NR4A1 mediates NK-cell dysfunction in hepatocellular carcinoma via the IFN-γ/p-STAT1/IRF1 pathway.

Hepatocellular carcinoma (HCC) is one of the most fatal tumours worldwide and has a high recurrence rate. Nevertheless, the mechanism of HCC genesis remains partly unexplored, while the efficiency of HCC treatments remains limited. The present study analysed the expression of nuclear receptor subfamily 4 group A member 1 (NR4A1) in tumour-infiltrating natural killer (NK) cells derived from both human patients with HCC and tumour-bearing mouse models, as well as the features of NR4A1high and NR4A1low NK cells. In addition, knockout of NR4A1 by CRISPR/Cas9 and adoptive transfer experiments were applied to verify the function of NR4A1 in both tumour-infiltrating NK cells and anti-PD-1 therapy. The present study found that NR4A1 was significantly highly expressed in tumour-infiltrating NK cells, which mediated the dysfunction of tumour-infiltrating NK cells by regulating the IFN-γ/p-STAT1/IRF1 signalling pathway. Knockout of NR4A1 in NK cells not only restored the antitumour function of NK cells but also enhanced the efficacy of anti-PD-1 therapy. The present findings suggest a regulatory role of NR4A1 in the immune progress of NK cells against HCC, which may provide a new direction for immunotherapies of HCC.

Erratum: PTPROt aggravates inflammation by enhancing NF-κB activation in liver macrophages during nonalcoholic steatohepatitis: Erratum.

[This corrects the article DOI: 10.7150/thno.42658.].

The cancer-testis lncRNA lnc-CTHCC promotes hepatocellular carcinogenesis by binding hnRNP K and activating YAP1 transcription.

Cancer-testis (CT) genes participate in the initiation and progression of cancer, but the role of CT-associated long non-coding RNAs (CT-lncRNAs) in hepatocellular carcinoma (HCC) is still elusive. Here, we discovered a conserved CT-lncRNA, named lnc-CTHCC, which was highly expressed in the testes and HCC. A lnc-CTHCC-knockout (KO) mouse model further confirmed that the global loss of lnc-CTHCC inhibited the occurrence and development of HCC. In vitro and in vivo assays also showed that lnc-CTHCC promoted HCC growth and metastasis. Mechanistically, lnc-CTHCC bound to heterogeneous nuclear ribonucleoprotein K (hnRNP K), which was recruited to the YAP1 promoter for its activation. Additionally, the N6-methyladenosine (m6A) modification was mediated by N6-adenosine-methyltransferase 70-kDa subunit (METTL3) and recognized by insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1)/IGF2BP3, which maintained lnc-CTHCC stability and increased its expression in HCC. Together, our results show that lnc-CTHCC directly binds to hnRNP K and promotes hepatocellular carcinogenesis and progression by activating YAP1 transcription, suggesting that lnc-CTHCC is a potential biomarker and therapeutic target of HCC.

A pan-cancer analysis of the prognostic and immunological roles of matrix metalloprotease-1 (MMP1) in human tumors.

Objective: Cancer remains the leading killer of human health worldwide. It has been shown that matrix metalloproteinase-1(MMP1) is related to poor prognosis in cancers such as BRCA, CESC and COAD. However, systematic pan-cancer analysis about the prognostic and immunological roles of MMP1 has not been explored. Here, the purpose of this study was to investigate the prognostic and immunological roles of MMP1 in pan-cancer and confirm cancer-promoting effect in pancreatic cancer. Methods: In our study, bioinformatics were first used to analyze data from multiple databases. Then, several bioinformatics tools were utilized to investigate the role of MMP1 in 33 tumor types. Finally, molecular biology experiments were carried out to prove the cancer-promoting effect of MMP1 in pancreatic cancer. Results: MMP1 expression was higher in tumor tissues than in control tissues in most tumor types. High expression of MMP1 was associated with poor overall survival (OS) and disease-free survival (DFS) in some tumor types. Further analysis of MMP1 gene mutation data showed that MMP1 mutations significantly influenced the prognosis of STAD. In addition, MMP1 expression was closely related to cancer-associated fibroblast (CAFs) infiltration in a variety of cancers and played an important role on immune infiltration score, tumor mutational burden (TMB) and microsatellite instability (MSI). Gene Ontology enrichment analysis indicated that these 20 genes were mainly related to extracellular structure organization/extracellular matrix organization/extracellular matrix disassembly/collagen metabolic process in the enriched biological processes. Finally, molecular biology experiments confirmed the cancer-promoting effect of MMP1 in pancreatic cancer. Conclusions: Our pan-cancer analysis comprehensively proved that MMP1 expression is related with clinical prognosis and tumor immune infiltration, and MMP1 can become a prognostic and immunological biomarker.

