Predicting lncRNA-disease associations based on combining selective similarity matrix fusion and bidirectional linear neighborhood label propagation.

Recent studies have revealed that long noncoding RNAs (lncRNAs) are closely linked to several human diseases, providing new opportunities for their use in detection and therapy. Many graph propagation and similarity fusion approaches can be used for predicting potential lncRNA-disease associations. However, existing similarity fusion approaches suffer from noise and self-similarity loss in the fusion process. To address these problems, a new prediction approach, termed SSMF-BLNP, based on organically combining selective similarity matrix fusion (SSMF) and bidirectional linear neighborhood label propagation (BLNP), is proposed in this paper to predict lncRNA-disease associations. In SSMF, self-similarity networks of lncRNAs and diseases are obtained by selective preprocessing and nonlinear iterative fusion. The fusion process assigns weights to each initial similarity network and introduces a unit matrix that can reduce noise and compensate for the loss of self-similarity. In BLNP, the initial lncRNA-disease associations are employed in both lncRNA and disease directions as label information for linear neighborhood label propagation. The propagation was then performed on the self-similarity network obtained from SSMF to derive the scoring matrix for predicting the relationships between lncRNAs and diseases. Experimental results showed that SSMF-BLNP performed better than seven other state of-the-art approaches. Furthermore, a case study demonstrated up to 100% and 80% accuracy in 10 lncRNAs associated with hepatocellular carcinoma and 10 lncRNAs associated with renal cell carcinoma, respectively. The source code and datasets used in this paper are available at: https://github.com/RuiBingo/SSMF-BLNP.

4 mC site recognition algorithm based on pruned pre-trained DNABert-Pruning model and fused artificial feature encoding.

DNA 4 mC plays a crucial role in the genetic expression process of organisms. However, existing deep learning algorithms have shortcomings in the ability to represent DNA sequence features. In this paper, we propose a 4 mC site identification algorithm, DNABert-4mC, based on a fusion of the pruned pre-training DNABert-Pruning model and artificial feature encoding to identify 4 mC sites. The algorithm prunes and compresses the DNABert model, resulting in the pruned pre-training model DNABert-Pruning. This model reduces the number of parameters and removes redundancy from output features, yielding more precise feature representations while upholding accuracy.Simultaneously, the algorithm constructs an artificial feature encoding module to assist the DNABert-Pruning model in feature representation, effectively supplementing the information that is missing from the pre-trained features. The algorithm also introduces the AFF-4mC fusion strategy, which combines artificial feature encoding with the DNABert-Pruning model, to improve the feature representation capability of DNA sequences in multi-semantic spaces and better extract 4 mC sites and the distribution of nucleotide importance within the sequence. In experiments on six independent test sets, the DNABert-4mC algorithm achieved an average AUC value of 93.81%, outperforming seven other advanced algorithms with improvements of 2.05%, 5.02%, 11.32%, 5.90%, 12.02%, 2.42% and 2.34%, respectively.

Ame-miR-980-3p participates in autophagy-mediated midgut remodelling in Apis mellifera via targeting Atg2B.

Autophagy is a process that serves to degrade damaged proteins and organelles, thereby promoting cell homeostasis, differentiation, development and survival. Many miRNAs have been found to have regulatory roles in autophagy. In insects, it has been shown that autophagy is involved in hormone-regulated programmed cell death during metamorphic midgut remodelling. However, whether this is also true during the remodelling of the honey bee midgut is unclear. In the present study, we explored the relationship between autophagy and midgut remodelling and sought to identify miRNAs involved in this physiological process. We found that autophagy occurred during midgut remodelling and that the inhibition of autophagy resulted in midgut dysplasia in prepupae. Differentially expressed miRNAs enriched in the autophagy signalling pathway during midgut remodelling were identified by small RNA-seq. Ame-miR-980-3p, which targets the autophagy-related gene Atg2B, was screened out. Furthermore, abnormal expression of ame-miR-980-3p in the pupal stage led to the thinning of the midgut wall of newly emerged bees (NE). When ame-miR-980-3p expression was inhibited, the intestinal villi of NE bees became significantly shorter and sparse, and the lipid signal in the peritrophic matrix of Pb almost disappeared, indicating that the adult midgut was underdeveloped and the lipid absorption ability was weakened. Taken together, ame-miR-980-3p targeted Atg2B to participate in the regulation of midgut autophagy in the pupae, and the abnormal expression of ame-miR-980-3p would interfere with cell proliferation and death in the process of midgut remodelling, hinder the formation of adult midgut and eventually lead to adult midgut dysplasia and affect the lipid absorption function of the midgut in Apis mellifera.

