Phase separation of RNF214 promotes the progression of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is one of the most common malignant tumors, and the expression and function of an uncharacterized protein RNF214 in HCC are still unknown. Phase separation has recently been observed to participate in the progression of HCC. In this study, we investigated the expression, function, and phase separation of RNF214 in HCC. We found that RNF214 was highly expressed in HCC and associated with poor prognosis. RNF214 functioned as an oncogene to promote the proliferation, migration, and metastasis of HCC. Mechanically, RNF214 underwent phase separation, and the coiled-coil (CC) domain of RNF214 mediated its phase separation. Furthermore, the CC domain was necessary for the oncogenic function of RNF214 in HCC. Taken together, our data favored that phase separation of RNF214 promoted the progression of HCC. RNF214 may be a potential biomarker and therapeutic target for HCC.

The P2 protein of wheat yellow mosaic virus acts as a viral suppressor of RNA silencing in Nicotiana benthamiana to facilitate virus infection.

Wheat yellow mosaic virus (WYMV) causes severe viral wheat disease in Asia. The WYMV P1 protein encoded by RNA2 has viral suppressor of RNA silencing (VSR) activity to facilitate virus infection, however, VSR activity has not been identified for P2 protein encoded by RNA2. In this study, P2 protein exhibited strong VSR activity in Nicotiana benthamiana at the four-leaf stage, and point mutants P70A and G230A lost VSR activity. Protein P2 interacted with calmodulin (CaM) protein, a gene-silencing associated protein, while point mutants P70A and G230A did not interact with it. Competitive bimolecular fluorescence complementation and competitive co-immunoprecipitation experiments showed that P2 interfered with the interaction between CaM and calmodulin-binding transcription activator 3 (CAMTA3), but the point mutants P70A and G230A could not. Mechanical inoculation of wheat with in vitro transcripts of WYMV infectious cDNA clone further confirmed that VSR-deficient mutants P70A and G230A decreased WYMV infection in wheat plants compared with the wild type. In addition, RNA silencing, temperature, ubiquitination and autophagy had significant effects on accumulation of P2 protein in N. benthamiana leaves. In conclusion, WYMV P2 plays a VSR role in N. benthamiana and promotes virus infection by interfering with calmodulin-related antiviral RNAi defense.

Insertion sequence transposition activates antimycobacteriophage immunity through an lsr2-silenced lipid metabolism gene island.

Insertion sequences (ISs) exist widely in bacterial genomes, but their roles in the evolution of bacterial antiphage defense remain to be clarified. Here, we report that, under the pressure of phage infection, the IS1096 transposition of Mycobacterium smegmatis into the lsr2 gene can occur at high frequencies, which endows the mutant mycobacterium with a broad-spectrum antiphage ability. Lsr2 functions as a negative regulator and directly silences expression of a gene island composed of 11 lipid metabolism-related genes. The complete or partial loss of the gene island leads to a significant decrease of bacteriophage adsorption to the mycobacterium, thus defending against phage infection. Strikingly, a phage that has evolved mutations in two tail-filament genes can re-escape from the lsr2 inactivation-triggered host defense. This study uncovered a new signaling pathway for activating antimycobacteriophage immunity by IS transposition and provided insight into the natural evolution of bacterial antiphage defense.

The regulation of intestinal flora on host's genes may play an essential role in the development of endometrial hyperplastic processes in yang deficiency individuals.

Yang-deficiency constitution (YADC) is linked to a higher vulnerability to various diseases, such as cold coagulation and blood stasis (CCBS) syndrome and infertility. Endometrial hyperplastic processes (EHPs) are a leading cause of infertility in women and are characterized by CCBS. However, it remains unclear whether YADC is related to the development of EHPs. METHODS: We recruited 202 EHPs patients including 147 with YADC (YEH group) and 55 with non-YADC (NYEH group). Fecal samples were collected from 8 YEH patients and 3 NYEH patients and analyzed using 16S rRNA V3-V4 sequencing for gut microbiota analysis. We obtained constitution survey data and a differential gut microbiota dataset from the literature for further analysis. Bioinformatics analysis was conducted using gut microbiota-related genes from public databases. RESULTS: YADC was significantly more prevalent in EHPs than non-YADC (P < 0.001), suggesting it as a potential risk factor for EHPs occurrence (ORpopulation survey = 13.471; ORhealthy women = 5.173). The YEH group had higher levels of inflammation, estrogen, and tamoxifen-related flora compared to NYEH and healthy YADC groups. There was an interaction between inflammation, estrogen, differential flora, and EHPs-related genes, particularly the TNF gene (related to inflammation) and the EGFR gene (related to estrogen), which may play a crucial role in EHPs development. CONCLUSION: YEH individuals exhibit significant changes in their gut microbiota compared to NYEH and healthy YADC. The interaction between specific microbiota and host genes is believed to play a critical role in the progression of EHPs.