Inter-stimulus phase coherence in steady-state somatosensory evoked potentials and its application in improving the performance of single-channel MI-BCI.

Objective. With the development of clinical applications of motor imagery-based brain-computer interfaces (MI-BCIs), a single-channel MI-BCI system that can be easily assembled is an attractive goal. However, due to the low quality of the spectral power features in the traditional MI-BCI paradigm, the recognition performance of current single-channel systems is far lower than that of multi-channel systems, impeding their use in clinical applications.Approach.In this study, the subjects' right and left hands were stimulated simultaneously at different frequencies to induce steady-state somatosensory evoked potentials (SSSEP). Subjects then performed motor imagery (MI) tasks. A new electroencephalography (EEG) index, inter-stimulus phase coherence (ISPC), was built to measure phase desynchronization of SSSEP caused by MI. Then, ISPC is introduced as a feature into left-hand and right-hand MI recognition.Main results.ISPC analysis found that left-handed MI can cause a significant decrease in phase synchronization in contralateral sensorimotor SSSEP, while right-handed MI has little effect on it, and vice versa. Combining ISPC features with traditional spectral power features, the single-channel left-hand versus right-hand MI recognition accuracy reaches 81.0%, which is much higher than that observed with traditional MI paradigms (about 60%).Significance.This work shows that the hybrid MI-SSSEP paradigm can provide more sensitive EEG features to decode motor intentions, demonstrating its potential for clinical applications.

Construction of circRNA-Based ceRNA Network to Reveal the Role of circRNAs in the Progression and Prognosis of Hepatocellular Carcinoma.

BACKGROUND: Circular RNAs (circRNAs) are now under hot discussion as novel promising biomarkers for patients with hepatocellular carcinoma (HCC). The purpose of our study is to identify several competing endogenous RNA (ceRNA) networks related to the prognosis and progression of HCC and to further investigate the mechanism of their influence on tumor progression. METHODS: First, we obtained gene expression data related to liver cancer from The Cancer Genome Atlas (TCGA) database (http://www.portal.gdc.cancer.gov/), including microRNA (miRNA) sequence, RNA sequence, and clinical information. A co-expression network was constructed through the Weighted Correlation Network Analysis (WGCNA) software package in R software. The differentially expressed messenger RNAs (DEmRNAs) in the key module were analyzed with the Database for Annotation Visualization and Integrated Discovery (DAVID) (https://david.ncifcrf.gov/summary.jsp) to perform functional enrichment analysis including Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO). The data of miRNA expression and clinical information downloaded from TCGA were utilized for survival analysis to detach the prognostic value of the DEmiRNAs of the key module. RESULTS: The 201 differentially expressed miRNAs (DEmiRNAs) and 3,783 DEmRNAs were preliminarily identified through differential expression analysis. The co-expression networks of DEmiRNAs and DEmRNAs were constructed with WGCNA. Further analysis confirmed four miRNAs in the most significant module (blue module) were associated with the overall survival (OS) of patients with liver cancer, including hsa-miR-92b-3p, hsa-miR-122-3p, hsa-miR-139-5p, and hsa-miR-7850-5p. DAVID was used for functional enrichment analysis of 286 co-expressed mRNAs. The GO analysis results showed that the top enriched GO terms were oxidation-reduction process, extracellular exosome, and iron ion binding. In KEGG pathway analysis, the top three enriched terms included metabolic pathways, fatty acid degradation, and valine, leucine, and isoleucine degradation. In addition, we intersected the miRNA-mRNA interaction prediction results with the differentially expressed and prognostic mRNAs. We found that hsa-miR-92b-3p can be related to CPEB3 and ACADL. By overlapping the data of predicted circRNAs by circBank and differentially expressed circRNAs of GSE94508, we screened has_circ_0077210 as the upstream regulatory molecule of hsa-miR-92b-3p. Hsa_circ_0077210/hsa-miR-92b-3p/cytoplasmic polyadenylation element binding protein-3 (CPEB3) and acyl-Coenzyme A dehydrogenase, long chain (ACADL) were validated in HCC tissue. CONCLUSION: Our research provides a mechanistic elucidation of the unknown ceRNA regulatory network in HCC. Hsa_circ_0077210 might serve a momentous therapeutic role to restrain the occurrence and development of HCC.