Honey bee larval culture in vitro: gut emptying determines the transition from larva to prepupa and recombinant AccApidaecin improves antibacterial activity.

In vitro rearing of honey bee larvae is ideal for bioassay studies; no honey bee stable cell lines are available. Inconsistency of internal development staging of reared larvae and a susceptibility to contamination are common problems encountered. Standardized protocols on rearing larvae in vitro to make the larvae growth and development more similar to that of natural colonies are necessary to ensure the accuracy of experimental results and promote honey bee research as a model organism. Here, we concluded that when larval fasting weight was >160 mg, the time point of gut emptying can be defined as the critical point separating the larval and prepupal stages. In this way, we can conduct precise studies on the prepupal stage, such as organ remodeling during metamorphosis. Simultaneously, we further verified that recombinant AccApidaecin in genetic engineered bacteria added to the larval diet upregulated antibacterial peptide gene expression, and did not stimulate the stress response in larvae, nor did it affect the pupation rate or eclosion rate. This demonstrated that feeding recombinant AccApidaecin can enhance the individual antibacterial ability at the molecular level.

The latest research progress on minimally invasive treatments for hepatocellular carcinoma.

BACKGROUND: Hepatocellular carcinoma (HCC) is the fourth leading cause of cancer-related death worldwide. Due to the high prevalence of hepatitis B virus (HBV) infection in China, the incidence of HCC in China is high, and liver cirrhosis caused by chronic hepatitis also brings great challenges to treatment. This paper reviewed the latest research progress on minimally invasive treatments for HCC, including percutaneous thermal ablation and new nonthermal ablation techniques, and introduced the principles, advantages, and clinical applications of various therapeutic methods in detail. DATA SOURCES: The data of treatments for HCC were systematically collected from the PubMed, ScienceDirect, American Chemical Society and Web of Science databases published in English, using "minimally invasive" and "hepatocellular carcinoma" or "liver cancer" as the keywords. RESULTS: Percutaneous thermal ablation is still a first-line strategy for the minimally invasive treatment of HCC. The effect of microwave ablation (MWA) on downgrading treatment before liver transplantation is better than that of radiofrequency ablation (RFA), while RFA is more widely used in the clinical practice. High-intensity focused ultrasound (HIFU) is mainly used for the palliative treatment of advanced liver cancer. Electrochemotherapy (ECT) delivers chemotherapeutic drugs to the target cells while reducing the blood supply around HCC. Irreversible electroporation (IRE) uses a microsecond-pulsed electric field that induces apoptosis and necrosis and triggers a systemic immune response. The nanosecond pulsed electric field (nsPEF) has achieved a good response in the ablation of mice with HCC, but it has not been reported in China for the treatment of human HCC. CONCLUSIONS: A variety of minimally invasive treatments provide a sufficient survival advantage for HCC patients. Nonthermal ablation will lead to a new wave with its unique advantage of antitumor recurrence and metastasis.

AmAtg2B-Mediated Lipophagy Regulates Lipolysis of Pupae in Apis mellifera.

