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Simple Summary: In this review, we have summarized the crucial role of G9a in cellular biology and disease. By synthesizing recent research discoveries, we delve into the functions of G9a in gene expression regulation, cell proliferation, and biological development. Additionally, we explore its potential involvement in cancer and discuss its prospects as a therapeutic target specifically in prostate cancer. In summary, this review provides a comprehensive perspective on G9a, enhances understanding of the significance of G9a in biology and cancer, and offers insights into future research and drug development. G9a, also named EHMT2, is a histone 3 lysine 9 (H3K9) methyltransferase responsible for catalyzing H3K9 mono- and dimethylation (H3K9me1 and H3K9me2). G9a contributes to various aspects of embryonic development and tissue differentiation through epigenetic regulation. Furthermore, the aberrant expression of G9a is frequently observed in various tumors, particularly in prostate cancer, where it contributes to cancer pathogenesis and progression. This review highlights the critical role of G9a in multiple cancer-related processes, such as epigenetic dysregulation, tumor suppressor gene silencing, cancer lineage plasticity, hypoxia adaption, and cancer progression. Despite the increased research on G9a in prostate cancer, there are still significant gaps, particularly in understanding its interactions within the tumor microenvironment and its broader epigenetic effects. Furthermore, this review discusses the recent advancements in G9a inhibitors, including the development of dual-target inhibitors that target G9a along with other epigenetic factors such as EZH2 and HDAC. It aims to bring together the existing knowledge, identify gaps in the current research, and suggest future directions for research and treatment strategies. [ABSTRACT FROM AUTHOR]

Phenotype plasticity and evolution adaptations are the two main ways in which allow populations to deal with environmental changes, but the potential relationship between them remains controversial. Using a reciprocal transplant approach with cattle adapted to the Tibetan Plateau and adjacent lowlands, we aim to investigate the relative contributions of evolutionary processes and phenotypic plasticity in driving both phenotypic and transcriptomic changes under natural conditions. We observed that while numerous genetic transcriptomic changes were evident during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes with ancestral plasticity are generally reversed by evolutionary adaptations and show a closer expression level to the ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotypes level, with a majority of biochemical and hemorheology phenotypes showing a tendency to revert to their ancestral patterns, suggesting the restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. The findings of our study contribute to the debate regarding the relative contributions of plasticity and genetic changes in mammal environment adaptation. Furthermore, we highlight that the restoration of ancestral phenotypes represents a general pattern in cattle new environment adaptation. Our findings reveal that while numerous genetic transcriptomic changes were observed during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes exhibiting ancestral plasticity generally undergo reversal through evolutionary adaptations, resulting in closer expression levels resembling their ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotype level, where a majority of biochemical and hemorheology traits displayed a tendency to revert to their ancestral patterns, suggesting that restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. [ABSTRACT FROM AUTHOR]

Objective: To identify key ferroptosis-related biomarkers and investigate immune infiltration in meniscus injuries among individuals of different age groups. Methods: (1) We obtained our training dataset from the GEO database and analyzed gene expression matrices from the GSE191157 gene chip dataset. Simultaneously, we downloaded relevant genes associated with ferroptosis for further analysis. (2)Using the "limma" package, we conducted differential gene expression analysis between elderly and young patients with meniscus injuries and performed weighted gene co-expression network analysis (WGCNA) on all genes in the GSE191157 gene chip dataset. (3) We selected two color modules most correlated with meniscus injury and then intersected the genes in these modules with ferroptosis-related genes. (4)Subsequently, we conducted ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses on the intersected genes. (5) Using LASSO regression in machine learning, we analyzed the intersected genes related to ferroptosis in meniscus injuries among individuals of different ages and extracted core genes. (6) Finally, we conducted gene set enrichment analysis (GSEA) and single-sample gene set enrichment variation analysis (ssG-SEA) for immune infiltration and confirmed the correlation between core genes and ferroptosis in meniscus injuries. Results: A total of 2 517 differentially expressed genes were identified, and the intersection of these genes with ferroptosis-related genes yielded 61 genes. After WGCNA analysis, the blue and yellow modules were found to be most relevant to the disease, resulting in 46 intersected genes. Through LASSO regression analysis, four core genes (BEX1, MMP13, PTPN18, and SLC38A1) were selected. GSEA results indicated that ferroptosis in meniscus injuries is primarily associated with Toll-like receptor signaling, RNA transcription and splicing, mTOR signaling, and ECM-receptor interaction. Immune cell infiltration analysis revealed a significant correlation between core gene expression and immune cell infiltration. MMP13 exhibited a negative correlation with effector memory CD8 T cells, CD56dim natural killer cells, and central memory CD4 T cells, while SLC38A1, BEX1, and PTPN18 were positively correlated. Conclusion: This study identified four key genes associated with ferroptosis in meniscus injuries among individuals of different age groups, namely BEX1, MMP13, PTPN18, and SLC38A1. Immune cell infiltration analysis demonstrated a clear correlation between core gene expression and immune cell infiltration. [ABSTRACT FROM AUTHOR]