Postoperative lenvatinib + PD-1 blockade reduces early tumor recurrence in hepatocellular carcinoma with microvascular invasion (Barcelona Clinic Liver Cancer stage 0 or A): a propensity score matching analysis.

BACKGROUND: This study aimed to determine the effectiveness of postoperative adjuvant lenvatinib + PD-1 blockade for patients with early-stage hepatocellular carcinoma (HCC) with microvascular invasion (MVI). METHODS: A total of 393 patients with HCC (Barcelona Clinic Liver Cancer stage 0 or A) who underwent curative hepatectomy with histopathologically proven MVI were enrolled according to the inclusion and exclusion criteria and assigned to 2 groups: surgery alone (surgery-alone group) and surgery with lenvatinib and PD-1 blockade (surgery + lenvatinib + PD-1 group) to compare recurrence-free survival (RFS), overall survival (OS), recurrence type, and annual recurrence rate after the application of propensity score matching (PSM). The Cox proportional hazards model was used for univariate and multivariate analyses. RESULTS: Overall, 99 matched pairs were selected using PSM. Patients in the surgery + lenvatinib + PD-1 group had significantly higher 3-year RFS rates (76.8%, 65.7%, and 53.5%) than patients in the surgery-alone group (60.6%, 45.5%, and 37.4%) (P = .012). The 2 groups showed no significant difference in recurrence types and OS. Surgery alone, MVI-M2, and alpha-fetoprotein of ≥200 ng/mL were independent risk factors for RFS (P < .05), and history of alcohol use disorder was an independent risk factor for OS (P = .022). CONCLUSION: Postoperative lenvatinib + PD-1 blockade improved the RFS in patients with HCC with MVI and was particularly beneficial for specific individuals.

Long-term combined blockade of CXCR4 and PD-L1 with in vivo reassembly for intensive tumor interference.

Negative immunoregulatory signal (PD-L1, CXCR4, et al.) and weak immunogenicity elicited immune system failing to detect and destroy cancerous cells. CXCR4 blockade promoted T cell tumor infiltration and increased tumor sensitivity to anti-PD-L1 therapy. Here, pH-responsive reassembled nanomaterials were constructed with anti-PD-L1 peptide and CXCR4 antagonists grafting (APAB), synergized with photothermal therapy for melanoma and breast tumor interference. The self-assembled APAB nanoparticles accumulated in the tumor and rapidly transformed into nanofibers in response to the acidic tumor microenvironment, leading to the exposure of grafted therapeutic agents. APAB enabling to reassemble around tumor cells and remained stable for over 96 h due to the aggregation induced retention (AIR) effect, led to long-term efficiently combined PD-L1 and CXCR4 blockade. Photothermal efficiency (ICG) induced immunogenic cell death (ICD) of tumor cells so as to effectively improve the immunogenicity. The combined therapy (ICG@APAB) could effectively inhibit the growth of primary tumor (∼83.52%) and distant tumor (∼76.24%) in melanoma-bearing mice, and significantly (p < 0.05) prolong the survival time over 42 days. The inhibition assay on tumor metastasis in 4 T1 model mice exhibited ICG@APAB almostly suppressed the occurrence of lung metastases and the expression levels of CD31, MMP-9 and VEGF in tumor decreased by 82.26%, 90.45% and 41.54%, respectively. The in vivo reassembly strategy will offer novel perspectives benefical future immunotherapies and push development of combined therapeutics into clinical settings.

