Autophagy-related IFNG is a prognostic and immunochemotherapeutic biomarker of COAD patients

BackgroundNumerous studies have shown autophagy affects cellular immune responses. This study aims to explore prognosis and immunotherapeutic biomarkers related to autophagy in colon adenocarcinoma (COAD).MethodsBased on R software, we performed the ssGSEA, differential expression analysis, Kaplan-Meier survival analysis, correlation analysis, and enrichment analysis. For wet experiment, we did qRT-PCR, immunohistochemistry and CCK-8 experiments.ResultsUsing autophagy-related genes (ARGs) and the ssGSEA, COAD patients were divided into low and high autophagy groups. For immune score, stromal score, tumor purity, tumor infiltrating immune cells, co-signaling molecules, tumor mutational burden, microsatellite instability, mismatch repair, immune-related pathways, immune signatures, somatic mutations and subtype analysis, high autophagy group might benefit more from immunotherapy. Among 232 ARGs, IFNG was generally significantly correlated with tumor immunotherapy biomarkers (PD-L1, CD8A and cytotoxic T lymphocytes (CTL)). The disease-free survival of high IFNG group was significantly longer than that of low group. On above-mentioned immune-related research, the high IFNG group reached the same conclusion. The qRT-PCR and IHC analysis confirmed that IFNG was significantly higher expressed in dMMR samples compared to pMMR samples. For chemotherapy, the autophagy and IFNG were significantly negatively related to the chemosensitivity to cisplatin; IFNG inhibitor glucosamine increased cisplatin chemoresistance while IFNG increased cisplatin chemosensitivity; IFNG could reverse glucosamine induced chemoresistance. The functional enrichment analysis of IFNG, PD-L1, CD8A and 20 similar proteins were related to the activation of the immune system. The GSEA and ceRNA network partly described interaction mechanisms of IFNG with PD-L1 and CD8A.ConclusionAutophagy score and IFNG expression were novel immunotherapy predictive biomarkers, which might play predictive effects through the JAK-STAT signaling pathway. IFNG might be a potential targeted therapy for cisplatin resistant colon cancer. Besides, IFNG was also a prognostic indicator

Comprehensive RNA-seq analysis of potential therapeutic targets of Gan–Dou–Fu–Mu decoction for treatment of Wilson disease using a toxic milk mouse model

Background: Gan–Dou–Fu–Mu decoction (GDFMD) improves liver fibrosis in experimental and clinical studies including those on toxic mouse model of Wilson disease (Model). However, the mechanisms underlying the effect of GDFMD have not been characterized. Herein, we deciphered the potential therapeutic targets of GDFMD using transcriptome analysis. Methods: We constructed a tx-j Wilson disease (WD) mouse model, and assessed the effect of GDFMD on the liver of model mice by hematoxylin and eosin, Masson, and immunohistochemical staining. Subsequently, we identified differentially expressed genes (DEGs) that were upregulated in the Model (Model vs. control) and those that were downregulated upon GDFMD treatment (compared to the Model) using RNA-sequencing (RNA-Seq). Biological functions and signaling pathways in which the DEGs were involved were determined by gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses. A protein–protein interaction (PPI) network was constructed using the STRING database, and the modules were identified using MCODE plugin with the Cytoscape software. Several genes identified in the RNA-Seq analysis were validated by real-time quantitative PCR. Results: Total of 2124 DEGs were screened through the Model vs. control and Model vs. GDFMD comparisons, and dozens of GO and KEGG pathway terms modulated by GDFMD were identified. Dozens of pathways involved in metabolism (including metabolic processes for organic acids, carboxylic acids, monocarboxylic acids, lipids, fatty acids, cellular lipids, steroids, alcohols, eicosanoids, long-chain fatty acids), immune and inflammatory response (such as complement and coagulation cascades, cytokine–cytokine receptor interaction, inflammatory mediator regulation of TRP channels, antigen processing and presentation, T-cell receptor signaling pathway), liver fibrosis (such as ECM-receptor interactions), and cell death (PI3K-Akt signaling pathway, apoptosis, TGF-beta signaling pathway, etc.) were identified as potential targets of GDFMD in the Model. Some hub genes and four modules were identified in the PPI network. The results of real-time quantitative PCR analysis were consistent with those of RNA-Seq analysis. Conclusions: We performed gene expression profiling of GDFMD-treated WD model mice using RNA-Seq analysis and found the genes, pathways, and processes effected by the treatment. Our study provides a theoretical basis to prevent liver fibrosis resulting from WD using GDFMD

Dysfunction of the Lenticular Nucleus Is Associated with Dystonia in Wilson’s Disease