Background: Copper and copper-binding proteins are key components of tumor progression as they play important roles in tumor invasion and migration, but their associations in gliomas remain unclear. Methods: Transcriptomic datasets of glioblastoma, low-grade glioma, and normal brain cortex were derived from the TCGA and GTEX databases. Differentially expressed genes (DEGs) of copper-binding proteins were screened and used to construct a prognostic model based on COX and LASSO regression, which was further validated by the CGGA datasets. The expressions of risk-model genes were selectively confirmed via anatomic feature-based expression analysis and immunohistochemistry. The risk score was stratified by age, gender, WHO grade, IDH1 mutation, MGMT promoter methylation, and 1p/19q codeletion status, and a nomogram was constructed and validated. Results: A total of 21 DEGs of copper-binding proteins were identified and a six-gene risk-score model was constructed, consisting of ANG, F5, IL1A, LOXL1, LOXL2, and STEAP3, which accurately predicted 1-, 3-, and 5-year overall survival rates, with the AUC values of 0.87, 0.88, and 0.82, respectively. The high-risk group had a significantly shorter OS (p < 0.0001) and was associated with old age, wild-type IDH1, a high WHO grade, an unmethylated MGMT promoter, and 1p/19q non-codeletion and had higher levels of immune cell infiltration, cancer-immunity suppressor, and immune checkpoint gene expression as well as a higher TMB. Conclusions: The model based on the genes of copper-binding proteins could contribute to prognosis prediction and provide potential targets against gliomas. [ABSTRACT FROM AUTHOR]

Purpose Aldo-keto reductase family 1 member C3 (AKR1C3) is important in prostate cancer progression, being a potential biomarker in metastatic castration-resistant prostate cancer (mCRPC). Previous explorations of AKR1C3 are mainly based on tissue samples. This study investigates using plasma-based liquid biopsy to validate the prognostic and predictive value of AKR1C3 in patients with mCRPC. Materials and Methods We prospectively recruited 62 patients with mCRPC. All patients received repeated prostate biopsies at the time of mCRPC diagnosis, and immunohistochemistry (IHC) staining was used to detect protein expression of AKR1C3 in the tissues. We took their blood simultaneously and performed digital droplet polymerase chain reaction (ddPCR) to measure expression levels of AKR1C3 in the exosomes. The detected plasma and tissue AKR1C3 expression levels were analyzed for patients' overall survival (OS) and progression-free survival under first-line abiraterone use (ABI-PFS). Results All other baseline characteristics were balanced between the 2 groups. 15/62 (24.2%) and 25/62 (40.3%) patients showed AKR1C3-EXO positive (≥20 copies/20 μL) and AKR1C3-IHC positive, respectively. Positive AKR1C3-EXO expression was associated with decreased patients' survival [ABI-PFS: 3.9 vs 10.1 months, P <.001; OS: 16.2 vs 32.5 months, P <.001]. AKR1C3-IHC positivity was also correlated with ABI-PFS and OS (P =.010, P =.016). In patients with worse baseline blood tests (including higher alkaline phosphatase (ALP) and lactate dehydrogenase (LDH) level and lower hemoglobin (HB) level), and lower ISUP/WHO group (<4), their OS was significantly worse when showing AKR1C3-EXO positive. Conclusion AKR1C3-EXO is associated with patient prognosis regarding OS and ABI-PFS and can be used as a biomarker in mCRPC. [ABSTRACT FROM AUTHOR]