Analysis of m6A-regulated genes and subtype classification in lupus nephritis.

BACKGROUND: Lupus nephritis (LN) is the most common and severe clinical manifestation of systemic lupus erythematosus (SLE). N6-methyladenosine (m6A) is a reversible RNA modification and has been implicated in various biological processes. However, the roles of m6A regulators in LN are not fully demonstrated. METHODS: We downloaded the kidney tissue transcriptome dataset of LN patients and normal controls from the GEO database and extracted the expression levels of m6A regulators. We constructed and compared Random Forest (RF) and Support Vector Machine (SVM) models, and subsequently selected featured genes to develop nomogram models. The m6A subtypes were identified based on significantly differentially expressed m6A regulators, and the m6A gene subtypes were identified based on m6A-associated differential genes, and the two m6A modification patterns were comprehensively evaluated. RESULTS: We obtained the GSE32591 and GSE112943 datasets from the GEO database, including 78 LN samples and 36 normal control samples. We extracted the expression levels of 20 m6A regulators. By RF analysis we identified 7 characteristic m6A regulators and constructed nomogramh models with these 7 genes. We identified two m6A subtypes based on these seven important m6A regulators, and the immune cell infiltration levels of the two subtype clusters were significantly different. We identified two more m6A gene subtypes based on m6A-associated DEGs. We calculated the m6A scores using the principal component analysis (PCA) algorithm and found that the m6A scores of m6A cluster A and gene cluster A were lower than those of m6A cluster B and gene cluster B. In addition, we found that the levels of inflammatory factors were also significantly different between m6A clusters and gene clusters. CONCLUSION: This study confirms that m6A regulators are involved in the LN process through different modes of action and provide new diagnostic and therapeutic targets for LN.

A rotary transformer cross-subject model for continuous estimation of finger joints kinematics and a transfer learning approach for new subjects.

Introduction: Surface Electromyographic (sEMG) signals are widely utilized for estimating finger kinematics continuously in human-machine interfaces (HMI), and deep learning approaches are crucial in constructing the models. At present, most models are extracted on specific subjects and do not have cross-subject generalizability. Considering the erratic nature of sEMG signals, a model trained on a specific subject cannot be directly applied to other subjects. Therefore, in this study, we proposed a cross-subject model based on the Rotary Transformer (RoFormer) to extract features of multiple subjects for continuous estimation kinematics and extend it to new subjects by adversarial transfer learning (ATL) approach. Methods: We utilized the new subject's training data and an ATL approach to calibrate the cross-subject model. To improve the performance of the classic transformer network, we compare the impact of different position embeddings on model performance, including learnable absolute position embedding, Sinusoidal absolute position embedding, and Rotary Position Embedding (RoPE), and eventually selected RoPE. We conducted experiments on 10 randomly selected subjects from the NinaproDB2 dataset, using Pearson correlation coefficient (CC), normalized root mean square error (NRMSE), and coefficient of determination (R2) as performance metrics. Results: The proposed model was compared with four other models including LSTM, TCN, Transformer, and CNN-Attention. The results demonstrated that both in cross-subject and subject-specific cases the performance of RoFormer was significantly better than the other four models. Additionally, the ATL approach improves the generalization performance of the cross-subject model better than the fine-tuning (FT) transfer learning approach. Discussion: The findings indicate that the proposed RoFormer-based method with an ATL approach has the potential for practical applications in robot hand control and other HMI settings. The model's superior performance suggests its suitability for continuous estimation of finger kinematics across different subjects, addressing the limitations of subject-specific models.

Cellular plasticity and fate determination in gastric carcinogenesis.

Cellular plasticity serves as a crucial biological phenomenon in humans, integral to tissue repair and maintenance of dynamic environmental homeostasis post-injury. However, dysregulated activation of this beneficial mechanism can pave the way for tumorigenesis and cancer progression. In this review, we synthesize recent advancements concerning the properties and roles of gastric epithelial cells, with a special emphasis on cellular plasticity and fate specification during the progress of gastric tumorigenesis. Notably, the attribute of stemness is not exclusive to gastric stem cells but also extends to differentiated cells in gastric units. We delve into the extent of plasticity and changes in cellular fate that contribute to malignant transformation in both stem and mature cells within the stomach. Moreover, we explore matrix-epithelial interactions, immunological modulation, and epigenomic alterations throughout the course of gastric tumorigenesis. A comprehensive understanding of the underlying cellular mechanisms governing plasticity and fate decisions could catalyze the development of innovative approaches for cancer prevention and antineoplastic therapies.