Lipophagy plays an important role in regulating lipid metabolism in mammals. The exact function of autophagy-related protein 2 (Atg2) has been investigated in mammals, but research on the existence and functions of Atg2 in Apis mellifera (AmAtg2) is still limited. Here, autophagy occurred in honeybee pupae, which targeted lipid droplets (LDs) in fat body, namely lipophagy, which was verified by co-localization of LDs with microtubule-associated protein 1A/1B light chain 3 beta (LC3). Moreover, AmAtg2 homolog B (AmAtg2B) was expressed specifically in pupal fat body, which indicated that AmAtg2B might have special function in fat body. Further, AmAtg2B antibody neutralization and AmAtg2B knock-down were undertaken to verify the functions in pupae. Results showed that low expression of AmAtg2B at the protein and transcriptional levels led to lipophagy inhibition, which down-regulated the expression levels of proteins and genes related to lipolysis. Altogether, results in this study systematically revealed that AmAtg2B interfered with lipophagy and then caused abnormal lipolysis in the pupal stage.

Multi-faceted role of pyroptosis mediated by inflammasome in liver fibrosis.

Liver fibrosis is a reversible pathological overreaction during the self-repair of liver injuries, and it is the common period of chronic liver diseases induced by different pathogenesis progress into cirrhosis and even hepatocellular carcinoma. Pyroptosis, a novel form of programmed cell death, is reported to take part in the pathogenesis and progression of acute or chronic liver diseases and liver fibrosis. Caspase-1 dependent canonical pathway and caspase-4/-5/-11 mediated noncanonical pathway are the two signalling pathways to induce pyroptosis. The activation of inflammasomes under the stimulation of pathogenic microorganisms and danger signals can initiate the pyroptotic pathway and release large amounts of proinflammatory and profibrotic cytokines. This article comprehensively summarizes recent researches focused on the mechanism of pyroptosis and its role in major hepatic cells, which can provide potential therapeutic strategies for liver fibrosis.

Circular RNA circ_GLIS2 suppresses hepatocellular carcinoma growth and metastasis.

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is one of the leading causes of tumour-related death. Here, we investigated the molecular mechanism of HCC by studying the function of circ_GLIS2. METHODS: Human HCC specimens and cell lines were used. Sanger sequencing, actinomycin D and RNase R treatment were performed to validate circular RNA features of circ_GLIS2. qRT-PCR, western blotting, immunostaining, and IHC were employed to examine levels of circ_GLIS2, GLIS2 mRNA, and EMT-related markers. CCK-8, colony formation, flow cytometry, wound healing assay, and transwell assays were performed to evaluate cancer cell proliferation, apoptosis, migration, and invasion. RIP and RNA pull-down assay were used to validate EIF4A3/GLIS2 mRNA interaction. MSP was performed to measure the methylation status of GLIS2 promoter. Nude mouse xenograft model was used to examine tumour growth and metastasis in vivo. RESULTS: Circ_GLIS2 and linear GLIS2 mRNA were reduced in human HCC tissues and cells. Their low levels correlated with a poor survival rate of HCC patients. Overexpression of circ_GLIS2 and GLIS2 suppressed HCC cell proliferation, migration, and invasion but promoted cell apoptosis. GLIS2 promoter region was hypermethylated in HCC cells. EIF4A3 was directly bound with GLIS2 mRNA and promoted circ_GLIS2/GLIS2 expression. Moreover, overexpression of circ_GLIS2 restrained HCC tumour growth and metastasis in vivo. CONCLUSION: Circ_GLIS2 suppresses HCC growth and metastasis by inhibiting cell proliferation, migration, and invasion, but promoting cell apoptosis. These findings provide molecular insights into the mechanism of HCC and indicate that circ_GLIS2 could serve as a diagnosis marker or therapeutic target for HCC.

Hyperbaric Oxygen Preconditioning Protects Against Cerebral Ischemia/Reperfusion Injury by Inhibiting Mitochondrial Apoptosis and Energy Metabolism Disturbance.