Background: Clear cell renal cell carcinoma (ccRCC) is the most common and highly heterogeneous subtype of renal cell carcinoma. Dysregulated basal cell adhesion molecule (BCAM) gene is associated with poor prognosis in various cancers. However, the dysregulated functions and related multi-omics features of BCAM in ccRCC stay unclear. Results: BCAM expression was aberrantly downregulated in ccRCC and correlated with adverse pathological parameters and poor prognosis. Low mRNA expression of BCAM was remarkably associated with its CpG methylation levels and BAP1 mutation status. Patients with lower-expressed BCAM concomitant with BAP1 mutation had a worse prognosis. Using RNA-seq data from The cancer genome atlas, we found that compared to the BCAM-high expression subgroup, ccRCC patients in the BCAM-low expression subgroup had significantly higher levels of immune infiltration, higher immune checkpoint expression levels and lower TIDE (tumor immune dysfunction and exclusion) score, indicating potential better response to immunotherapy. Data from the Clinical Proteomic Tumor Analysis Consortium further validated the association between low BCAM expression and CD8 + inflamed phenotype at protein level. Meanwhile, our results suggested that the angiogenesis-related pathways were enriched in the BCAM-high expression subgroup. More importantly, according to the data from the GDSC database, we revealed that the BCAM-high expression subgroup should be more sensitive to anti-angiogenetic therapies, including sorafenib, pazopanib and axitinib. Conclusions: These results suggest that BCAM could serve as a biomarker distinguishing different tumor microenvironment phenotypes, predicting prognosis and helping therapeutic decision-making for patients with ccRCC. [ABSTRACT FROM AUTHOR]

Nitrogen enters the terrestrial ecosystem through deposition. High nitrogen levels can affect physical and chemical properties of soil and inhibit normal growth and reproduction of forest plants. Nitrogen modulates the composition of soil microorganisms. Strigolactones inhibits plant branching, promotes root growth, nutrient absorption, and promotes arbuscular fungal mycelia branching. Plants are subjected to increasing atmospheric nitrogen deposition. Therefore, it is imperative to explore the relationship between strigolactone and nitrogen deposition of plants and abundance of soil microorganisms. In the present study, the effects of strigolactone on genetic responses and soil microorganisms of Torreya grandis , under simulated nitrogen deposition were explored using high-throughput sequencing techniques. T. grandis is a subtropical economic tree species in China. A total of 4,008 differentially expressed genes were identified in additional N deposition and GR24 treatment. These genes were associated with multiple GO terms and metabolic pathways. GO enrichment analysis showed that several DEGs were associated with enrichment of the transporter activity term. Both additional nitrogen deposition and GR24 treatment modulated the content of nutrient elements. The content of K reduced in leaves after additional N deposition treatment. The content of P increased in leaves after GR24 treatment. A total of 20 families and 29 DEGs associated with transporters were identified. These transporters may be regulated by transcription factors. A total of 1,402,819 clean reads and 1,778 amplicon sequence variants (ASVs) were generated through Bacterial 16S rRNA sequencing. Random forest classification revealed that Legionella, Lacunisphaera, Klebsiella, Bryobacter, and Janthinobacterium were significantly enriched in the soil in the additional N deposition group and the GR24 treatment group. Co-occurrence network analysis showed significant differences in composition of soil microbial community under different treatments. These results indicate a relationship between N deposition and strigolactones effect. The results provide new insights on the role of strigolactones in plants and composition of soil microorganisms under nitrogen deposition. [ABSTRACT FROM AUTHOR]

Hypoxic-ischemic encephalopathy (HIE) is one of the leading causes of neonatal death and permanent neurological disability. Here, we designed to quest therapeutic effects of diazoxide (DZ) on HIE and its mechanism. The cell model of HIE was established. CCK8 and flow cytometry were applied to test cell viability and apoptosis. RT-qPCR and western blotting was evaluated to the expression of miR-21, PDCD4, PI3K, and p-AKT/AKT. Commercial kits were employed to detect SOD, MDA, LDH. DCFH-DA was used to measure intracellular ROS. ELISA was performed to estimate IL-1β, IL-6 and TNF-α. Dual-luciferase reporter gene and RIP assay were applied to confirm the binding relationships between miR-21 and PDCD4. In H19-7 cells and PC12 cells stimulated by OGD, with low cell viability, high apoptosis, miR-21 high expression and PDCD4 low expression. However, the functions were all reversed by DZ administration. Furthermore, miR-21 inhibitor could abolish the beneficial effects of DZ on OGD-induced cells. Besides, miR-21 could interact with PDCD4. In addition, PDCD4 involved with the regulation of DZ to OGD-induced cells via PI3K/AKT pathway. DZ enhanced miR-21 level and inhibited PDCD4 level via PI3K/AKT pathway to resisted HIE. [ABSTRACT FROM AUTHOR]

