Establishment of a selectable marker recycling system for iterative gene editing in Fusarium fujikuroi.

Gibberellic acid (GA3) is a vital plant growth hormone widely used in agriculture. Currently, GA3 production relies on liquid fermentation by the filamentous fungus Fusarium fujikuroi. However, the lack of an effective selection marker recycling system hampers the application of metabolic engineering technology in F. fujikuroi, as multiple-gene editing and positive-strain screening still rely on a limited number of antibiotics. In this study, we developed a strategy using pyr4-blaster and CRISPR/Cas9 tools for recycling orotidine-5'-phosphate decarboxylase (Pyr4) selection markers. We demonstrated the effectiveness of this method for iterative gene integration and large gene-cluster deletion. We also successfully improved GA3 titers by overexpressing geranylgeranyl pyrophosphate synthase and truncated 3-hydroxy-3-methyl glutaryl coenzyme A reductase, which rewired the GA3 biosynthesis pathway. These results highlight the efficiency of our established system in recycling selection markers during iterative gene editing events. Moreover, the selection marker recycling system lays the foundation for further research on metabolic engineering for GA3 industrial production.

Improving the productivity of gibberellic acid by combining small-molecule compounds-based targeting technology and transcriptomics analysis in Fusarium fujikuroi.

Gibberellic acid (GA3), produced industrially by Fusarium fujikuroi, stands as a crucial plant growth regulator extensively employed in the agriculture filed while limited understanding of the global metabolic network hinders researchers from conducting rapid targeted modifications. In this study, a small-molecule compounds-based targeting technology was developed to increase GA3 production. Firstly, various small molecules were used to target key nodes of different pathways and the result displayed that supplement of terbinafine improved significantly GA3 accumulation, which reached to 1.08 g/L. Subsequently, lipid and squalene biosynthesis pathway were identified as the key pathways influencing GA3 biosynthesis by transcriptomic analysis. Thus, the strategies including in vivo metabolic engineering modification and in vitro supplementation of lipid substrates were adopted, both contributed to an enhanced GA3 yield. Finally, the engineered strain demonstrated the ability to achieve a GA3 yield of 3.24 g/L in 5 L bioreactor when utilizing WCO as carbon source and feed.

Improving Gibberellin GA3 Production with the Construction of a Genome-Scale Metabolic Model of Fusarium fujikuroi.

Liquid fermentation is the primary method for GA3 production usingFusarium fujikuroi. However, production capacity is limited due to unknown metabolic pathways. To address this, we constructed a genome-scale metabolic model (iCY1235) with 1753 reactions, 1979 metabolites, and 1235 genes to understand the GA3 regulation mechanisms. The model was validated by analyzing growth rates under different glucose uptake rates and identifying essential genes. We used the model to optimize fermentation conditions, including carbon sources and dissolved oxygen. Through the OptForce algorithm, we identified 20 reactions as targets. Overexpressing FFUJ_02053 and FFUJ_14337 resulted in a 37.5 and 75% increase in GA3 titers, respectively. These targets enhance carbon flux toward GA3 production. Our model holds promise for guiding the metabolic engineering of F. fujikuroi to achieve targeted overproduction. In summary, our study utilizes the iCY1235 model to understand GA3 regulation, optimize fermentation conditions, and identify specific targets for enhancing GA3 production through metabolic engineering.

CCLHunter: An efficient toolkit for cancer cell line authentication.

Cancer cell lines are essential in cancer research, yet accurate authentication of these cell lines can be challenging, particularly for consanguineous cell lines with close genetic similarities. We introduce a new Cancer Cell Line Hunter (CCLHunter) method to tackle this challenge. This approach utilizes the information of single nucleotide polymorphisms, expression profiles, and kindred topology to authenticate 1389 human cancer cell lines accurately. CCLHunter can precisely and efficiently authenticate cell lines from consanguineous lineages and those derived from other tissues of the same individual. Our evaluation results indicate that CCLHunter has a complete accuracy rate of 93.27%, with an accuracy of 89.28% even for consanguineous cell lines, outperforming existing methods. Additionally, we provide convenient access to CCLHunter through standalone software and a web server at https://ngdc.cncb.ac.cn/cclhunter.

Oscillator Strengths and Cross Sections of the Valence-Shell Excitations of HBr Studied by Fast Electron Impact.