Preparation and characterization of furfural residue derived char-based catalysts for biomass tar cracking.

This study proposed an innovative strategy of catalytic cracking of tar during biomass pyrolysis/gasification using furfural residue derived biochar-based catalysts. Fe, Co, and Ni modified furfural residue char (FRC-Fe, FRC-Co, and FRC-Ni) were prepared by one-step impregnation method. The influences of cracking temperature and metal species on the tar cracking characteristics were investigated. The results showed that the tar conversion efficiency for all catalysts were improved with the cracking temperature increasing, the higher tar conversion efficiency achieved at 800 °C were 66.72 %, 89.58 %, 84.58 %, and 94.70 % for FRC, FRC-Fe, FRC-Co, and FRC-Ni respectively. FRC-Ni achieved the higher gas (H2, CO, CH4, CO2) yield 681.81 mL/g. At 800 °C, the catalyst (FRC-Ni) still reached a high tar conversion efficiency over 85.90 % after 5 cycles. SEM-EDS results showed that the distribution of Ni particles on the biochar support was uniform. TGA results demonstrated that FRC-Ni exhibited better thermal stability. XRD results indicated that there was no significant change in the grain size of Ni before and after the reaction. The FRC-Ni catalyst was reasonably stable due to its better anti-sintering and coke-resistant capabilities.

One-pot reaction for the preparation of diatom hemostatic particles with effective hemostasis and economic benefits.

Effective hemostatic materials have been in demand for rapid pre-hospital hemostasis in emergency situations, which can significantly reduce accidental deaths. The development of emergency hemostatic materials with rapid hemostasis, biosafety, and economical preparation is a great challenge. In this study, Ca(OH)2-complexed diatom powder hemostatic particles (Ca(OH)2-Php) were prepared based on a one-pot reaction by directly mixing various raw materials and by rotary granulation. High-temperature calcination was able to carbonate and consume the organic matter in the hemostatic particles. The crosslinked hydrogen bonds in those particles were converted to silica-oxygen bonds, the particles became more stable, and the porous structure of diatom biosilica (DBs) was exposed. Ca(OH)2-Php has high porosity, can quickly adsorb the water in blood (water absorption: 75.85 ± 6.93%), and exhibits rapid hemostasis capacity (clotting time was shortened by 43% compared with that of the control group), good biocompatibility (hemolysis rate <7%, no cytotoxicity), and simplicity of handling (conveniently debride, no residues, no tissue inflammation). This study provides a new idea for the preparation of emergency hemostatic materials, and Ca(OH)2-Php prepared by one-pot reaction has various high-quality characteristics including rapid hemostasis, wide applicability, economical preparation, and potential for large-scale production.

α-synuclein-lack expression rescues methamphetamine-induced mossy fiber degeneration in dorsal hippocampal CA3.

Methamphetamine (METH) - induced cognitive impairments may be related to synaptic degeneration at mossy fiber terminals, critical for spatial memory formation in hippocampal circuits. We have previously found METH-induced neurodegeneration in the striatum by increasing the α-synuclein (α-SYN) level. However, whether and how the METH-induced mossy fiber degeneration is also blamed for the abnormal accumulation of α-SYN remains to be elucidated. Chronic METH exposure decreased mossy fiber density but upregulatedα-SYN and phosphorylated TAU (TAU-pSer396) in hippocampal CA3, associated with glial cell overactivation, axonal neuropathies, and memory impairment. Notably, the knockout of the α-SYN gene significantly alleviated the METH-induced mossy fiber degeneration and memory impairment. Meanwhile, the TAU-pSer396 accumulation and glial activation were ameliorated by α-SYN knockout. Our findings suggest an essential role of α-SYN in mediating METH-induced mossy fiber degeneration, providing promising therapeutic and prophylactic targets for METH-related neurodegenerative diseases.

