACKGROUND: Intracardiac echocardiography (ICE) technology has been increasingly accepted as an integral part of atrial fibrillation (AF) ablation procedures. It is still unknown whether ICE can routinely replace transesophageal echocardiography (TEE) for routine thrombus screening in non-selective AF patients. OBJECTIVE: To assess whether ICE can routinely replace TEE in screening for left atrial (LA)/left atrial appendage (LAA) thrombus in general patients undergoing catheter ablation for AF. METHODS: A total of 2003 consecutive patients undergoing AF ablation were included. 1155 patients (ICE group) received intra-procedural ICE examination for LA/LAA thrombus screening, while 848 patients (TEE group) received pre-procedure TEE examination. The incidence of thrombus, peri-procedure complications, and hospital efficiency were assessed. RESULTS: The LA and LAA were adequately visualized in all patients. Five patients in the ICE group and 15 patients in the TEE group were found to have LAA thrombus. The incidence of major periprocedural thrombo-embolic events was comparable between two groups (0.2% vs. 0.1%, p = .76), none were due to undetected LA/LAA thrombus. Other major periprocedural complications occurred at similar rates in both groups, while post-procedure fever was less common in the ICE group (12.7% vs. 17.4%, p < .001). Procedure times and hospital length of stay were both shorter in the ICE group (142 min [87-197 min] vs. 150 min [95-205 min], and 3[2-4] day vs. 4[3-5] day, respectively, both p < .001). CONCLUSIONS: ICE can replace TEE for atrial thrombus screening in AF patients undergoing ablation without increased complications. An "ICE replacing TEE" workflow can also reduce the incidence of postoperative fever and improve hospital efficiency.

Insomniacs show greater prefrontal activation during verbal fluency task compared to non-insomniacs: a functional near-infrared spectroscopy investigation of depression in patients.

BACKGROUND: Previous studies have shown that insomnia affects human prefrontal function and that there are specific patterns of brain activation to counteract sleep and improve cognition. However, the effects of insomnia on the prefrontal cortex of MDD (major depressive disorder) patients and the patterns of activation to counteract sleep in MDD patients remain unclear. The aim of this study is to examine this using fNIRS (functional near-infrared spectroscopy). METHODS: Eighty depressed patients and 44 healthy controls were recruited for this study. fNIRS was used to assess changes in the concentration of oxygenated hemoglobin ([oxy-Hb]) in the prefrontal cortex of all participants during the VFT (verbal fluency test) and to record the number of words created to assess cognitive ability. The Pittsburgh Sleep Quality Index was used to assess sleep quality, and the Hamilton Rating Scale for Depression (24-item) and Hamilton Rating Scale for Anxiety (14-item) were used to assess the severity of depression and anxiety. RESULTS: When comparing patients, the healthy control group had significantly higher [oxy-Hb] values in the bilateral prefrontal cortex during VFT than the MDD group. In the MDD group, the [oxy-Hb] values in all brain regions except the right DLPFC were significantly higher in the group with insomnia than in the group without insomnia, but their VFT performance was significantly lower than in the group without insomnia and the healthy group. PSQI scores were positively correlated with [oxy-Hb] values in some left-brain regions, whereas HAMD and HAMA scores were not correlated with [oxy-Hb] values. CONCLUSION: The PFC was significantly less active during VFT in those with MDD than in healthy controls. All brain regions, except the right DLPFC, were significantly more active in MDD patients with insomnia than in those without insomnia, suggesting that sleep quality needs to be an important indicator in fNIRS screening. In addition, there was a positive correlation between the severity of insomnia in the left VLPFC and the level of activation, suggesting a role for the left brain region in the neurophysiology of overcoming sleepiness in MDD patients. these findings may provide new ideas for the treatment of MDD patients in the future. TRIAL REGISTRATION: Our experiment was registered in the China Clinical Trial Registry (registration number ChiCTR2200065622) on November 10.( The first patient was recruited in 10/11/2022.).

Gel Electrophoresis Chip Using Joule Heat Self-Dissipation, Short Run Time, and Online Dynamic Imaging.