The oscillator strengths and cross sections of the valence-shell excitations of HBr were determined by fast electron scattering with an incident electron energy of 1500 eV and an energy resolution of 80 meV. The momentum transfer dependence behaviors of the generalized oscillator strengths have been used to elucidate the transition characteristics. The present results show that the strong spin-orbital interaction results in the observation of some triplet states in the (Λ, S) coupling and the constant generalized oscillator strength ratios for the pair states with the same electronic configuration and quantum number Ω, and the quantitative spin-orbit coupling coefficients of b3Π1(v = 0) and C1Π(v = 0) are determined. The optical oscillator strengths of the valence-shell excitations were obtained by extrapolating the generalized oscillator strengths to the limit of zero squared momentum transfer. The present optical oscillator strengths give an independent cross-check of the previous experimental and theoretical results, and the comparison shows that the line-saturation effect is more severe for the high Rydberg states with large intensities and narrow natural widths. The integral cross sections of the valence-shell excitations of HBr were obtained from the excitation threshold to 5000 eV by the BE-scaling method. The present oscillator strengths and cross sections supplement the fundamental molecular database of HBr and can be used for modeling in the semiconductor industry, astrophysics, and atmospheric chemistry.

Efficacy and Safety of Panax notoginseng Saponins in the Treatment of Adults With Ischemic Stroke in China: A Randomized Clinical Trial.

Importance: Preclinical and clinical studies have suggested the neuroprotective effect of Panax notoginseng saponins (Xuesaitong soft capsules). However, robust evidence in patients with ischemic stroke is lacking. Objective: To assess the efficacy and safety of Xuesaitong soft capsules in patients with ischemic stroke. Design, Setting, and Participants: This multicenter, double-blind, placebo-controlled randomized clinical trial was conducted at 67 tertiary health centers in China from July 1, 2018, to June 30, 2020. Included patients were aged 18 to 75 years with a diagnosis of ischemic stroke and a National Institutes of Health Stroke Scale score between 4 and 15. Interventions: Eligible patients were randomly assigned within 14 days after symptom onset to receive either treatment with Xuesaitong soft capsules (120 mg orally twice daily) or placebo (120 mg orally twice daily) for 3 months. Main Outcomes and Measures: The primary outcome was functional independence at 3 months, defined as a modified Rankin Scale score of 0 to 2. Results: Among 3072 eligible patients with ischemic stroke who were randomized, 2966 (96.5%) were included in the modified intention-to-treat cohort (median [IQR] age, 62 [55-68] years; 1982 male [66.8%]). The number of patients who achieved functional independence at 3 months was 1328 (89.3%) in the Xuesaitong group and 1218 (82.4%) in the control group (odds ratio, 1.95; 95% CI, 1.56-2.44; P < .001). In the safety cohort, serious adverse events occurred in 15 of 1488 patients (1.0%) in the Xuesaitong group and 16 of 1482 (1.1%) in the control group (P = .85). Conclusions and Relevance: In this randomized clinical trial, Xuesaitong soft capsules significantly increased the likelihood of functional independence at 3 months in patients with ischemic stroke, indicating that this may be a safe and effective alternative therapy to improve prognosis in this population. Trial Registration: Chinese Clinical Trial Registry Identifier: ChiCTR1800016363.

Variation characteristics of climatic potential yield and resources utilization efficiency of maize under the background of climate change in agro-pastoral transitional zone of Gansu, China.

To evaluate the effects of changes in radiation, accumulative temperature, precipitation and climate resources on climate resource utilization efficiency in the agro-pastoral transitional zone of Gansu Province, we analyzed the variations of climate potential yield loss rate, light, heat, precipitation and comprehensive utilization efficiency of climate resources in the agro-pastoral transitional zone of Gansu Province by the step-by-step correction and indexation method, with the 1971-2020 weather data from 45 meteorological sites and the maize phenology data. The results showed that solar radiation showed fluctuating downward trend at a rate of -22.03 MJ·m-2·(10 a)-1, the accumulative ≥11 ℃ temperature showed significant upward trend at a rate of 60.89 ℃·(10 a)-1, the precipitation showed slow upward trend at a rate of 2.05 mm·(10 a)-1 during the study period. The climate potential yield loss rate due to temperature and precipitation limitations was relatively high in Gannan and the northern part of Longzhong, while it was relatively low in the most areas of Longdong. Except for the central part of the study area and part of Longdong, the climate potential yield loss rate due to temperature and precipitation limitations in other regions of the study area showed decreased trend at the rate of -2.0%·(10 a)-1 and -0.6%·(10 a)-1. The low-value areas of light and heat utilization efficiency distributed in the northern and southern parts of Longzhong and part of Gannan, the low-value area of precipitation utilization efficiency distributed in Gannan, and the low value of comprehensive utilization efficiency distributed in Lanzhou and Baiyin which were 0.41 and 0.47, respectively. Longdong was the most suitable for maize planting, where the climate resources utilization efficiency of maize was highest, followed by Gannan and Longzhong. The average tendency rate of light, heat, precipitation and climate resources comprehensive utilization efficiency in the study area showed increased trend, which were 0.1%·(10 a)-1, 0.07 kg·hm-2·â„ƒ-1·d-1·(10 a)-1, 1.17 kg·hm-2·mm-1·(10 a)-1 and 0.05 ·(10 a)-1, respectively, showing a good potential to increase maize yield.