Reducing False Triggering Caused by Irrelevant Mental Activities in Brain-Computer Interface Based on Motor Imagery.

In recent years, the brain-computer interface (BCI) based on motor imagery (MI) has been considered as a potential post-stroke rehabilitation technology. However, the recognition of MI relies on the event-related desynchronization (ERD) feature, which has poor task specificity. Further, there is the problem of false triggering (irrelevant mental activities recognized as the MI of the target limb). In this paper, we discuss the feasibility of reducing the false triggering rate using a novel paradigm, in which the steady-state somatosensory evoked potential (SSSEP) is combined with the MI (MI-SSSEP). Data from the target (right hand MI) and nontarget task (rest) were used to establish the recognition model, and three kinds of interference tasks were used to test the false triggering performance. In the MI-SSSEP paradigm, ERD and SSSEP features modulated by MI could be used for recognition, while in the MI paradigm, only ERD features could be used. The results showed that the false triggering rate of interference tasks with SSSEP features was reduced to 29.3%, which was far lower than the 55.5% seen under the MI paradigm with ERD features. Moreover, in the MI-SSSEP paradigm, the recognition rate of the target and nontarget task was also significantly improved. Further analysis showed that the specificity of SSSEP was significantly higher than that of ERD (p < 0.05), but the sensitivity was not significantly different. These results indicated that SSSEP modulated by MI could more specifically decode the target task MI, and thereby may have potential in achieving more accurate rehabilitation training.

A radiomics-based model on non-contrast CT for predicting cirrhosis: make the most of image data.

BACKGROUND: To establish and validate a radiomics-based model for predicting liver cirrhosis in patients with hepatitis B virus (HBV) by using non-contrast computed tomography (CT). METHODS: This retrospective study developed a radiomics-based model in a training cohort of 144 HBV-infected patients. Radiomic features were extracted from abdominal non-contrast CT scans. Features selection was performed with the least absolute shrinkage and operator (LASSO) method based on highly reproducible features. Support vector machine (SVM) was adopted to build a radiomics signature. Multivariate logistic regression analysis was used to establish a radiomics-based nomogram that integrated radiomics signature and other independent clinical predictors. Performance of models was evaluated through discrimination ability, calibration and clinical benefits. An internal validation was conducted in 150 consecutive patients. RESULTS: The radiomics signature comprised 25 cirrhosis-related features and showed significant differences between cirrhosis and non-cirrhosis cohorts (P < 0.001). A radiomics-based nomogram that integrates radiomics signature, alanine transaminase, aspartate aminotransferase, globulin and international normalized ratio showed great calibration and discrimination ability in the training cohort (area under the curve [AUC]: 0.915) and the validation cohort (AUC: 0.872). Decision curve analysis confirmed the most clinical benefits can be provided by the nomogram compared with other methods. CONCLUSIONS: Our developed radiomics-based nomogram can successfully diagnose the status of cirrhosis in HBV-infected patients, that may help clinical decision-making.