Dysfunction of the lenticular nucleus is thought to contribute to neurological symptoms in Wilson’s disease (WD). However, very little is known about whether and how the lenticular nucleus influences dystonia by interacting with the cerebral cortex and cerebellum. To solve this problem, we recruited 37 WD patients (20 men; age, 23.95 ± 6.95 years; age range, 12–37 years) and 37 age- and sex-matched healthy controls (HCs) (25 men; age, 25.19 ± 1.88 years; age range, 20–30 years), and each subject underwent resting-state functional magnetic resonance imaging (RS-fMRI) scans. The muscle biomechanical parameters and Unified Wilson Disease Rating Scale (UWDRS) were used to evaluate the level of dystonia and clinical representations, respectively. The lenticular nucleus, including the putamen and globus pallidus, was divided into 12 subregions according to dorsal, ventral, anterior and posterior localization and seed-based functional connectivity (FC) was calculated for each subregion. The relationships between FC changes in the lenticular nucleus with muscle tension levels and clinical representations were further investigated by correlation analysis. Dystonia was diagnosed by comparing all WD muscle biomechanical parameters with healthy controls (HCs). Compared with HCs, FC decreased from all subregions in the putamen except the right ventral posterior part to the middle cingulate cortex (MCC) and decreased FC of all subregions in the putamen except the left ventral anterior part to the cerebellum was observed in patients with WD. Patients with WD also showed decreased FC of the left globus pallidus primarily distributed in the MCC and cerebellum and illustrated decreased FC from the right globus pallidus to the cerebellum. FC from the putamen to the MCC was significantly correlated with psychiatric symptoms. FC from the putamen to the cerebellum was significantly correlated with muscle tension and neurological symptoms. Additionally, the FC from the globus pallidus to the cerebellum was also associated with muscle tension. Together, these findings highlight that lenticular nucleus–cerebellum circuits may serve as neural biomarkers of dystonia and provide implications for the neural mechanisms underlying dystonia in WD

Identification of 6 Hub Proteins and Protein Risk Signature of Colorectal Cancer

Background. Colorectal cancer (CRC) is the second most common cause of cancer death in the United States and the third most common cancer globally. The incidence of CRC tends to be younger, and we urgently need a reliable prognostic assessment strategy. Methods. Protein expression profile and clinical information of 390 CRC patients/samples were downloaded from the TCPA and TCGA database, respectively. The Kaplan-Meier, Cox regression, and Pearson correlation analysis were applied in this study. Results. Based on the TCPA and TCGA database, we screened 6 hub proteins and first constructed protein risk signature, all of which were significantly associated with CRC patients’ overall survival (OS). The risk score was an independent prognostic factor and significantly related with the size of the tumor in situ (T). 6 hub proteins were differentially expressed in cancer and normal tissues and in different CRC stages, which were validated at the ONCOMINE database. Next, 40 coexpressed proteins of 6 hub proteins were extracted from the TCPA database. In the protein-protein interaction (PPI) network, HER1, HER2, and CTNNB1 were at the center. Function enrichment analysis illustrated that 46 proteins were mainly involved in the EGFR (HER1) tyrosine kinase inhibitor resistance pathway. Conclusion. Studies indicated that 6 hub proteins might be considered as new targets for CRC therapies, and the protein risk signature can be used to predict the OS of CRC patients

Activated gastric cancer-associated fibroblasts contribute to the malignant phenotype and 5-FU resistance via paracrine action in gastric cancer

Abstract Background Cancer-associated fibroblasts (CAFs) play important roles in tumor progression. However, the behaviors of activated CAFs in gastric cancer remain to be determined. The aim of the present study was to investigate the correlations between activated gastric CAFs and the prognosis of patients with gastric cancer, and to determine the effects of activated CAFs on the malignant phenotype and 5-fluorouracil resistance in this cancer. Methods Ninety-five patients with primary gastric cancer were enrolled in this study. Activation states of gastric CAFs were evaluated by immunohistochemistry. A modified method for the primary culture of gastric CAFs was employed. Types of CAFs and activation states were identified by immunocytochemical and immunofluorescent staining. Cell co-culture and gastric CAF conditioned medium transfer models were established to investigate the paracrine effects of activated CAFs on the migration and invasion of gastric cell lines. The half maximal inhibitory concentration of 5-fluorouracil and levels of cell apoptosis were examined using cell viability assay and flow cytometry, respectively. Protein expression levels of associated molecules were measured by Western blotting. Results Kaplan–Meier survival curves showed that activated gastric CAFs identified via fibroblast activation protein were significantly related to poorer cumulative survival in gastric cancer patients. Five strains of CAFs were successfully cultured via the modified culture method, and three gastric CAFs strains were identified as activated gastric CAFs. The migration and invasion abilities of gastric cells were significantly enhanced in both the co-culture group and the conditioned medium group. The half maximal inhibitory concentration for 5-fluorouracil in BGC-823 cells was elevated after treatment with conditioned medium, and early apoptosis was inhibited. Additionally, an obvious elevation of epithelial–mesenchymal transition level was observed in the conditioned medium group. Conclusions Activated gastric CAFs correlate with a poor prognosis of cancer patients and may contribute to the malignant phenotype and the development of resistance to 5-fluorouracil via paracrine action in gastric cancer. Gastric CAFs with a specific activation state might be used as a tumor biomarker within the microenvironment for prognosis and as a new therapeutic target for chemoresistant gastric cancer

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Additional file 3. Wound-healing assay in MKN-45 and SGC-7901 cell lines. MKN-45 and SGC-7901 cells were co-cultured with GCAFs or CM from GCAFs for 72 hours before the wounds were generated. And the scratch area after 48 hours was measured to evaluate the migration abilities of cancer cells (scale bar=500 Âľm)

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Additional file 2. Correlations between FAP staining and the clinicopathology of gastric cancer. The table in this file shows the correlations between FAP staining in GCAFs and the clinicopathology of gastric cancer

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Additional file 1. Information data of the cases enrolled in this study. This file includes the clinicopathological information of cases enrolled in this study