Structure optimization and mechanical study on lifting mechanism of the multifunctional car transporter.

In order to realize the multifunctional purpose, the rear column of the car transporter is replaced by a lifting mechanism which can be regarded as a four-bar mechanism. However, for the multifunctional car transporter, lifting difficulty and lifting lock occur shortly after the beginning of lifting. Dynamic analysis of the lifting mechanism is carried out, and the computational results reveal that the unreasonable structure of the lifting mechanism is the main reason for the above problems. In order to overcome lifting difficulty and lifting lock, and to improve lifting performance, a back push bar combined lifting mechanism is proposed to replace the original lifting mechanism, and dynamic analysis and finite element analysis (FEA) are carried out in both lifting mechanisms. After using the back push bar combined lifting mechanism, the numerical results show that the required hydraulic cylinder thrust is reduced to a certain degree, and the horizontal pulling force imposed on the front column by the upper platform is declined sharply; the lifting test shows that the lifting process becomes fluent and labor-saving.

Expression Profiles and Functional Analysis of Plasma Exosomal Circular RNAs in Acute Myocardial Infarction.

Acute myocardial infarction (AMI) is a common cardiovascular disease with high rates of morbidity and mortality globally. The dysregulation of circular RNAs (circRNAs) has been shown to be closely related to various pathological aspects of AMI. However, the function of exosomal circRNAs in AMI has yet to be investigated. The purpose of this study was to investigate the expression profiles of plasma exosomal circRNAs in AMI and explore their potential functionality. The expression profiles of plasma exosomal circRNAs in patients with AMI, stable coronary heart atherosclerotic disease (CAD), and healthy controls were obtained from a GEO expression dataset (GSE159657). We also analyzed bioinformatics functionality, potential pathways, and interaction networks related to the microRNAs associated with the differentially expressed circRNAs. A total of 253 exosomal circRNAs (184 up- and 69 down-regulated) and 182 exosomal circRNAs (94 up- and 88 down-regulated) were identified as being differentially expressed between the control group and the AMI and CAD patients, respectively. Compared with the CAD group, 231 different exosomal circRNAs (177 up- and 54 down-regulated) were identified in the AMI group. Functional analysis suggested that the parental genes of exosomal has_circ_0061776 were significantly enriched in the biological process of lysine degradation. Pathway interaction network analysis further indicated that exosomal has_circ_0061776 was associated with has-miR-133a, has-miR-214, has-miR-423, and has-miR-217 and may play a role in the pathogenesis of AMI through the MAPK signaling pathway. This study identified the differential expression and functionality of exosomal circRNAs in AMI and provided further understanding of the potential pathogenesis of an exosomal circRNA-related competing endogenous RNA (ceRNA) network in AMI.

Recent Development of Advanced Biotechnology in the Oleaginous Fungi for Arachidonic Acid Production.

Arachidonic acid is an essential ω-6 polyunsaturated fatty acid, which plays a significant role in cardiovascular health and neurological development, leading to its wide use in the food and pharmaceutical industries. Traditionally, ARA is obtained from deep-sea fish oil. However, this source is limited by season and is depleting the already threatened global fish stocks. With the rapid development of synthetic biology in recent years, oleaginous fungi have gradually attracted increasing attention as promising microbial sources for large-scale ARA production. Numerous advanced technologies including metabolic engineering, dynamic regulation of fermentation conditions, and multiomics analysis were successfully adapted to increase ARA synthesis. This review summarizes recent advances in the bioengineering of oleaginous fungi for ARA production. Finally, perspectives for future engineering approaches are proposed to further improve the titer yield and productivity of ARA.