PTPROt aggravates inflammation by enhancing NF-κB activation in liver macrophages during nonalcoholic steatohepatitis.

Rationale: Inflammation plays a crucial role in the progression of nonalcoholic steatohepatitis (NASH). Protein tyrosine phosphatase receptor type O truncated isoform (PTPROt) is an integral membrane protein that has been identified in osteoclasts, macrophages, and B lymphocytes. However, its relationship between inflammation and NASH is largely unknown. Herein, we aimed to study the function of PTPROt in NASH progression. Methods: We established a NASH mouse model in wild-type (WT), PTPRO knockout mice by western diet (WD) and methionine-choline-deficient diet (MCD). In addition, MCD-induced NASH model was established in BMT mice. Moreover, we determined the expression of PTPROt in liver macrophages in human subjects without steatosis, with simple steatosis, and with NASH to confirm the relationship between PTPROt and NASH. In vitro assays were also performed to study the molecular role of PTPROt in NASH progression. Results: Human samples and animal model results illustrated that PTPROt is increased in liver macrophages during NASH progression and is positively correlated with the degree of NASH. Our animal model also showed that PTPROt in liver macrophages can enhance the activation of the NF-κB signaling pathway, which induces the transcription of genes involved in the inflammatory response. Moreover, PTPROt promotes the transcription of pro-oxidant genes and inhibits antioxidant and protective genes via increased activation of the NF-κB signaling pathway, thereby causing an increased level of reactive oxygen species (ROS) and damaged mitochondria. This triggers the NLRP3-IL1ß axis and causes a heightened inflammatory response. Notably, PTPROt partially limits inflammation and ROS production by promoting mitophagy, which participates in a negative feedback loop in this model. Conclusions: Our data strongly indicate that PTPROt plays a dual role in inflammation via the NF-κB signaling pathway in liver macrophages during NASH. Further studies are required to explore therapeutic strategies and prevention of this common liver disease through PTPROt.

VersicanV1 promotes proliferation and metastasis of hepatocellular carcinoma through the activation of EGFR-PI3K-AKT pathway.

Versican has been reported to participate in carcinogenesis in several malignant tumors. However, the accurate role of VersicanV1, a predominant isoform of Versican in liver, remains an enigma in hepatocellular carcinoma (HCC). The expression of VersicanV1 in HCC tissues and adjacent tissues was detected by Reverse Transcription-Polymerase Chain Reaction (RT-PCR), Western Blot (WB) and inmumohistochemistry (IHC). Gain and loss of function assays were performed to examine the role of VersicanV1 in proliferation and metastasis of HCC. Measurement of oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) in vitro and PET-CT (positron emission tomography/computed tomography) analysis in vivo were applied to evaluate the effects of VersicanV1 on glycolysis. RNA sequencing, Co-IP (Co-immunoprecipitation) and MS (mass spectrometry) were utilized to investigate the molecular mechanisms. Our current study reveals that VersicanV1, regulated by direct interaction with Linc01225, is significantly upregulated in HCC tissues and correlates with poor prognosis. Both in vitro and in vivo experiments show that knockdown of VersicanV1 in HCC cells attenuates cancer cells malignancy. Further studies identify the positive role of VersicanV1 in aerobic glycolysis. Mechanistic investigation discovers the activation of EGFR-PI3K-AKT pathway in HCC cells expressing high VersicanV1. Moreover, EGF-like motif is indispensable for VersicanV1 to promote Warburg effect of HCC cells and subsequently, proliferation, invasion, and metastasis ability via activation of EGFR-PI3K-AKT axis. In sum, our research highlights a novel role of VersicanV1 in the progression of HCC, suggesting that VersicanV1 is an indicator for prognosis and a potential therapeutic target of HCC.