Automatic Detection of Feral Pigeons in Urban Environments Using Deep Learning.

The overpopulation of feral pigeons in Hong Kong has significantly disrupted the urban ecosystem, highlighting the urgent need for effective strategies to control their population. In general, control measures should be implemented and re-evaluated periodically following accurate estimations of the feral pigeon population in the concerned regions, which, however, is very difficult in urban environments due to the concealment and mobility of pigeons within complex building structures. With the advances in deep learning, computer vision can be a promising tool for pigeon monitoring and population estimation but has not been well investigated so far. Therefore, we propose an improved deep learning model (Swin-Mask R-CNN with SAHI) for feral pigeon detection. Our model consists of three parts. Firstly, the Swin Transformer network (STN) extracts deep feature information. Secondly, the Feature Pyramid Network (FPN) fuses multi-scale features to learn at different scales. Lastly, the model's three head branches are responsible for classification, best bounding box prediction, and segmentation. During the prediction phase, we utilize a Slicing-Aided Hyper Inference (SAHI) tool to focus on the feature information of small feral pigeon targets. Experiments were conducted on a feral pigeon dataset to evaluate model performance. The results reveal that our model achieves excellent recognition performance for feral pigeons.

Worldwide productivity and research trend of publications concerning extracellular vesicles role in fibrosis: A bibliometric study from 2013 to 2022.

Background: Fibrosis is a heavy burden on the global healthcare system. Recently, an increasing number of studies have demonstrated that Extracellular vesicles play an important role in intercellular communication under both physiological and pathological conditions. This study aimed to explore the role of extracellular vesicles' in fibrosis using bibliometric methods. Methods: Original articles and reviews related to extracellular vesicles and fibrosis were obtained from the Web of Science Core Collection database on November 9, 2022. VOSviewer was used to obtain general information, including co-institution, co-authorship, and co-occurrence visualization maps. The CiteSpace software was used to analyze citation bursts of keywords and references, a timeline view of the top clusters of keywords and cited articles, and the dual map. R package "bibliometrix" was used to analyze annual production, citation per year, collaboration network between countries/regions, thematic evolution map, and historiography network. Results: In total, 3376 articles related to extracellular vesicles and fibrosis published from 2013 to 2022 were included in this study, with China and the United States being the top contributors. Shanghai Jiao Tong University has the highest number of publications. The main collaborators were Giovanni Camussi, Stefania Bruno, Marta Tepparo, and Cristina Grange. Journals related to molecular, biology, genetics, health, immunology, and medicine tended to publish literature on extracellular vesicles and fibrosis. "Recovery," "heterogeneity," "degradation," "inflammation," and "mesenchymal stem cells" are the keywords in this research field. Literature on extracellular vesicles and fibrosis associated with several diseases, including "kidney disease," "rheumatoid arthritis," and "skin regeneration" may be the latest hot research field. Conclusions: This study provides a comprehensive perspective on extracellular vesicles and fibrosis through a bibliometric analysis of articles published between 2013 and 2022. We identified the most influential countries, institutions, authors, and journals. We provide information on recent research frontiers and trends for scholars interested in the field of extracellular vesicles and fibrosis. Their role in biological processes has great potential to initiate a new upsurge in future research.

METFORMIN MITIGATES SEPSIS-ASSOCIATED PULMONARY FIBROSIS BY PROMOTING AMPK ACTIVATION AND INHIBITING HIF-1α-INDUCED AEROBIC GLYCOLYSIS.

ABSTRACT: Recent research has revealed that aerobic glycolysis has a strong correlation with sepsis-associated pulmonary fibrosis (PF). However, at present, the mechanism and pathogenesis remain unclear. We aimed to test the hypothesis that the adenosine monophosphate-activated protein kinase (AMPK) activation and suppression of hypoxia-inducible factor 1α (HIF-1α)-induced aerobic glycolysis play a central role in septic pulmonary fibrogenesis. Cellular experiments demonstrated that lipopolysaccharide increased fibroblast activation through AMPK inactivation, HIF-1α induction, alongside an augmentation of aerobic glycolysis. By contrast, the effects were reversed by AMPK activation or HIF-1α inhibition. In addition, pretreatment with metformin, which is an AMPK activator, suppresses HIF-1α expression and alleviates PF associated with sepsis, which is caused by aerobic glycolysis, in mice. Hypoxia-inducible factor 1α knockdown demonstrated similar protective effects in vivo . Our research implies that targeting AMPK activation and HIF-1α-induced aerobic glycolysis with metformin might be a practical and useful therapeutic alternative for sepsis-associated PF.