Background: Colon adenocarcinoma (COAD) is one of the most common malignant tumors in the world. The histopathological features are crucial for the diagnosis, prognosis, and therapy of COAD. Methods: We downloaded 719 whole-slide histopathological images from TCIA, and 459 corresponding HTSeq-counts mRNA expression and clinical data were obtained from TCGA. Histopathological image features were extracted by CellProfiler. Prognostic image features were selected by the least absolute shrinkage and selection operator (LASSO) and support vector machine (SVM) algorithms. The co-expression gene module correlated with prognostic image features was identified by weighted gene co-expression network analysis (WGCNA). Random forest was employed to construct an integrative prognostic model and calculate the histopathological-genomic prognosis factor (HGPF). Results: There were five prognostic image features and one co-expression gene module involved in the model construction. The time-dependent receiver operating curve showed that the prognostic model had a significant prognostic value. Patients were divided into high-risk group and low-risk group based on the HGPF. Kaplan-Meier analysis indicated that the overall survival of the low-risk group was significantly better than the high-risk group. Conclusions: These results suggested that the histopathological image features had a certain ability to predict the survival of COAD patients. The integrative prognostic model based on the histopathological images and genomic features could further improve the prognosis prediction in COAD, which may assist the clinical decision in the future. [ABSTRACT FROM AUTHOR]

Background: The tumor necrosis factor-stimulated gene-6 (TSG-6) has been confirmed to inhibit inflammation. It is now generally accepted that local inflammatory stimulation around shoulder capsule causes proliferative fibrosis. This study aims to investigate the mechanism of recombinant TSG-6 protein inhibiting the growth of capsule fibroblasts in frozen shoulder via the TGF-β/Smad2 signal pathway. Methods: Human frozen shoulder capsule tissue was taken for primary and passage culture, and the 3rd generation fibroblasts from pathological frozen shoulder capsule were treated with different concentrations of recombinant TSG-6 protein, or with TGF-β1 agonist SRI-011381. Immunoconfocal analysis was used to identify the isolated fibroblasts, and MTT assay, colony formation assay, and flow cytometry were used to detect the viability, proliferation, and apoptosis rate of fibroblast. The contents of fibrosis and inflammation indexes COL1A1, TNF-α, IL-6, and IL-1β in the cell supernatant were detected using ELISA and then further examined by qRT-PCR. The expression of Bax, Bcl-2, and proteins related to TGF-β/Smad2 pathway were detected by Western Blot. Results: Compared with the blank control group, fibroblasts intervened with TSG-6 (2 μg and 5 μg) showed significantly decreased viability and proliferation ability and enhanced cell apoptosis, concurrent with the reductions in Bcl-2 expression; COL1A1, TNF-α, IL-6, and IL-1β levels; and the expression of TGF-β1 and phosphorylated Smad22, and an increase in Bax expression, while SRI-011381 treatment would reverse the effect of recombinant TSG-6 protein. Conclusion: Recombinant TSG-6 protein inhibited the growth of primary fibroblasts from human frozen shoulder capsule by suppressing the TGF-β/Smad2 signaling pathway. [ABSTRACT FROM AUTHOR]

Background: To use ddPCR to quantify plasma exosomal class III β‐tubulin (βIII‐tubulin, TUBB3, encoded by the TUBB3 gene) mRNA expression in metastatic castration‐resistant prostate cancer (mCRPC) patients, and study the association of this expression with abiraterone efficacy. Methods: Blood samples were prospectively collected from 52 mCRPC patients using abiraterone as first‐line therapy to measure plasma exosomal TUBB3 mRNA expression value before the initiation of abiraterone. Study endpoints were PSA response rate, PSA‐progression‐free survival (PSA‐PFS), and overall survival (OS, from CRPC to death). Results: Patients with positive exosomal TUBB3 expression showed shorter PSA‐PFS (negative TUBB3 vs. positive TUBB3: 11.0 vs. 7.9 months; p = 0.014). Further analysis demonstrated that patients with strongly positive exosomal TUBB3 (>20 copies/20 µl) was associated with even shorter PSA‐PFS (negative TUBB3 vs. positive TUBB3 [<20 copies/20 µl] vs. strongly positive TUBB3 [>20 copies/20 µl]: 11.0 vs. 8.3 vs. 3.6 months, p = 0.005). In multivariate analyzes, TUBB3 (+) (HR: 2.114, p = 0.033) and ECOG score >2 (HR: 3.039, p = 0.006) were independent prognosticators of poor PSA‐PFS. PSA response and OS did not present significant differences. Conclusion: The exosomal TUBB3 mRNA expression level is associated with poor PSA‐PFS of abiraterone in mCRPC patients. The detection of exosomal TUBB3 can be valuable in their management. [ABSTRACT FROM AUTHOR]