Hyperbaric oxygen (HBO) therapy is considered a safe and feasible method that to provide neuroprotection against ischemic stroke. However, the therapy mechanisms of HBO have not been fully elucidated. We hypothesized that the mechanism underlying the protective effect of HBO preconditioning (HBO-PC) against cerebral ischemia/reperfusion injury was related to inhibition of mitochondrial apoptosis and energy metabolism disorder. To test this hypothesis, an ischemic stroke model was established by middle cerebral artery occlusion (MCAO) in rats. HBO-PC involved five consecutive days of pretreatment before MCAO. In additional experiments, X chromosome-linked inhibitor of apoptosis protein (XIAP) and second mitochondria-derived activator of caspases (SMAC) shRNA and NC plasmids were intraventricularly injected into rat brains after MCAO (2 h). After 24 h, all rats underwent motor function evaluation, which was assessed by modified Garcia scores. TTC staining for the cerebral infarct and cerebral edema, and TUNEL staining for cell apoptosis, were also analyzed. Reactive oxygen species and antioxidative enzymes in rat brains were detected, as well as mitochondrial complex enzyme activities, ATP levels, and Na+/K+ ATPase activity. Western blot was used to detect apoptotic proteins including Bcl-2, Bax, caspase-3, caspase-9, cyc-c, XIAP, and SMAC. HBO-PC remarkably reduced the infarct volume and improved neurological deficits. Furthermore, HBO-PC alleviated oxidative stress and regulated the expression of apoptosis-related proteins. Moreover, HBO-PC inhibited the decrease in ATP levels, mitochondrial complex enzyme activities, and Na+/K+ ATPase activity to maintain stable energy metabolism. XIAP knockdown weakened the protective effect of HBO, whereas SMAC knockdown strengthened its protective effect. The effects of HBO-PC can be attributed to inhibition of ischemia/hypoxia-induced mitochondrial apoptosis and energy metabolism disturbance. The action of HBO-PC is related to the XIAP and SMAC signaling pathways.

The Phenotypic and Genetic Spectrum of Paroxysmal Kinesigenic Dyskinesia in China.

BACKGROUND: Paroxysmal kinesigenic dyskinesia is a spectrum of involuntary dyskinetic disorders with high clinical and genetic heterogeneity. Mutations in proline-rich transmembrane protein 2 have been identified as the major pathogenic factor. OBJECTIVES: We analyzed 600 paroxysmal kinesigenic dyskinesia patients nationwide who were identified by the China Paroxysmal Dyskinesia Collaborative Group to summarize the clinical phenotypes and genetic features of paroxysmal kinesigenic dyskinesia in China and to provide new thoughts on diagnosis and therapy. METHODS: The China Paroxysmal Dyskinesia Collaborative Group was composed of departments of neurology from 22 hospitals. Clinical manifestations and proline-rich transmembrane protein 2 screening results were recorded using unified paroxysmal kinesigenic dyskinesia registration forms. Genotype-phenotype correlation analyses were conducted in patients with and without proline-rich transmembrane protein 2 mutations. High-knee exercises were applied in partial patients as a new diagnostic test to induce attacks. RESULTS: Kinesigenic triggers, male predilection, dystonic attacks, aura, complicated forms of paroxysmal kinesigenic dyskinesia, clustering in patients with family history, and dramatic responses to antiepileptic treatment were the prominent features in this multicenter study. Clinical analysis showed that proline-rich transmembrane protein 2 mutation carriers were prone to present at a younger age and have longer attack duration, bilateral limb involvement, choreic attacks, a complicated form of paroxysmal kinesigenic dyskinesia, family history, and more forms of dyskinesia. The new high-knee-exercise test efficiently induced attacks and could assist in diagnosis. CONCLUSIONS: We propose recommendations regarding diagnostic criteria for paroxysmal kinesigenic dyskinesia based on this large clinical study of paroxysmal kinesigenic dyskinesia. The findings offered some new insights into the diagnosis and treatment of paroxysmal kinesigenic dyskinesia and might help in building standardized paroxysmal kinesigenic dyskinesia clinical evaluations and therapies. © 2020 International Parkinson and Movement Disorder Society.

