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1.
Diagn Pathol ; 19(1): 105, 2024 Aug 02.
Article in English | MEDLINE | ID: mdl-39095799

ABSTRACT

Hepatocellular carcinoma (HCC) is a malignant tumor. It is estimated that approximately 50-80% of HCC cases worldwide are caused by hepatitis b virus (HBV) infection, and other pathogenic factors have been shown to promote the development of HCC when coexisting with HBV. Understanding the molecular mechanisms of HBV-induced hepatocellular carcinoma (HBV-HCC) is crucial for the prevention, diagnosis, and treatment of the disease. In this study, we analyzed the molecular mechanisms of HBV-induced HCC by combining bioinformatics and deep learning methods. Firstly, we collected a gene set related to HBV-HCC from the GEO database, performed differential analysis and WGCNA analysis to identify genes with abnormal expression in tumors and high relevance to tumors. We used three deep learning methods, Lasso, random forest, and SVM, to identify key genes RACGAP1, ECT2, and NDC80. By establishing a diagnostic model, we determined the accuracy of key genes in diagnosing HBV-HCC. In the training set, RACGAP1(AUC:0.976), ECT2(AUC:0.969), and NDC80 (AUC: 0.976) showed high accuracy. They also exhibited good accuracy in the validation set: RACGAP1(AUC:0.878), ECT2(AUC:0.731), and NDC80(AUC:0.915). The key genes were found to be highly expressed in liver cancer tissues compared to normal liver tissues, and survival analysis indicated that high expression of key genes was associated with poor prognosis in liver cancer patients. This suggests a close relationship between key genes RACGAP1, ECT2, and NDC80 and the occurrence and progression of HBV-HCC. Molecular docking results showed that the key genes could spontaneously bind to the anti-hepatocellular carcinoma drugs Lenvatinib, Regorafenib, and Sorafenib with strong binding activity. Therefore, ECT2, NDC80, and RACGAP1 may serve as potential biomarkers for the diagnosis of HBV-HCC and as targets for the development of targeted therapeutic drugs.


Subject(s)
Biomarkers, Tumor , Carcinoma, Hepatocellular , Computational Biology , Liver Neoplasms , Machine Learning , Carcinoma, Hepatocellular/virology , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/diagnosis , Liver Neoplasms/virology , Liver Neoplasms/genetics , Liver Neoplasms/diagnosis , Humans , Biomarkers, Tumor/genetics , Hepatitis B virus/genetics , GTPase-Activating Proteins/genetics , Hepatitis B/complications , Hepatitis B/diagnosis , Hepatitis B/virology , Gene Expression Profiling/methods , Gene Expression Regulation, Neoplastic , Databases, Genetic
2.
Int J Biochem Cell Biol ; 174: 106635, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39098591

ABSTRACT

ArfGAP with coiled-coil, ankyrin repeat and PH domains 3 (ACAP3) level has been confirmed to be downregulated in papillary thyroid carcinoma (PTC). Histone deacetylase inhibitors (HDACIs) have therapeutic effects on PTC. Accordingly, this study probed into the potential relation of histone deacetylase 2 (HDAC2) and ACAP3 in PTC. Expressions of ACAP3 and HDAC2 in PTC were investigated by quantitative real-time polymerase chain reaction (qRT-PCR). The relationship between HDAC2 and ACAP3 was predicted by Pearson analysis. Cell functional assays (cell counting kit-8, transwell, wound healing and flow cytometry assays) and rescue assay were carried out to determine the effects of HDAC2/ACAP3 axis on biological behaviors of PTC cells. Expressions of apoptosis-, epithelial-mesenchymal transition-, Protein Kinase B (AKT)-, and P53-related proteins were measured by Western blot. ACAP3 level was downregulated in PTC tissues and cells. ACAP3 overexpression (oe-ACAP3) suppressed viability, proliferation, migration and invasion of PTC cells, facilitated apoptosis, downregulated the expressions of Protein Kinase B (Bcl-2) and N-cadherin, upregulated the expressions of Bcl-2 associated protein X (Bax) and E-cadherin, diminished the p-AKT/AKT ratio and elevated the p-p53/p53 ratio; however, ACAP3 silencing or HDAC2 overexpression (oe-HDAC2) did the opposite. HDAC2 negatively correlated with ACAP3. The tumor-suppressing effect of oe-ACAP3 in PTC was reversed by oe-HDAC2. Collectively, ACAP3 negatively regulated by HDAC2 suppresses the proliferation and metastasis while facilitating apoptosis of PTC cells.