Gel electrophoresis (GE) is one of the most general tools in biomedicine. However, it suffers from low resolution, and its mechanism has not been fully revealed yet. Herein, we presented the dispersion model of w2 (t) ∝ Tt, showing the band dispersion (w) via temperature (T) and running time (t) control. Second, we designed an efficient GE chip via the time control and rapid Joule heat self-dissipation by thermal conductive plastic (TCP) and electrode buffer. Third, we conducted the simulations on TCP and polymethylmethacrylate (PMMA) chips, unveiling that (i) the temperature of TCP was lower than the PMMA one, (ii) the temperature uniformity of TCP was better than the PMMA one, and (iii) the resolution of TCP was superior to the PMMA one. Fourth, we designed both TCP and PMMA chips for experimentally validating the dispersion model, TCP chip, and simulations. Finally, we applied the TCP chip to thalassemia and model urine protein assays. The TCP chip has merits of high resolution, rapid run of 6-10 min, and low cost. This work paves the way for greatly improving electrophoretic techniques in gel, chip, and capillary via temperature and time control for biologic study, biopharma quality control, clinical diagnosis, and so on.

A facile online multi-gear capacitively coupled contactless conductivity detector for an automatic and wide range monitoring of high salt in HPLC.

Sensing the electrolyte solution or aqueous-organic mixture has attracted much interest in chemical separation, pharmaceutical engineering, bioprocess, and biochemical experiments. However, reports on online contactless sensor with automatic and wide range sensing of high content electrolyte have been rarely presented. Herein, a facile model and theory of online multi-gear capacitively coupled contactless conductivity detection (M-C4D) sensor was proposed using one excitation electrode and multiple detection electrodes. Further, the relevant digital computation based on the M-C4D theory was developed for parameter optimization: the electrode gap of 5-150 mm, inner radius of 0.25-0.75 mm, electrode length of 10-60 mm, and frequency of 40-250 kHz using MATLAB. To demonstrate the model, theory, and digital computation, liquid chromatography (LC) was chosen as the model of bioprocess, and the sensor was designed and used as an online sensing device for the automatic monitoring of high salt elution in LC. The experiments showed that (i) the detection results were in agreement with the digital data, validating the digital computation, theory, and model of M-C4D and (ii) the monitoring data of M-C4D were in agreement with those via the traditional meter, further validating the model and theory. Finally, the developed sensor was applied to the automated detection of high salt gradient in LC. In contrast to the currently used meters and C4D, the developed M-C4D sensor had the following merits: (i) facile and automatic online detection avoiding cumbersome manual switching of detector heads, (ii) fair linear range of 0.015-20 mS cm-1 (equivalently 0.1-159 mM KCl) that does not fit the range of traditional C4D, and (iii) fair accuracy of less than 1.50% relative error. All these results indicate that the developed model, theory, and sensor have potential for the process monitoring of high content electrolytes transfer in biochemical engineering and clinic pre-warning.

CUL4B renders breast cancer cells tamoxifen-resistant via miR-32-5p/ER-α36 axis.

Tamoxifen (TAM) resistance is a significant clinical challenge in endocrine therapies for estrogen receptor (ER)-positive breast cancer patients. Cullin 4B (CUL4B), which acts as a scaffold protein in CUL4B-RING ubiquitin ligase complexes (CRL4B), is frequently overexpressed in cancer and represses tumor suppressors through diverse epigenetic mechanisms. However, the role and the underlying mechanisms of CUL4B in regulating drug resistance remain unknown. Here, we showed that CUL4B promotes TAM resistance in breast cancer cells through a miR-32-5p/ER-α36 axis. We found that upregulation of CUL4B correlated with decreased TAM sensitivity of breast cancer cells, and knockdown of CUL4B or expression of a dominant-negative CUL4B mutant restored the response to TAM in TAM-resistant MCF7-TAMR and T47D-TAMR cells. Mechanistically, we demonstrated that CUL4B renders breast cancer cells TAM-resistant by upregulating ER-α36 expression, which was mediated by downregulation of miR-32-5p. We further showed that CRL4B epigenetically represses the transcription of miR-32-5p by catalyzing monoubiquitination at H2AK119 and coordinating with PRC2 and HDAC complexes to promote trimethylation at H3K27 at the promoter of miR-32-5p. Pharmacologic or genetic inhibition of CRL4B/PRC2/HDAC complexes significantly increased TAM sensitivity in breast cancer cells in vitro and in vivo. Taken together, our findings thus establish a critical role for the CUL4B-miR-32-5p-ER-α36 axis in the regulation of TAM resistance and have important therapeutic implications for combined application of TAM and the inhibitors of CRL4B/PRC2/HDAC complex in breast cancer treatment. © 2021 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

High-quality gene/disease embedding in a multi-relational heterogeneous graph after a joint matrix/tensor decomposition.