Background: Histopathological image features offer a quantitative measurement of cellular morphology, and probably help for better diagnosis and prognosis in head and neck squamous cell carcinoma (HNSCC). Methods: We first used histopathological image features and machine‐learning algorithms to predict molecular features of 212 HNSCC patients from The Cancer Genome Atlas (TCGA). Next, we divided TCGA‐HNSCC cohort into training set (n = 149) and test set (n = 63), and obtained tissue microarrays as an external validation set (n = 126). We identified the gene expression profile correlated to image features by bioinformatics analysis. Results: Histopathological image features combined with random forest may predict five somatic mutations, transcriptional subtypes, and methylation subtypes, with area under curve (AUC) ranging from 0.828 to 0.968. The prediction model based on image features could predict overall survival, with 5‐year AUC of 0.831, 0.782, and 0.751 in training, test, and validation sets. We next established an integrative prognostic model of image features and gene expressions, which obtained better performance in training set (5‐year AUC = 0.860) and test set (5‐year AUC = 0.826). According to histopathological transcriptomics risk score (HTRS) generated by the model, high‐risk and low‐risk patients had different survival in training set (HR = 4.09, p < 0.001) and test set (HR=3.08, p = 0.019). Multivariate analysis suggested that HTRS was an independent predictor in training set (HR = 5.17, p < 0.001). The nomogram combining HTRS and clinical factors had higher net benefit than conventional clinical evaluation. Conclusions: Histopathological image features provided a promising approach to predict mutations, molecular subtypes, and prognosis of HNSCC. The integration of image features and gene expression data had potential for improving prognosis prediction in HNSCC. [ABSTRACT FROM AUTHOR]

Background: Clear cell renal cell carcinoma (ccRCC) is one of the most common malignancies in urinary system, and radiomics has been adopted in tumor staging and prognostic evaluation in renal carcinomas. This study aimed to integrate image features of contrast-enhanced CT and underlying genomics features to predict the overall survival (OS) of ccRCC patients. Method: We extracted 107 radiomics features out of 205 patients with available CT images obtained from TCIA database and corresponding clinical and genetic information from TCGA database. LASSO-COX and SVM-RFE were employed independently as machine-learning algorithms to select prognosis-related imaging features (PRIF). Afterwards, we identified prognosis-related gene signature through WGCNA. The random forest (RF) algorithm was then applied to integrate PRIF and the genes into a combined imaging-genomics prognostic factors (IGPF) model. Furthermore, we constructed a nomogram incorporating IGPF and clinical predictors as the integrative prognostic model for ccRCC patients. Results: A total of four PRIF and four genes were identified as IGPF and were represented by corresponding risk score in RF model. The integrative IGPF model presented a better prediction performance than the PRIF model alone (average AUCs for 1-, 3-, and 5-year were 0.814 vs. 0.837, 0.74 vs. 0.806, and 0.689 vs. 0.751 in test set). Clinical characteristics including gender, TNM stage and IGPF were independent risk factors. The nomogram integrating clinical predictors and IGPF provided the best net benefit among the three models. Conclusion: In this study we established an integrative prognosis-related nomogram model incorporating imaging-genomic features and clinical indicators. The results indicated that IGPF may contribute to a comprehensive prognosis assessment for ccRCC patients. [ABSTRACT FROM AUTHOR]

Lung adenocarcinoma (LUAD) is one of the leading fatal malignancy with high morbidity and mortality worldwide. However, due to its complicated mechanism and lack of effective clinical therapeutics, early diagnosis and prognosis are still unsatisfactory. Most of the previous studies focused on cancer stem cells (CSCs), the relationship between cancer stemness (stem-like characteristics) and anti-tumor immunity has not been clearly revealed. Therefore, this study aimed to comprehensively analyze the role of cancer stemness and tumor microenvironment (TME) in LUAD using weighted gene co-expression network analysis (WGCNA). We constructed a gene co-expression network, identified key modules, and hub genes, and further explored the relationship between hub gene expression and cancer immunological characteristics through a variety of algorithms, including Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) and Gene Set Enrichment Analysis (GSEA). The hub genes were renamed stemness related genes (SRGs), whose functions were examined at the transcription and protein levels through survival analysis with additional samples, Oncomine database, immunohistochemistry, single cell RNA sequencing (scRNA-seq) and single-sample Gene Set Enrichment Analysis (ssGSEA). Subsequently, Tumor Immune Dysfunction and Exclusion (TIDE) and Connectivity Map (CMap) were implemented for treatment and prognosis analyses. As a result, 15 co-expressed SRGs (CCNA2, CCNB1, CDC20, CDCA5, CDCA8, FEN1, KIF2C, KPNA2, MCM6, NUSAP1, RACGAP1, RRM2, SPAG5, TOP2A, and TPX2) were identified. The overexpression of which was discovered to be associated with reduced immune infiltration in LUAD. It was discovered that there was a general negative correlation between cancer stemness and immunity. The expression of SRGs could probably affect our tumor occurrence, progression, the efficacy of chemotherapy and immunotherapy, and clinical outcomes. In conclusion, the 15 SRGs reported in our study may be used as potential candidate biomarkers for prognostic indicators and therapeutic targets after further validation. [ABSTRACT FROM AUTHOR]