Naoxintong Capsule for Secondary Prevention of Ischemic Stroke: A Multicenter, Randomized, and Placebo-Controlled Trial.

OBJECTIVE: To examine whether the combination of Naoxintong Capsule with standard care could further reduce the recurrence of ischemic stroke without increasing the risk of severe bleeding. METHODS: A total of 23 Chinese medical centers participated in this trial. Adult patients with a history of ischemic stroke were randomly assigned in a 1:1 ratio using a block design to receive either Naoxintong Capsule (1.2 g orally, twice a day) or placebo in addition to standard care. The primary endpoint was recurrence of ischemic stroke within 2 years. Secondary outcomes included myocardial infarction, death due to recurrent ischemic stroke, and all-cause mortality. The safety of drugs was monitored. Results were analyzed using the intention-to-treat principle. RESULTS: A total of 2,200 patients were enrolled from March 2015 to March 2016, of whom 143 and 158 in the Naoxintong and placebo groups were lost to follow-up, respectively. Compared with the placebo group, the recurrence rate of ischemic stroke within 2 years was significantly lower in the Naoxintong group [6.5% vs. 9.5%, hazard ratio (HR): 0.665, 95% confidence interval (CI): 0.492-0.899, P=0.008]. The two groups showed no significant differences in the secondary outcomes and safety, including rates of severe hemorrhage, cerebral hemorrhage and subarachnoid hemorrhage (P>0.05). CONCLUSION: The combination of Naoxintong Capsule with standard care reduced the 2-year stroke recurrence rate in patients with ischemic stroke without increasing the risk of severe hemorrhage in high-risk patients. (Trial registration No. NCT02334969).

First report of Botryosphaeria dothidea as the causal agent of a new fruit rot disease of pepper in China.

Pepper is an important and widely cultivated economic vegetable in the world (Yin et al., 2021). In June 2021, approximately 25% to 33.3% of the pepper plants had rot disease symptoms in Zhuanghang Comprehensive Experimental Base (30.894829 °N, 121.391374 °E), Fengxian district, Shanghai city, China. Water-soaked spots appeared on fruits that increased in size and leading to smelly fruit decay. To isolate the pathogen, three pepper samples with severe symptoms were collected. The samples were surface disinfected with 70% ethanol for 30 sec, 10% chlorine bleach for 10 min, rinsing with sterile water for three times and the rot tissues were cut and dried on sterile filter paper. The dried paper was later placed on potato dextrose agar (PDA) medium and incubated at 28°C (Tang et al., 2021). After 2-3 days, four types of colonies with different colony appearances were observed, in which only one can induce fruit rot phenotype (data not shown). Four isolates were cultured for molecular identification in each type. ITS1/ITS4, T1/ßt-2b and EF1-526F/EF1-1567R primers were used to amplify the internal transcribed spacer region (ITS), the beta-tubulin (TUB2) and the translation elongation factor I alpha (EF1-α) genes, respectively (Chen et al., 2018) and corresponding sequences from the isolates were analyzed with BLAST. Sequences of the isolate which can induce pepper decay were submitted to GenBank under the accession numbers of OM663701 (ITS), OM720127 (TUB2) and OM720128 (EF1-α). The results showed that the pathogen had 99% sequence homology to most strains of Botryosphaeria dothidea (B. dothidea) and displayed the highest sequence similarity to strain LBSX-1 (ITS: KF55123), strain JGT01 (TUB2: MW202404) and isolate CZA (EF1-α: MN025271). Based on molecular characterization, the isolate was identified as B. dothidea isolate SH01. A phylogenetic tree was constructed using Maximum Parsimony (MP) methods by MEGA7, and showed that SH01 was closely related to isolate CMW9075. To confirm the pathogenicity, five healthy pepper fruits were surface sterilized, 500µl of conidial suspension (1×103 conidia/ml) were injected into pepper (sterilized distilled water as control). Six days post inoculation (dpi), fruit rot symptoms appeared and the pepper decayed at 12 dpi. Four days post inoculation with mycelium plugs (from a 4-day-old culture on PDA, PDA plugs as control), hyphae were observed in the inoculation site and B. dothidea was re-isolated from the symptomatic areas, thus fulfilling Koch's postulates (Back et al., 2021, Chen et al., 2020). The pepper rotted severely at 7 dpi. The colonies of SH01 were pale to white and gradually turned into gray in 4-6 days. Conidia of the pathogen were unicellular, aseptate, hyaline and fusiform to fusoid, with dimensions of 19.7-23.5 µm × 3.8-5.2 µm (average = 21.9 µm × 4.8 µm, n = 50). Hyphae were transparent, branched and composed of multiple cells. The characteristic was consistent with the descriptions of B. dothidea (Vasic et al., 2013). B. dothidea belongs to Botryosphaeriaceae, causing widespread diseases in many plant species, commonly associated with cankers and dieback of woody plants and economic crops, such as plumcot trees (Back et al., 2021), eucalyptus (Yu et al., 2009) and soybeans (Chen et al., 2020) in China and Korea. Our findings reported for the first time that B. dothidea (SH01) can induce the pepper rot disease and future work on its pathogenesis may provide strategies for disease control against this fungus.