Integrating bulk and single-cell RNA sequencing data reveals epithelial-mesenchymal transition molecular subtype and signature to predict prognosis, immunotherapy efficacy, and drug candidates in low-grade gliomas.

Objective: Epithelial-mesenchymal transition (EMT) is a tightly regulated and dynamic process occurring in both embryonic development and tumor progression. Our study aimed to comprehensively explore the molecular subtypes, immune landscape, and prognostic signature based on EMT-related genes in low-grade gliomas (LGG) in order to facilitate treatment decision-making and drug discovery. Methods: We curated EMT-related genes and performed molecular subtyping with consensus clustering algorithm to determine EMT expression patterns in LGG. The infiltration level of diverse immune cell subsets was evaluated by implementing the single-sample gene set enrichment analysis (ssGSEA) and ESTIMATE algorithms. The distinctions in clinical characteristics, mutation landscape, and immune tumor microenvironment (TME) among the subtypes were subjected to further investigation. Gene Set Variation Analysis (GSVA) was performed to explore the biological pathways that were involved in subtypes. The chemo drug sensitivity and immunotherapy of subtypes were estimated through GDSC database and NTP algorithm. To detect EMT subtype-related prognostic gene modules, the analysis of weighted gene co-expression network (WGCNA) was performed. The LASSO algorithm was utilized to construct a prognostic risk model, and its efficacy was verified through an independent CGGA dataset. Finally, the expression of the hub genes from the prognostic model was evaluated through the single-cell dataset and in-vitro experiment. Results: The TCGA-LGG dataset revealed the creation of two molecular subtypes that presented different prognoses, clinical implications, TME, mutation landscapes, chemotherapy, and immunotherapy. A three-gene signature (SLC39A1, CTSA and CLIC1) based on EMT expression pattern were established through WGCNA analysis. Low-risk patients showed a positive outlook, increased immune cell presence, and higher expression of immune checkpoint proteins. In addition, several promising drugs, including birinapant, fluvastatin, clofarabine, dasatinib, tanespimycin, TAK-733, GDC-0152, AZD8330, trametinib and ingenol-mebutate had great potential to the treatment of high risk patients. Finally, CTSA and CLIC1 were highly expressed in monocyte cell through single-cell RNA sequencing analysis. Conclusion: Our research revealed non-negligible role of EMT in the TME diversity and complexity of LGG. A prognostic signature may contribute to the personalized treatment and prognostic determination.

Anisotropic structure deformation of ß-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine under high pressure: vibration spectra calculation and resolution based on AIMD simulation.

The phase transition of the ß-HMX crystal has been widely studied under high pressure, but the microscopic transition mechanism is not sufficiently understood. In this article, we perform a series of ab initio molecular dynamics simulations focusing on structure deformation and the corresponding vibration spectra resolution of ß-HMX at 0-40 GPa. Several typical pressure-induced phase transition processes are confirmed by analyzing the chemical bond, dihedral angle, charge transfer, and IR and Raman spectra. The corresponding relationship between molecular structure and spectral signal is constructed through the partial spectra calculations of special functional groups within the HMX molecule. The anisotropic effects of different groups on the initial structural phase transition are uncovered. The equatorial C-N and axial N-N bonds have the largest compression ratio as pressure increases, which is the intrinsic factor for the initiation of structure transformation. The C-N molecular ring plays an important role in the entire phase transition process. In addition, the phase transition of ß â†’ ζ is also closely related to the deformation of NO2, while that of ζ → ε is induced by the axial N-NO2 group. Regarding the higher-pressure phase transition, the synergetic effect of N-NO2, CH2 groups, and molecular rings becomes more considerable.