Autophagy and the Metabolism of Misfolding Protein.

Autophagy is a major intracellular degradative process that delivers cytoplasmic materials to the lysosome for degradation. An increasing number of studies on the physiological and pathological roles of autophagy in a variety of autophagy knockout models and human diseases were carried out. Among them, the clearance of misfolded proteins is the important function of autophagy. Impairment at different steps of the autophagy system, such as the ubiquitin-proteasome and the autophagy-lysosome pathways, may result in the accumulation of misfolded proteins in insoluble aggregates. Abnormal accumulation of misfolded proteins in cells can lead to a variety of human diseases. Here, we review the major advances in autophagy and the metabolism of misfolding protein in human diseases. Current studies about the promising therapeutic strategy in autophagy-modulating are also summarized.

Clinical characteristics of impulse control and related disorders in Chinese Parkinson's disease patients.

BACKGROUND: Impulse control and related disorders (ICRDs) are clinically complications in Parkinson's disease (PD). However, the clinical characteristics of ICRDs in Chinese PD patients were rarely reported. We aimed to explore the prevalence and the clinical profile of ICRDs in Chinese patients with PD. METHODS: 142 Chinese PD patients were consecutively enrolled. The symptoms of ICRDs were assessed with the Questionnaire for Impulsive-Compulsive Disorders. The clinical characteristics of patients with ICRDs and without ICRDs were compared. RESULTS: ICRDs were present in 31% of our patients. The most common ICRDs were compulsive medication use (11.3%) and punding (9.2%); the least frequent were walkabout (1.4%). Variables independently associated with ICRDs were earlier onset of the disease (≤55 years), severe cognitive impairment (MMSE 10-20), the dose of dopamine agonist (>1 mg/d) and dyskinesia. CONCLUSIONS: ICRDs was commonly found in Chinese PD patients. Earlier onset of the disease, the dose of dopamine agonist, severe cognitive impairment and dyskinesia are independent factors associated with ICRDs. Our results will be benefit for clinicians to assess the risk of developing ICRDs before delivering dopaminergic medication.

STEMI could be the primary presentation of acute aortic dissection.

BACKGROUND: Stanford type A aortic dissection (TAAD) may lead to coronary artery occlusion and malfunction. However, TAAD manifesting as acute ST-segment elevation myocardial infarction (STEMI) has not been studied. In the present study, we reported 8 TAAD cases with STEMI as the primary presentation, and analyzed their clinical characteristics and outcome. METHODS: The records were reviewed for patients admitted to the large comprehensive university hospital for PCI due to STEMI from January 1, 2002 to January 1, 2017. RESULTS: The incidence of STEMI secondary to TAAD in our center was 0.51% (8/1,576). A total of 5 patients underwent urgent coronary angiography (CAG) without awareness of TAAD. Compression at the ostium of right coronary artery (RCA) was found in 2 patients, dissected flap of RCA in 1 patient, and heterogeneous filling and false lumen in RCA in 1 patient. Three of these 5 patients received surgery and survived. One patient accepted urgent RCA stenting because of cardiogenic shock and died after refusal of surgical therapy and failure of medical treatment. Another 2 patients received thrombolytic therapy died prior to CAG. Thus, the total in-hospital mortality was 37.5% (3/8). CONCLUSIONS: TAAD presenting as STEMI was a rare condition that predominantly involved RCA. A quick and correct clinical diagnosis of STEMI caused by TAAD prior to invasive procedure would be important. Urgent CAG without awareness of TAAD could provide important information for a timely diagnosis. High level of suspicion and awareness is the key to establishing the diagnosis and achieving optimal clinical outcome.

Waveguide-coupled hybrid plasmonic modulator based on graphene.