Background: Tongue squamous cell carcinoma (TSCC) is the most common malignant tumor derived from the oral cavity, yet its specific molecular mechanisms have not been fully clarified. The aim of this study was to evaluate the association between potential genes and clinical features through constructing gene co‐expression networks. Methods: The weighted gene co‐expression network analysis was used to construct gene co‐expression networks and to identify candidate key modules and hub genes. The gene expression profiles of GSE31056 obtained from the Gene Expression Omnibus (GEO) database was used to construct co‐expression networks. Results: Five hub genes (FAP, AGTRAP, PLOD1, POSTN, and TSHZ3) were identified and validated at transcriptional levels. Moreover, the protein levels of these five hub genes were also found significantly higher in tumor tissues. Among them, FAP was most associated with immune infiltration. Conclusions: These five candidate biomarkers and therapeutic targets are worthy of further investigation and discussion. [ABSTRACT FROM AUTHOR]

Abstract: NAP (NAPVSIPQ) is a short peptide derived from activity-dependent neuroprotective protein (ADNP) sequence, whose potent and direct neuroprotective capabilities have been widely accepted. However, due to the high risk and inconvenience of intraocular injections, NAP is difficult to be clinically administered as therapeutic agent in treating retinal diseases. Currently, stable transfection of this octapeptide into cells has not been reported, partly because of its small size and lacking of 5’ signal sequence. Here, we have developed a novel NT4-NAP fusion gene by attaching the 5’ nonfunctional preproregion of neurotrophin 4 (NT4) to NAP cDNA. Recombinant adeno-associated virus was established to introduce NT4-NAP construct into cultured rat retinal Müller cells (RMC), resulting in sustained high level NAP production from stable transfection. Functional analyses of RMC cells transfected with NAP revealed the remarkably reduced cytotoxicity and apoptosis of the cells under hypoxia. Furthermore, coculturing of transfected RMC-NAP cells with primary rat retinal neural cells offer marked protection to the latter against hypoxia induced cellular damages. Together our data indicate that stable transfection of NAP into retinal Müller cells with constant NAP production is possible. NAP produced from cellular transfection maintained its biological neuroprotective activities. This targeted gene expression may provide an effective treatment for retinal diseases in the near future. [Copyright &y& Elsevier]

Abstract: It has been widely reported that IAPs family are overexpressed in various malignancies, and their expression patterns are associated with clinical outcome of these diseases. Adenoid cystic carcinoma (ACC) of lachrymal gland is a malignant tumor with a poor prognosis, while, pleomorphic adenoma (PA) is the benign tumor of lachrymal gland epithelia. It was the first time that we investigated the expression profile of IAPs in tissues from ACC and PA, and evaluated the prognostic significance of IAPs. Paraffin-embedded tissues with 27 cases of ACC and 33 cases of PA were enrolled, and another 17 fresh frozen tissues were also collected. Expression of cIAP1, cIAP2, XIAP, Survivin and Livin in embedded tissues was analyzed by immunohistochemistry, and expression of five IAPs in fresh tissues was evaluated by semiquantitive RT-PCR and Western blot. Prognostic significance of IAPs with clinicopathological variables and outcome was then investigated with univariate and multivariate analysis. Survivin and cIAP2 expression in ACC were significantly higher than that of in PA (p < 0.05). cIAP1 and XIAP tended to show stronger expression in ACC than in PA, although the differences were not statistically significant. Livin expression was almost undetectable in both malignancy and benign lesion of lachrymal gland. Survivin expression in lachrymal tumors was localized in cytoplasm exclusively, and its expression was related to T staging and proliferative index in ACC, multivariate analysis demonstrated that Survivin was the only factor that could independently predict poor prognosis of ACC (RR = 3.681, 95%CI: 1.068–12.688, p = 0.039). Furthermore, Survivin expression was associated with progression of PA. Expression of cIAP1, cIAP2, XIAP and Survivin was higher in ACC than in PA tissues, however, only differential expression of Survivin and cIAP2 between ACC and PA was significant. Different prognosis between ACC and PA might be attributable to the different expression profiles of IAPs. Overexpression of Survivin in ACC was associated with poorer survival, which may have clinical impact on diagnosis and therapeutic considerations of this malignancy. [Copyright &y& Elsevier]