Correction: VersicanV1 promotes proliferation and metastasis of hepatocellular carcinoma through the activation of EGFR-PI3K-AKT pathway.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Computational Prediction of Protein Epsilon Lysine Acetylation Sites Based on a Feature Selection Method.

AIM AND OBJECTIVE: Lysine acetylation, as one type of post-translational modifications (PTM), plays key roles in cellular regulations and can be involved in a variety of human diseases. However, it is often high-cost and time-consuming to use traditional experimental approaches to identify the lysine acetylation sites. Therefore, effective computational methods should be developed to predict the acetylation sites. In this study, we developed a position-specific method for epsilon lysine acetylation site prediction. MATERIAL AND METHODS: Sequences of acetylated proteins were retrieved from the UniProt database. Various kinds of features such as position specific scoring matrix (PSSM), amino acid factors (AAF), and disorders were incorporated. A feature selection method based on mRMR (Maximum Relevance Minimum Redundancy) and IFS (Incremental Feature Selection) was employed. RESULTS: Finally, 319 optimal features were selected from total 541 features. Using the 319 optimal features to encode peptides, a predictor was constructed based on dagging. As a result, an accuracy of 69.56% with MCC of 0.2792 was achieved. We analyzed the optimal features, which suggested some important factors determining the lysine acetylation sites. CONCLUSION: We developed a position-specific method for epsilon lysine acetylation site prediction. A set of optimal features was selected. Analysis of the optimal features provided insights into the mechanism of lysine acetylation sites, providing guidance of experimental validation.

Insight into selective removal of copper from high-concentration nickel solutions with XPS and DFT: New technique to prepare 5N-nickel with chelating resin.

An efficient and profitable separation process was proposed to prepare 5N (the purity of the metal solution reaches 99.999%) high-purity nickel from 3N nickel-solutions using Purolite S984. The adsorption performance of this superior resin, especially its selectivity for metal ions, was explored quantitatively. The maximum adsorption capacity for copper was 2.286mmol/g calculated by the Langmuir model, which was twice as large as that for nickel. In the binary systems, the adsorption capacity for nickel was decreased by 45%, indicating direct competition for the active sites. The infinite separation factor for copper versus nickel exceeded 300, revealing the feasibility of preparing 5N-level high-purity nickel solutions, which was further verified using the 800BV (bed volume) effluent in the column dynamic process. According to the cost-benefit analysis, purification contributed to a profit of approximately 60,000USD per cycle, and the investment return period was less than 1/3years. Density functional theory analysis confirmed that four nitrogen atoms would be involved in the coordination complex and thus a structure involving two five-membered rings could be achieved. The X-ray photoelectron spectra confirmed the involvement of nitrogen atoms, implying a coordination ratio of approximately 1:1.

Integrated adsorptive technique for efficient recovery of m-cresol and m-toluidine from actual acidic and salty wastewater.

An integrated adsorptive technique combining an m-cresol adsorption unit, an acid retardation unit and an m-toluidine adsorption unit in sequence was designed to recover m-cresol and m-toluidine from highly acidic and salty m-cresol manufacturing wastewater. In the first column packed with hypercrosslinked polymeric resin (NDA-99), most m-cresol was captured through π-π and hydrogen-bonding interactions as well as the salting-out effect, while m-toluidine was not absorbed due to protonation. To separate acid from salt, an acid retardation unit was introduced successively to adsorb sulfuric acid by strong base anion exchange resin (201×7). After the acid retardation unit and mild neutralization reaction, the last column filled with NDA-99 was applied to trap neutral m-toluidine from the salty effluent. Moreover, the eluent of the acid retardation unit was utilized as the regenerant to recover m-toluidine, and the recycled high-acidity and low-salinity solution of m-toluidine was directly used to produce m-cresol as the raw material. Therefore, the proposed method not only efficiently recycled m-cresol and m-toluidine, but also reduced the consumption of alkali dramatically (saving 0.1628t/t wastewater). These findings will inspire design of integrated adsorptive techniques for treating complex organic wastewater with high efficiency and low cost.