In this paper, we propose a low-transmission-loss, high-speed, graphene-based electro-absorption modulator with a hybrid plasmonic waveguide at 1.55 µm. In the proposed device, double-layer graphene is placed on top of the horizontal hybrid plasmonic waveguide to enhance the light-graphene interaction. The adjustment of the in-plane permittivity of the anisotropy graphene causes a significant modulation of the absorption at the operating bandwidth of 0.4 THz, with modulation length of 8.5 µm and modulator footprint of 1.6 µm2. A taper silicon coupler is used for waveguide coupling, and 80% coupling efficiency is achieved. In addition, the modulation potential on a smaller footprint is further shown.

Effect of nicotine on L-dopa-induced dyskinesia in animal models of Parkinson's disease: a systematic review and meta-analysis.

L-dopa-induced dyskinesias (LIDs) are abnormal involuntary movements (AIM) that develop with long-term L-dopa therapy for Parkinson's disease (PD). In this study, we used these tools to describe the efficacy of nicotine reduced LID in animal models of PD. Studies were identified by electronic searching of six online databases up to September of 2013 to identify preclinical trials involving nicotine for LID in animal model. Data were extracted for AIM compared with LID animals. Pre-specified subgroup analysis was carried out according to method of model, gender, anesthetic used, and species. Combined standardized mean difference (SMD) estimates and 95 % confidence intervals (CIs) were calculated using a random-effects model. Eleven studies involving 181 animals which described the effect of nicotine on LID were included in the meta-analysis. Nicotine was efficacious in reducing total AIM compared with control group (SMD -3.77, 95 % CI -5.30 to -2.23, P < 0.00001). Meanwhile, four studies showed certain effects of nicotine for improving the axial AIM (SMD -2.21, 95 % CI -4.17 to -0.24, P = 0.03); oral AIM and forelimb AIM were obvious improved in six studies in the nicotine group (SMD -3.00, 95 % CI -4.55 to -1.44, P = 0.0002; SMD -2.52, 95 % CI -3.52 to -1.53, P < 0.00001, respectively). We conclude that nicotine appears to have efficacy in animal models of LID. Large randomized clinical trials testing the effect of nicotine in PD patients with LID are warranted.

The association between the LRRK2 G2385R variant and the risk of Parkinson's disease: a meta-analysis based on 23 case-control studies.

Clinical diagnosis of Parkinson's disease (PD) is essential but misdiagnosis of PD-like diseases is quite common. LRRK2 G2385R variants have been extensively examined for the association to the risk of Parkinson's disease. However, results from different studies are inconsistent. The purpose of this meta-analysis was to assess the association between the LRRK2 G2385R variants and the risk of PD. A systematic literature search was performed for 6 databases up to January of 2014 to identify case-control studies involving LRRK2 G2385R variants and the risk of PD. A total of 12,915 cases and 12,451 controls in 23 case-control studies were included in this meta-analysis. The results indicated that the variant A allele carriers (GA + AA) increased risk of PD when compared with the homozygote GG (GA + AA vs. GG: OR = 2.4, 95 % CI = 1.97 to 2.92, P < 0.00001). In the subgroup analysis by ethnicity, increased risks were identified among Chinese (OR = 2.69, 95 % CI = 2.1-3.45, P < 0.00001) as well as in non-Chinese (OR = 2.17, 95 % CI 1.75-2.69, P < 0.00001). In the subgroup analysis by age of onset, significant associations were found in both later-onset PD (LOPD) and early-onset PD (EOPD) cases. And there was no significant difference of the allele frequency between patients with LOPD and EOPD (OR = 1.18, 95 % CI = 0.77-1.80, P = 0.45). Our results suggest that the LRRK2 G2385R variants contribute to the susceptibility of PD especially in Chinese PD. Meanwhile, it is possible that age is not the risk factor to facilitate G2385R gene mutation.

Bilateral pulmonary artery aneurysms, coronary artery aneurysm, and ventricular pseudoaneurysm in Behçet disease.