Subject(s)
Apoptosis , Cell Proliferation , GTPase-Activating Proteins , Histone Deacetylase 2 , Thyroid Cancer, Papillary , Thyroid Neoplasms , Humans , Histone Deacetylase 2/metabolism , Histone Deacetylase 2/genetics , Histone Deacetylase 2/antagonists & inhibitors , Thyroid Cancer, Papillary/pathology , Thyroid Cancer, Papillary/genetics , Thyroid Cancer, Papillary/metabolism , Thyroid Neoplasms/pathology , Thyroid Neoplasms/metabolism , Thyroid Neoplasms/genetics , Cell Line, Tumor , Apoptosis/drug effects , Cell Proliferation/drug effects , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Gene Expression Regulation, Neoplastic/drug effects , Epithelial-Mesenchymal Transition/drug effects , Cell Movement/drug effects , Male , Female , Middle Aged
3.
Sci Rep ; 14(1): 18720, 2024 08 12.
Article in English | MEDLINE | ID: mdl-39134572

ABSTRACT

ARHGAP25, a member of the ARHGAP family, encodes a negative regulator of Rho-GTPase that is important for actin remodeling, cell polarity, and cell migration. ARHGAP25 is down-regulated in a variety of solid tumors and promotes cancer cell growth, migration, and invasion. However, nothing is understood about ARHGAP25's biological function in osteosarcoma. This work used qPCR and WB to confirm the expression of ARHGAP25 in osteosarcoma following the initial analysis of its expression in pan-cancer. For GO and KEGG analysis, we have chosen 300 genes from the TARGET osteosarcoma data that had the strongest positive correlation with ARHGAP25, and we created nomogram and calibration charts. We simultaneously overexpressed ARHGAP25 in osteosarcoma cells to examine its impact on apoptosis and proliferation. By using MSP, we determined their methylation status in osteosarcoma cells and normal bone cells. We observed that ARHGAP25 was significantly downregulated in a range of malignancies, including osteosarcoma, and was associated with poor patient outcomes. The decrease of ARHGAP25 expression in osteosarcoma is related to DNA methylation. Overexpression of ARHGAP25 induced apoptosis and inhibited the proliferation of osteosarcoma cells in vitro. In addition, ARHGAP25 is also associated with immune-related pathways in osteosarcoma. These findings suggest that ARHGAP25 is a valuable prognostic biomarker in osteosarcoma patients.


Subject(s)
Apoptosis , Bone Neoplasms , Cell Proliferation , Computational Biology , DNA Methylation , GTPase-Activating Proteins , Gene Expression Regulation, Neoplastic , Osteosarcoma , Osteosarcoma/genetics , Osteosarcoma/pathology , Osteosarcoma/metabolism , Humans , GTPase-Activating Proteins/genetics , GTPase-Activating Proteins/metabolism , Computational Biology/methods , Bone Neoplasms/genetics , Bone Neoplasms/pathology , Bone Neoplasms/metabolism , Bone Neoplasms/mortality , Apoptosis/genetics , Cell Line, Tumor , Cell Proliferation/genetics , Prognosis , Male , Female , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Clinical Relevance
4.
Cancer Med ; 13(15): e70043, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39087856