MOTIVATION: Node embedding of biological entity network has been widely investigated for the downstream application scenarios. To embed full semantics of gene and disease, a multi-relational heterogeneous graph is considered in a scenario where uni-relation between gene/disease and other heterogeneous entities are abundant while multi-relation between gene and disease is relatively sparse. After introducing this novel graph format, it is illuminative to design a specific data integration algorithm to fully capture the graph information and bring embeddings with high quality. RESULTS: First, a typical multi-relational triple dataset was introduced, which carried significant association between gene and disease. Second, we curated all human genes and diseases in seven mainstream datasets and constructed a large-scale gene-disease network, which compromising 163,024 nodes and 25,265,607 edges, and relates to 27,165 genes, 2,665 diseases, 15,067 chemicals, 108,023 mutations, 2,363 pathways, and 7.732 phenotypes. Third, we proposed a Joint Decomposition of Heterogeneous Matrix and Tensor (JDHMT) model, which integrated all heterogeneous data resources and obtained embedding for each gene or disease. Forth, a visualized intrinsic evaluation was performed, which investigated the embeddings in terms of interpretable data clustering. Furthermore, an extrinsic evaluation was performed in the form of linking prediction. Both intrinsic and extrinsic evaluation results showed that JDHMT model outperformed other eleven state-of-the-art (SOTA) methods which are under relation-learning, proximity-preserving or message-passing paradigms. Finally, the constructed gene-disease network, embedding results and codes were made available. DATA AND CODES AVAILABILITY: The constructed massive gene-disease network is available at: https://hzaubionlp.com/heterogeneous-biological-network/. The codes are available at: https://github.com/bionlp-hzau/JDHMT.

Use of a coronary guidewire to facilitate transseptal puncture: A randomized comparison with a conventional technique.

INTRODUCTION: Transseptal puncture (TSP) is routinely performed for left heart intervention, but it can sometimes be complex and life-threatening. This study introduced a safe and effective method to facilitate TSP for left atrial access. METHODS AND RESULTS: A total of 200 patients (190 with atrial fibrillation, 10 with a left accessory pathway) were prospectively analyzed. In the guidewire group, TSP was performed using a SWARTZ sheath and a Brockenbrough needle with a 0.014-inch coronary guidewire instead of an inner stylet. The needle tip position was confirmed by pushing the guidewire into the left superior pulmonary vein after initial puncture in 100 patients. In the contrast group, TSP was performed in 100 patients using standard devices by injecting contrast to confirm needle-tip position. Left atrial access was achieved successfully in all patients in the two groups without serious complications. The guidewire group showed a higher first-pass rate for left atrial access compared with the contrast group (81.1% vs. 75% p < .001, respectively). CONCLUSION: Coronary guidewire TSP is safe and is associated with a high success rate, and it is thus a useful alternative to conventional TSP. This method is useful for patients with septal aneurysms and contrast allergies.

Sustained ER stress promotes hyperglycemia by increasing glucagon action through the deubiquitinating enzyme USP14.

Endoplasmic reticulum (ER) stress plays an important role in metabolic diseases like obesity and type 2 diabetes mellitus (T2DM), although the underlying mechanisms and regulatory pathways remain to be elucidated. Here, we induced chronic low-grade ER stress in lean mice to levels similar to those in high-fat diet (HFD)-fed obese mice and found that it promoted hyperglycemia due to enhanced hepatic gluconeogenesis. Mechanistically, sustained ER stress up-regulated the deubiquitinating enzyme ubiquitin-specific peptidase 14 (USP14), which increased the stability and levels of 3',5'-cyclic monophosphate-responsive element binding (CREB) protein (CBP) to enhance glucagon action and hepatic gluconeogenesis. Exogenous overexpression of USP14 in the liver significantly increased hepatic glucose output. Consistent with this, liver-specific knockdown of USP14 abrogated the effects of ER stress on glucose metabolism, and also improved hyperglycemia and glucose intolerance in obese mice. In conclusion, our findings show a mechanism underlying ER stress-induced disruption of glucose homeostasis, and present USP14 as a potential therapeutic target against T2DM.