Hepatitis B virus (HBV) infection is a critical factor for the initiation and progression of hepatocellular carcinoma (HCC). Gene expression profiles for HBV-associated HCC may provide valuable insight for the diagnosis and treatment of this type of HCC. The present study aimed to screen the differential genes in human HCC tissues based on high-throughput sequencing and to predict the potential therapeutic targets. Total mRNA was extracted from human HCC tissues and paracancerous tissues and sequenced using the Hiseq4000 sequencing platform. Differential gene expressions were screened and further analyzed using quantitative PCR and immunohistochemistry. A total of 2,386 differentially expressed genes were screened. Of these, 1119 were upregulated and 1,267 were downregulated in paracancerous tissues compared with tumor tissues. Gene Ontology term analysis demonstrated that differentially expressed genes were involved in carboxylic acid catabolism, monocarboxylic acid metabolic processes and α-amino acid metabolic processes. Molecular functional analysis revealed that the differentially expressed genes functioned in oxidoreductase activity, for example acting on CH-OH group of donors and permitting identical protein binding, anion binding, coenzyme binding and monocarxylic acid transporter activity. The Kyoto Encyclopedia of Genes and Genomes analysis reported that the differentially expressed genes were primarily concentrated in 20 signaling pathways, such as valine, leucine and leucine degradation, retinol metabolism and the cell cycle. Differential expression of proteins regulating the cell cycle, including stratifin, cyclin B1 and cyclin-dependent kinase 1, were significantly higher in tumor tissue compared with those in paracancerous tissue at both the mRNA and protein levels. These results were consistent with those obtained from high-throughput sequencing, indicating the reliability of the high-throughput sequencing. Together, these results identified differentially expressed genes and predicted the subsequent signaling pathways, which may be involved in the occurrence and development of HCC. Therefore, the present study may provide novel implications in the therapeutic and diagnosis of HCC. [ABSTRACT FROM AUTHOR]

Background: Head and neck squamous cell carcinoma (HNSCC) is the sixth most common tumor in human. Research has shown that HPV status HNSCC is a unique prognosis factor, which may due to its immune infiltration landscape. But the underlying mechanism is unclear.Methods: In this study, we used a combination of several bioinformatics tools, including WCGNA, ssGSEA, CIBERSORT, TIDE,etc., to explore significant genes both related to HPV infection status and immune cell infiltration in HNSCC patients.Results: Combined with several bioinformatics algorithms, eight hub genes were identified, including LTB, CD19, CD3D, SKAP1, KLRB1, CCL19, TBC1D10C and ARHGAP4. In HNSCC population, the hub genes had a stable co-expression, which was related to immune cell infiltration, especially CD8+ T cells, and the infiltrative immune cells were in a dysfunctional status. Samples with high hub genes expression presented with better response to immune check point block (ICB) therapy and sensitivity to bleomycin and methotrexate.Conclusions: The eight hub genes we found presented with a stable co-expression in immune cell infiltration of HPV + ve HNSCC population. The co-expression of hub genes related to an immune microenvironment featuring an increase in immune cells but high degree of immune dysfunction status. Patients with high hub gene expression had a better response to ICB treatment, bleomycin and methotrexate. The co-expression of hub genes may be related to immune infiltration status in patients. The concrete molecular mechanism of hub genes function demands further exploration. [ABSTRACT FROM AUTHOR]

• We identified 23 co-expressed immune-related genes (IRGs) in laryngeal cancer samples. • These IRGs showed robust expression characteristics in multiple independent data sets. • The IRGs were significantly related to immune infiltration patterns and function. • The IRGs were related to prediction of patients' responses to ICB therapy. • The IRGs were also associated with sensitivity prediction of chemotherapeutic drugs. Laryngeal cancer is a common malignant tumor that originates from the larynx, yet its molecular mechanisms have not been thoroughly explored. The purpose of this study was to identify and evaluate immune-related genes in laryngeal cancer through gene co-expression networks, which may serve as biomarkers for its immunotherapy. We applied ESTIMATE to evaluate the immune-infiltration landscape of tumor microenvironment. The co-expression networks were constructed by weighted gene co expression network analysis (WGCNA) and compared with the existing human immune related genes (IRGs) to determine the co-expressed IRGs. GSVA combined with CIBERSORT and ssGSEA illustrated the correlation of hub genes and immune infiltration patterns. TIDE algorithm and Subclass mapping evaluated the function of hub genes in predicting immune function and immunotherapeutic sensitivity. The pRRophetic was employed in the sensitivity prediction of chemotherapeutic drugs. A total of 23 co-expressed IRGs were identified and showed robust expression characteristics. These genes were significantly related to immune infiltration patterns, immune function and sensitivity prediction of immunotherapy and chemotherapeutic drugs for laryngeal cancer patients. Genetic alteration in somatic mutation level and related pathways were also revealed. The 23 co-expressed IRGs may act as immunotherapeutic biomarkers and potential therapeutic targets for laryngeal cancer with certain expression robustness. The molecular mechanisms deserve further investigation, which will guide clinical treatment in the future. [ABSTRACT FROM AUTHOR]