The Application of Two-Stage Operation for High-Risk Patients with Oesophageal Cancer Following Gastrectomy.

BACKGROUND: Oesophageal replacement by colonic interposition remains a major challenge due to its complexity and high incidence of complications; here we applied the two-stage operation strategy to oesophageal replacement by colonic interposition in high-risk oesophageal cancer patients following gastrectomy. METHODS: We performed a retrospective analysis on the data of patients with a history of distal gastrectomy who underwent one-stage and two-stage oesophageal replacement by colonic interposition from February 2012 to February 2020, and explored the relationship between the staging strategy and postoperative outcomes. RESULTS: The clinical data of 93 patients were collected and analysed. There were no significant differences in the patients' characteristics between the two groups (all p > 0.05), except for comorbidities and Charlson Comorbidity Index (all p < 0.05). The Clavien-Dindo score between the two groups was also not significantly different (p > 0.05). The logistic regression models revealed that patients who had received preoperative therapy had a higher Clavien-Dindo score (p < 0.05), but the stage strategy did not (p > 0.05). CONCLUSIONS: The two-stage operation is feasible in high-risk patients who need to undergo colonic interposition for oesophageal replacement. At the same time, it lowers the technical threshold of colonic interposition for oesophageal replacement, increasing this surgical technique's acceptability.

Clinical scoring model based on age, NIHSS, and stroke-history predicts outcome 3 months after acute ischemic stroke.

Background: The clinical nomogram is a popular decision-making tool that can be used to predict patient outcomes, bringing benefits to clinicians and patients in clinical decision-making. This study established a simple and effective clinical prediction model to predict the 3-month prognosis of acute ischemic stroke (AIS), and based on the predicted results, improved clinical decision-making and improved patient outcomes. Methods: From 18 December 2021 to 8 January 2022, a total of 146 hospitalized patients with AIS confirmed by brain MR were collected, of which 132 eligible participants constituted a prospective study cohort. The least absolute shrinkage and selection operator (LASSO) regression was applied to a nomogram model development dataset to select features associated with poor prognosis in AIS for inclusion in the logistic regression of our risk scoring system. On this basis, the nomogram was drawn, evaluated for discriminative power, calibration, and clinical benefit, and validated internally by bootstrap. Finally, the optimal cutoff point for each independent risk factor and nomogram was calculated using the Youden index. Results: A total of 132 patients were included in this study, including 85 men and 47 women. Good outcome was found in 94 (71.212%) patients and bad outcome in 38 (28.788%) patients during the follow-up period. A total of eight (6.061%) deaths were reported over this period, of whom five (3.788%) died during hospitalization. Five factors affecting the 3-month prognosis of AIS were screened by LASSO regression, namely, age, hospital stay, previous stroke, atrial fibrillation, and NIHSS. Further multivariate logistic regression revealed three independent risk factors affecting patient outcomes, namely, age, previous stroke, and NIHSS. The area under the curve of the nomogram was 0.880, and the 95% confidence interval was 0.818-0.943, suggesting that the nomogram model has good discriminative power. The p-value for the calibration curve is 0.925, indicating that the nomogram model is well-calibrated. According to the decision curve analysis results, when the threshold probability is >0.01, the net benefit obtained by the nomogram is the largest. The concordance index for 1,000 bootstrapping calculations is 0.869. The age cutoff for predicting poor patient outcomes using the Youden index was 76.5 years (specificity 0.777 and sensitivity 0.684), the cutoff for the NIHSS was 7.5 (specificity 0.936, sensitivity 0.421), and the cutoff for total nomogram score was 68.8 (sensitivity 81.6% and specificity 79.8%). Conclusion: The nomogram model established in this study had good discrimination, calibration, and clinical benefits. A nomogram composed of age, previous stroke, and NIHSS might predict the prognosis of stroke after AIS. It might intuitively and individually predict the risk of poor prognosis in 3 months of AIS and provide a reference basis for screening the treatment plan of patients.