ABSTRACT

BACKGROUND: Recent research indicates a positive correlation between DEP structural domain-containing 1B (DEPDC1B) and the cell cycle in various tumors. However, the role of DEPDC1B in the infiltration of the tumor immune microenvironment (TIME) remains unexplored. METHODS: We analyzed the differential expression and prognostic significance of DEPDC1B in colon adenocarcinoma (COAD) using the R package "limma" and the Gene Expression Profiling Interactive Analysis (GEPIA) website. Gene set enrichment analysis (GSEA) was employed to investigate the functions and interactions of DEPDC1B expression in COAD. Cell Counting Kit-8 (CCK-8) assays and colony formation assays were utilized to assess the proliferative function of DEPDC1B. Correlations between DEPDC1B expression and tumor-infiltrating immune cells, immune checkpoints, tumor mutational burden (TMB), and microsatellite instability (MSI) status were examined using Spearman correlation analysis and CIBERSORT. RESULTS: DEPDC1B was highly expressed in COAD. Elevated DEPDC1B expression was associated with lower epithelial-to-mesenchymal transition (EMT) and TNM stages, leading to a favorable prognosis. DEPDC1B mRNA was prominently expressed in COAD cell lines. CCK-8 and colony formation assays demonstrated that DEPDC1B inhibited the proliferation of COAD cells. Analysis using the CIBERSORT database and Spearman correlation revealed that DEPDC1B correlated with four types of tumor-infiltrating immune cells. Furthermore, high DEPDC1B expression was linked to the expression of PD-L1, CTLA4, SIGLEC15, PD-L2, TMB, and MSI-H. High DEPDC1B expression also indicated responsiveness to anti-PD-L1 immunotherapy. CONCLUSIONS: DEPDC1B inhibits the proliferation of COAD cells and positively regulates the cell cycle, showing a positive correlation with CCNB1 and PBK expression. DEPDC1B expression in COAD is associated with tumor-infiltrating immune cells, immune checkpoints, TMB, and MSI-H in the tumor immune microenvironment. This suggests that DEPDC1B may serve as a novel prognostic marker and a potential target for immunotherapy in COAD.


Subject(s)
Adenocarcinoma , Colonic Neoplasms , GTPase-Activating Proteins , Gene Expression Regulation, Neoplastic , Tumor Microenvironment , Humans , Colonic Neoplasms/genetics , Colonic Neoplasms/immunology , Colonic Neoplasms/pathology , Colonic Neoplasms/metabolism , Adenocarcinoma/genetics , Adenocarcinoma/immunology , Adenocarcinoma/pathology , Tumor Microenvironment/immunology , Tumor Microenvironment/genetics , Prognosis , GTPase-Activating Proteins/genetics , GTPase-Activating Proteins/metabolism , Cell Line, Tumor , Cell Proliferation , Lymphocytes, Tumor-Infiltrating/immunology , Lymphocytes, Tumor-Infiltrating/metabolism , Epithelial-Mesenchymal Transition/genetics , Epithelial-Mesenchymal Transition/immunology , Genes, Tumor Suppressor , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Microsatellite Instability , Male , B7-H1 Antigen/genetics , B7-H1 Antigen/metabolism , Cyclin B1/genetics , Cyclin B1/metabolism , Female
5.
Cell Death Dis ; 15(7): 533, 2024 Jul 27.
Article in English | MEDLINE | ID: mdl-39068164

ABSTRACT

Renal cell carcinoma (RCC) is considered a "metabolic disease" characterized by elevated glycolysis in patients with advanced RCC. Tyrosine kinase inhibitor (TKI) therapy is currently an important treatment option for advanced RCC, but drug resistance may develop in some patients. Combining TKI with targeted metabolic therapy may provide a more effective approach for patients with advanced RCC. An analysis of 14 RCC patients (including three needle biopsy samples with TKI resistance) revealed by sing-cell RNA sequencing (scRNA-seq) that glycolysis played a crucial role in poor prognosis and drug resistance in RCC. TCGA-KIRC and glycolysis gene set analysis identified DEPDC1 as a target associated with malignant progression and drug resistance in KIRC. Subsequent experiments demonstrated that DEPDC1 promoted malignant progression and glycolysis of RCC, and knockdown DEPDC1 could reverse TKI resistance in RCC cell lines. Bulk RNA sequencing (RNA-seq) and non-targeted metabolomics sequencing suggested that DEPDC1 may regulate RCC glycolysis via AKT/mTOR/HIF1α pathway, a finding supported by protein-level analysis. Clinical tissue samples from 98 RCC patients demonstrated that DEPDC1 was associated with poor prognosis and predicted RCC metastasis. In conclusion, this multi-omics analysis suggests that DEPDC1 could serve as a novel target for TKI combined with targeted metabolic therapy in advanced RCC patients with TKI resistance.