Characterization of DNA Damage Repair Related Signature and Molecular Feature in Low-Grade Gliomas to Aid Chemotherapy and Drug Discovery.

BACKGROUND: DNA damage repair (DDR) related genes are associated with the development, progression, aggressiveness, and heterogeneity of low-grade gliomas (LGG). However, the precise role of DDR in LGG prognosis and molecular subtypes remains to be elucidated. METHODS: We analyzed 477 and 594 LGG samples from the Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) to develop a prognostic model using the random forest algorithm and Cox regression. Independent prognostic factors were incorporated into a nomogram, and its performance was assessed using receiver operating characteristic and calibration curves. We also used Connectivity Map analysis to identify potential small molecule drugs targeting DDR. Molecular subtypes based on DDR were identified by consensus cluster analysis, and the clinical characteristics, mutation landscape, immune tumor microenvironment, and drug sensitivity of patients with different subtypes in the TCGA and CGGA datasets were further compared. The Boruta algorithm was used to select features from the differentially expressed genes between clusters to generate DDR scores. Results were further validated in the Glioma Longitudinal AnalySiS consortium dataset. Statistical analysis and tests were implemented using R software version 4.0.2. RESULTS: We developed a prognostic model containing six DDR-related genes, which served as a potential independent prognostic indicator in LGG across three datasets. The area under the curve (AUC) values for 1-, 3-, and 5-year survival in the TCGA dataset were 0.901, 0.832, and 0.771, respectively. The nomogram demonstrated high accuracy in predicting 1-, 3-, and 5-year survival, with AUC values greater than 0.8. Additionally, we identified and validated two molecular subtypes based on DDR genes. These subtypes exhibited significant differences in somatic mutations, clinical prognosis, and immune cell infiltration. One subtype showed higher immune and stromal scores, worse prognosis, and increased sensitivity to common chemotherapeutic agents. Finally, we established a DDR score which served as another promising prognostic predictor for LGG. CONCLUSIONS: The prognostic model and molecular subtypes based on DDR genes can help in more detailed classification and provide insights for personalized management of LGG and clinical drug development.

Multi-omics analysis reveals CLIC1 as a therapeutic vulnerability of gliomas.

Introduction: Despite advances in comprehending cancer biology, malignant gliomas remain incurable. The present work conducted a multi-omics analysis for investigating the significance of chloride intracellular channel 1 (CLIC1) in gliomas. Methods: Multi-omics data of glioma covering transcriptomics, genomics, DNA methylation and single-cell transcriptomics from multiple public cohorts were enrolled for analyzing CLIC1. In vitro experiments were conducted to measure apoptosis and cell mobility in U251 and U373 glioma cells following transfection of CLIC1 siRNAs. Results: Elevated CLIC1 expression was proven to stably and independently estimate worse survival outcomes. CLIC1 expression was higher in more advanced stage, wild-type IDH and unmethylated MGMT samples. Tumorigenic and anticancer immunity pathways were remarkably enriched in CLIC1-up-regulated tumors. Additionally, CLIC1 was positively linked with cancer-immunity cycle, stromal activation, DNA damage repair and cell cycle. Suppressing CLIC1 resulted in apoptosis and attenuated cell motility of glioma cells. More frequent genomic alterations were found in CLIC1-up-regulated tumors. CLIC1 expression presented a remarkably negative connection to DNA methylation. High CLIC1 expression samples were more sensitive to camptothecin, cisplatin, doxorubicin, erlotinib, paclitaxel, rapamycin, clofarabine, tanespimycin, methotrexate, everolimus, TAK-733, trametinib and AZD8330. Tumors with upregulated CLIC1 presented abundant immune cell infiltration, higher expression of immune-checkpoints and -modulators and similar transcriptome profiling, indicative of well response to immune-checkpoint blockade (ICB). Nevertheless, due to elevated TIDE score, tumors with CLIC1 upregulation appeared to be resistant to ICB. Single-cell analysis unveiled that CLIC1 was expressed ubiquitously in tumor cells and tumor microenvironment. Conclusions: Overall, CLIC1 was a promising treatment vulnerability in glioma.