NCAPG2 Is a Novel Prognostic Biomarker and Promotes Cancer Stem Cell Maintenance in Low-Grade Glioma.

Gliomas account for 75% of all primary malignant brain tumors in adults and are associated with high mortality. Mounting evidence has shown that NCAPG2 is differentially expressed in various cancers. However, the prognostic value and immune functions of NCAPG2 in low-grade glioma (LGG) remain unresolved. In the present study, we revealed that NCAPG2 was up-regulated in LGG, and its higher expression was associated with adverse clinical outcomes and poor clinical characteristics, including WHO grade, IDH mutation, 1p/19q codeletion, and primary therapy outcome. The results of the Cox regression analysis revealed that NCAPG2 was an independent factor for the prognosis of low-grade glioma. Meanwhile, we also established a nomogram based on NCAPG2 to predict the 1-, 3-, or 5-year survival in LGG patients. Furthermore, we found that Copy number variation (CNV) and DNA hypomethylation results in its overexpression in LGG. In addition, functional annotation confirmed that NCAPG2 was mainly involved in the immune regulation and WNT signaling pathways. Finally, we determined that increased expression of NCAPG2 was correlated with infiltration levels of various immune cells and immune checkpoint in LGG. Importantly, we found that NCAPG2 was highly expressed in glioma stem cells lines and knockdown of NCAPG2 significantly inhibited the self-renewal ability of GSC. This is the first study to identify NCAPG2 as a new potential prognostic biomarker and characterize the functional roles of NCAPG2 in the progression of LGG, and provides a novel potential diagnostic and therapeutic biomarker for LGG in the future.

Extra Spindle Pole Bodies-Like 1 Serves as a Prognostic Biomarker and Promotes Lung Adenocarcinoma Metastasis.

Extra spindle pole bodies-like 1 (ESPL1), a cysteine endopeptidase, plays a vital role in chromosome inheritance. However, the association of ESPL1 with prognosis and immune infiltration in lung adenocarcinoma (LUAD) has not yet been explored. Here, we analyzed the expression level, prognostic values, diagnostic value, and immune infiltration level in LUAD using various databases. Immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR) assays were used to detect the expression of ESPL1 in LUAD tissues and cell lines. In this study, we found that ESPL1 was upregulated in LUAD and a higher expression of ESPL1 was correlated with unfavorable prognosis in LUAD. Meanwhile, Cox hazard regression analysis results suggested that ESPL1 may be an independent prognostic factor for LUAD. Moreover, we demonstrated that ESPL1 expression was significantly correlated with immune infiltration of Th2 and dendritic cells in LUAD. We also confirmed that DNA copy number amplification and DNA hypo-methylation were positively correlated with ESPL1 expression in LUAD. Additionally, DNA copy number amplification was significantly associated with adverse clinical outcomes in LUAD. Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) confirmed that ESPL1 was mainly involved in the DNA replication and glycolysis signaling pathway. Finally, we revealed that ESPL1 was highly expressed in LUAD tissues and cell lines. Knockdown of ESPL1 significantly inhibited cell migration and the invasion abilities of LUAD. Our study comprehensively confirmed that ESPL1 expression may serve as a novel prognostic biomarker for both the clinical outcome and immune cell infiltration in LUAD.

DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression.