Subject(s)
Carcinoma, Renal Cell , Glycolysis , Hypoxia-Inducible Factor 1, alpha Subunit , Kidney Neoplasms , Proto-Oncogene Proteins c-akt , TOR Serine-Threonine Kinases , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/drug therapy , Humans , Glycolysis/drug effects , TOR Serine-Threonine Kinases/metabolism , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Kidney Neoplasms/drug therapy , Kidney Neoplasms/genetics , Proto-Oncogene Proteins c-akt/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Cell Line, Tumor , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Signal Transduction , Mice , Animals , Male , Female , Mice, Nude , Drug Resistance, Neoplasm/drug effects , Gene Expression Regulation, Neoplastic
6.
Cardiovasc Diabetol ; 23(1): 258, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39026321

ABSTRACT

BACKGROUND: Insulin signaling regulates cardiac substrate utilization and is implicated in physiological adaptations of the heart. Alterations in the signaling response within the heart are believed to contribute to pathological conditions such as type-2 diabetes and heart failure. While extensively investigated in several metabolic organs using phosphoproteomic strategies, the signaling response elicited in cardiac tissue in general, and specifically in the specialized cardiomyocytes, has not yet been investigated to the same extent. METHODS: Insulin or vehicle was administered to male C57BL6/JRj mice via intravenous injection into the vena cava. Ventricular tissue was extracted and subjected to quantitative phosphoproteomics analysis to evaluate the insulin signaling response. To delineate the cardiomyocyte-specific response and investigate the role of Tbc1d4 in insulin signal transduction, cardiomyocytes from the hearts of cardiac and skeletal muscle-specific Tbc1d4 knockout mice, as well as from wildtype littermates, were studied. The phosphoproteomic studies involved isobaric peptide labeling with Tandem Mass Tags (TMT), enrichment for phosphorylated peptides, fractionation via micro-flow reversed-phase liquid chromatography, and high-resolution mass spectrometry measurements. RESULTS: We quantified 10,399 phosphorylated peptides from ventricular tissue and 12,739 from isolated cardiomyocytes, localizing to 3,232 and 3,128 unique proteins, respectively. In cardiac tissue, we identified 84 insulin-regulated phosphorylation events, including sites on the Insulin Receptor (InsrY1351, Y1175, Y1179, Y1180) itself as well as the Insulin receptor substrate protein 1 (Irs1S522, S526). Predicted kinases with increased activity in response to insulin stimulation included Rps6kb1, Akt1 and Mtor. Tbc1d4 emerged as a major phosphorylation target in cardiomyocytes. Despite limited impact on the global phosphorylation landscape, Tbc1d4 deficiency in cardiomyocytes attenuated insulin-induced Glut4 translocation and induced protein remodeling. We observed 15 proteins significantly regulated upon knockout of Tbc1d4. While Glut4 exhibited decreased protein abundance consequent to Tbc1d4-deficiency, Txnip levels were notably increased. Stimulation of wildtype cardiomyocytes with insulin led to the regulation of 262 significant phosphorylation events, predicted to be regulated by kinases such as Akt1, Mtor, Akt2, and Insr. In cardiomyocytes, the canonical insulin signaling response is elicited in addition to regulation on specialized cardiomyocyte proteins, such as Kcnj11Y12 and DspS2597. Details of all phosphorylation sites are provided. CONCLUSION: We present a first global outline of the insulin-induced phosphorylation signaling response in heart tissue and in isolated adult cardiomyocytes, detailing the specific residues with changed phosphorylation abundances. Our study marks an important step towards understanding the role of insulin signaling in cardiac diseases linked to insulin resistance.


Subject(s)
Insulin , Mice, Inbred C57BL , Mice, Knockout , Myocytes, Cardiac , Phosphoproteins , Proteomics , Signal Transduction , Animals , Myocytes, Cardiac/metabolism , Male , Insulin/metabolism , Phosphorylation , Phosphoproteins/metabolism , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Receptor, Insulin/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Mice
7.
Int J Biol Macromol ; 275(Pt 1): 133594, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38960258