Massive hemoptysis in Behçet disease (BD) is rare but often fatal. This report presents a 28-year-old man with recurrent massive hemoptysis. He was diagnosed with bilateral multiple pulmonary artery aneurysms (PAAs), coronary artery aneurysm, and ventricular pseudoaneurysm from BD. The patient underwent emergency right lower lobectomy with no obvious complications. No hemoptysis recurred during an 18-month follow-up. This report also reviews the occurrence of PAAs in BD, with an emphasis on the treatment approaches.

Direct Fuzzy Adaptive Regulation for High-Order Delayed Systems: A Lyapunov-Razumikhin Function Method.

A slow time-delay assumption restricts the application of control approaches for numerous systems which are constantly affected by multiple uncertainties, including parameters, control coefficients, and the asymmetric dead-zone input. This work presents a new adaptive method for a class of high-order nonlinear delayed systems by removing the so-called slow time-delay assumption and multiple uncertainties. Remarkably, with a novel Lyapunov-Razumikhin (L-R) function and a direct fuzzy adaptive regulation scheme, a memoryless adaptive feedback controller is skillfully constructed to guarantee that the output tracks the given reference signal while keeping the boundedness of all closed-system signals. Finally, the presented scheme is applied to control a single-link robot system.

Prediction of miRNA-disease associations based on strengthened hypergraph convolutional autoencoder.

Most existing graph neural network-based methods for predicting miRNA-disease associations rely on initial association matrices to pass messages, but the sparsity of these matrices greatly limits performance. To address this issue and predict potential associations between miRNAs and diseases, we propose a method called strengthened hypergraph convolutional autoencoder (SHGAE). SHGAE leverages multiple layers of strengthened hypergraph neural networks (SHGNN) to obtain robust node embeddings. Within SHGNN, we design a strengthened hypergraph convolutional network module (SHGCN) that enhances original graph associations and reduces matrix sparsity. Additionally, SHGCN expands node receptive fields by utilizing hyperedge features as intermediaries to obtain high-order neighbor embeddings. To improve performance, we also incorporate attention-based fusion of self-embeddings and SHGCN embeddings. SHGAE predicts potential miRNA-disease associations using a multilayer perceptron as the decoder. Across multiple metrics, SHGAE outperforms other state-of-the-art methods in five-fold cross-validation. Furthermore, we evaluate SHGAE on colon and lung neoplasms cases to demonstrate its ability to predict potential associations. Notably, SHGAE also performs well in the analysis of gastric neoplasms without miRNA associations.

Transcriptional regulation of Glis2 in hepatic fibrosis.

The role of Gli-similar 2 (Glis2) in hepatic fibrosis (HF) is controversial. In this study, we focused on the functional and molecular mechanisms involved in the Glis2-mediated activation of hepatic stellate cells (HSCs)-a milestone event leading to HF. The expression levels of Glis2 mRNA and protein were significantly decreased in the liver tissues of patients with severe HF and in mouse fibrotic liver tissues as well as HSCs activated by TGFß1. Functional studies indicated that upregulated Glis2 significantly inhibited HSC activation and alleviated BDL-induced HF in mice. Downregulation of Glis2 was found to correlate significantly with DNA methylation of the Glis2 promoter mediated by methyltransferase 1 (DNMT1), which restricted the binding of hepatic nuclear factor 1-α (HNF1-α), a liver-specific transcription factor, to Glis2 promoters. In addition, the enrichment of DNMT1 in the Glis2 promoter region was mediated by metastasis-associated lung adenocarcinoma transcriptor-1 (MALAT1) lncRNA, leading to transcriptional silencing of Glis2 and activation of HSCs. In conclusion, our findings reveal that the upregulation of Glis2 can maintain the resting state of HSCs. The decreased expression of Glis2 under pathological conditions may lead to the occurrence and development of HF with the expression silencing of DNA methylation mediated by MALAT1 and DNMT1.