We revealed that SNX20 was up-regulated in LGG, and its higher expression was associated with adverse clinical outcomes and poor clinical characteristics, including WHO grade, IDH mutation, 1p/19q codeletion, and primary therapy outcome. The results of the Cox regression analysis revealed that SNX20 was an independent factor for the prognosis of low-grade glioma. Meanwhile, we also established a nomogram based on SNX20 to predict the 1-, 3-, or 5-year survival in LGG patients. Furthermore, we found that DNA hypomethylation results in its overexpression in LGG. In addition, functional annotation confirmed that SNX20 was mainly involved in the immune response and inflammatory response related signaling pathways, including the T cell receptor signaling pathway, natural killer cell-mediated cytotoxicity, and the NF-kappa B signaling pathway. Finally, we determined that increased expression of SNX20 was correlated with infiltration levels of various immune cells and immune checkpoint in LGG. Importantly, we found that SNX20 was highly expressed in glioma cell lines. Depletion of SNX20 significantly inhibits glioma cell proliferation and migration abilities. This is the first study to identify SNX20 as a new potential prognostic biomarker and characterize the functional roles of SNX20 in the progression of LGG, and provides a novel potential diagnostic and therapeutic biomarker for LGG in the future.

Long Non-Coding RNA AP000695.2 Acts as a Novel Prognostic Biomarker and Regulates the Cell Growth and Migration of Lung Adenocarcinoma.

Long non-coding RNAs (lncRNAs) are tumor-associated biological molecules and have been found to be implicated in the progression of lung adenocarcinoma (LUAD). LncRNA-AP000695.2 (ENSG00000248538) is a long non-coding RNA (lncRNA) that is widely increased in many tumor types including lung adenocarcinoma (LUAD). However, the aberrant expression profile, clinical significance, and biological function of AP000695.2 in human lung adenocarcinoma (LUAD) need to be further investigated. This study mines key prognostic AP000695.2 and elucidates its potential role and molecular mechanism in regulating the proliferation and metastasis of LUAD. Here, we discovered that AP000695.2 was significantly upregulated in lung adenocarcinoma tissues compared with healthy adjacent lung tissue and higher in LUAD cell lines than in normal human bronchial epithelial cell lines. A higher expression of AP000695.2 was positively correlated with aggressive clinicopathological characteristics, and AP000695.2 served as an independent prognostic indicator for the overall survival, disease-free survival, and progression-free survival in patients with LUAD. Receiver operating curve (ROC) analysis revealed the significant diagnostic ability of AP000695.2 (AUC = 0.838). Our in vivo data confirmed that AP000695.2 promotes the proliferation, migration, and invasion of LUAD cells. GSEA results suggested that AP000695.2 co-expressed genes were mainly enriched in immune-related biological processes such as JAK-STAT signaling pathway and toll-like receptor signaling pathway. Single-sample GSEA analysis showed that AP000695.2 is correlated with tumor-infiltrating immune cells in lung adenocarcinoma. Our findings confirmed that AP000695.2 was involved in the progression of lung adenocarcinoma, providing a novel prognostic indicator and promising diagnostic biomarker in the future.

DNA methylation-regulated YTHDF2 correlates with cell migration and immune cell infiltration in glioma.

BACKGROUND: Glioma is a lethal malignant brain tumor, it comprises about 80% of all malignant brain tumours. Mounting evidence has reported that YTHDF2 plays a significant role in the cancer progression. However, the effects of YTHDF2 on the prognosis of low-grade gliomas (LGGs) and its correlation with tumor immune infiltration are unclear. The present study was designed to determine the biological functions of YTHDF2 in glioma and to evaluate the association of YTHDF2 expression with glioma progression. METHODS: Clinical data on patients with glioma were obtained from The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), the Gene Expression Omnibus (GEO), as well as the Rembrandt and Gravendeel databases. The correlations among YTHDF2 expression, pathological characteristics, glioma progression and clinical outcome were evaluated. In addition, the correlation of YTHDF2 expression with immune cell infiltration was analyzed too. RESULTS: We found that YTHDF2 was significantly up-regulated in LGGs which correlated with tumor grade and poor prognosis. Interestingly, we showed that YTHDF2 expression in LGG was associated with copy number variation, DNA hypomethylation, and induced transcription factor YY1. Besides, KEGG pathway analysis shows that YTHDF2 mainly participates in the immune response and oncogenic signaling pathway. Additionally, YTHDF2 is positively associated with diverse immune cells infiltration, immune cells, and multiple immune checkpoint molecules. Finally, we confirmed that YTHDF2 was highly expressed in LGGs tissues and correlated with the tumor grade with immunohistochemistry assay. More importantly, our results demonstrated that YTHDF2 was elevated in GBM cells. Knockdown of YTHDF2 significantly inhibits the proliferation and migration of GBM cells. CONCLUSION: YTHDF2 correlates with glioma progression and immune cell infiltration, suggesting that YTHDF2 may be a useful prognostic biomarker for glioma.