Yishen Gushu Formula (YSGSF) is composed of Epimedium, prepared Rehmannia, Drynaria, Eucommia, Dodder, ginseng, Astragalus, Ligusticum wallichii, Aucklandia and Panax notoginseng. It can improve bone mineral density by regulating bone metabolism. However, the mechanism of YSGSF in the treatment of Postmenopausal osteoporosis (PMOP) remains unclear. The compounds, targets, and molecular mechanisms of YSGSF in the treatment of PMOP were investigated using broad-spectrum target metabolomics from plants, combined with network pharmacology and animal studies, leading to a discussion on a novel approach to understanding YSGSF's action in PMOP treatment. Using ultra-performance liquid chromatography coupled with triple quadrupole-linear ion trap tandem mass spectrometry (UPLC-QTRAP-MS/MS) within a comprehensive targeted metabolomics framework, the active constituents of YSGSF were identified. This, alongside network pharmacology and molecular docking, facilitated the identification of critical signaling pathways and targets pertinent to YSGSF's therapeutic effect on PMOP. Subsequently, an animal model for PMOP was developed. Following intervention grouping, rats' weight changes were recorded; serum bone metabolic factors were assessed via ELISA; bone microstructure was examined using HE staining and Micro-CT; and key signaling pathway proteins and genes were analyzed through immunohistochemistry to validate YSGSF's potential mechanism in PMOP treatment. A total of 84 main active components of YSGSF were identified. The key signaling pathways affected by YSGSF in the treatment of PMOP were the TNF and IL-7 signaling pathways, closely related to TNF-α, IL-1β, c-jun and other protein targets. The results of animal experiments showed that YSGSF could downregulate the expression of TNF-a, IL-1β and c-Jun proinflammatory factors by regulating the TNF and IL-7 signaling pathways and regulate the inflammatory response, osteocyte differentiation and apoptosis to control the development of PMOP. YSGSF activates the TNF-α and IL-7 signaling pathways in PMOP rats, reducing TNF-α and IL-1β levels, the c-Jun inflammatory response, and osteocyte differentiation and apoptosis, thus playing a significant role in treating PMOP. [Display omitted] [ABSTRACT FROM AUTHOR]

Objectives: To evaluate the efficacy of interleukin-8 (IL-8) as a possible biomarker for diagnosis and treatment of benign prostatic hyperplasia (BPH) with chronic prostatitis. Histologic inflammation can be demonstrated in most BPH pathologic specimens. To provide objective parameters of inflammation, this prospective study quantified the IL-8 in expressed prostatic secretion (EPS) from BPH patients with or without histologic inflammation. Methods: White blood cell (WBC) count and enzyme-linked immunosorbent assays of the EPS for IL-8 were done in 44 patients who underwent transurethral prostatic resection because of benign prostatic enlargement before the operations. The correlation between IL-8 and WBC count in EPS; prostatic specific antigen; and International Prostate Symptom Score, irritative, and obstructive subscores was determined by Pearson correlation analysis. Results: IL-8 was detectable in all patients (the threshold of detection for IL-8 is 5 pg/mL). Twenty-one (47.7%) BPH patients had chronic prostatitis. The mean level of IL-8 in EPS was higher in BPH with chronic prostatitis than in simple BPH (median ± SE, 8175 ± 3789 pg/mL vs 2806 ± 1009 pg/mL). The catheter and age seemed to have no impact on the level of IL-8 in EPS. Statistically significant correlation was only found between IL-8 and WBC count. The sensitivity and specificity of IL-8 in EPS identifying the BPH with chronic prostatitis from the simple BPH were 85.7% and 91.3% respectively, at a cut-point of 3992 pg/mL. Conclusions: IL-8 is significantly elevated in BPH patients with chronic prostatitis. IL-8 in EPS can serve as a reliable biomarker applicable to identifying BPH with chronic prostatitis from simple BPH. [Copyright &y& Elsevier]