ABSTRACT

Exosomal miRNAs have vital functions in mediating intercellular communication as well as tumor occurrence and development. Thus, our research was aimed at exploring the regulatory mechanisms of exosomal miR-130b-3p/DEP domain containing 1 (DEPDC1)/transforming growth factor-ß (TGF-ß) signaling pathway in non-small cell lung cancer (NSCLC). Here we indicated that exosomal miR-130b-3p expression decreased in the serum of NSCLC patients, and it was of significant diagnostic value. Moreover, elevated miR-130b-3p levels suppressed the proliferation and migration of NSCLC cells, and enhanced their apoptosis. Conversely, miR-130b-3p down-regulation led to an opposite effect. As the upstream of DEPDC1, miR-130b-3p directly bound to 3'UTR in DEPDC1 to regulate its expression. DEPDC1 levels affected the proliferation, migration, and apoptosis of NSCLC cells via TGF-ß signaling pathway. Exosomal miR-130b-3p was highly expressed in BEAS-2B cells, besides, BEAS-2B cells transferred exosomal miR-130b-3p to NSCLC cells. Finally, exosomal miR-130b-3p suppressed NSCLC cell growth and migration, promoted their apoptosis via TGF-ß signaling pathway by decreasing DEPDC1 expression, and suppressed epithelial-mesenchymal transition (EMT) in NSCLC cells. In conclusion, exosomal miR-130b-3p has the potential to be a predictive biomarker for NSCLC, thereby stimulating the exploration of diagnostic and therapeutic approaches targeting NSCLC.


Subject(s)
Apoptosis , Carcinoma, Non-Small-Cell Lung , Cell Movement , Cell Proliferation , Exosomes , Gene Expression Regulation, Neoplastic , Lung Neoplasms , MicroRNAs , Signal Transduction , Transforming Growth Factor beta , Humans , Carcinoma, Non-Small-Cell Lung/genetics , Carcinoma, Non-Small-Cell Lung/pathology , Carcinoma, Non-Small-Cell Lung/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Transforming Growth Factor beta/metabolism , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Lung Neoplasms/metabolism , Cell Proliferation/genetics , Cell Movement/genetics , Cell Line, Tumor , Apoptosis/genetics , Exosomes/metabolism , Exosomes/genetics , GTPase-Activating Proteins/genetics , GTPase-Activating Proteins/metabolism , Male , Female , Neoplasm Metastasis , Middle Aged
8.
Life Sci Alliance ; 7(10)2024 Oct.
Article in English | MEDLINE | ID: mdl-39084876

ABSTRACT

Phagocytosis is an important immune response that protects the host from pathogen invasion. Rit1 GTPase is known to be involved in diverse cellular processes. However, its role in FcγR-mediated phagocytosis remains unclear. Our live-cell imaging analysis revealed that Rit1 was localized to the membranes of F-actin-rich phagocytic cups in RAW264 macrophages. Rit1 knockout and expression of the GDP-locked Rit1 mutant suppressed phagosome formation. We also found that TBC1D10B, a GAP for the Rab family GTPases, colocalizes with Rit1 in the membranes of phagocytic cups. Expression and knockout studies have shown that TBC1D10B decreases phagosome formation in both Rab-GAP activity-dependent and -independent manners. Notably, the expression of the GDP-locked Rit1 mutant or Rit1 knockout inhibited the dissociation of TBC1D10B from phagocytic cups. In addition, the expression of the GTP-locked Rit1 mutant promoted the dissociation of TBC1D10B in phagocytic cups and restored the rate of phagosome formation in TBC1D10B-expressing cells. These data suggest that Rit1-TBC1D10B signaling regulates FcγR-mediated phagosome formation in macrophages.


Subject(s)
GTPase-Activating Proteins , Macrophages , Phagocytosis , Phagosomes , Receptors, IgG , Signal Transduction , Animals , Receptors, IgG/metabolism , Mice , Phagosomes/metabolism , Macrophages/metabolism , Phagocytosis/genetics , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , RAW 264.7 Cells , rab GTP-Binding Proteins/metabolism , rab GTP-Binding Proteins/genetics , Actins/metabolism
9.
Arch Microbiol ; 206(8): 339, 2024 Jul 03.
Article in English | MEDLINE | ID: mdl-38958759

ABSTRACT

Cordyceps cicadae is recognized for its medicinal properties, attributed to bioactive constituents like polysaccharides and adenosine, which have been shown to improve kidney and liver functions and possess anti-tumor properties. Rho GTPase activating proteins (Rho GAPs) serve as inhibitory regulators of Rho GTPases in eukaryotic cells by accelerating the GTP hydrolysis of Rho GTPases, leading to their inactivation. In this study, we explored the function of the CcRga8 gene in C. cicadae, which encodes a Rho-type GTPase activating protein. Our study found that the knockout of CcRga8 resulted in a decrease in polysaccharide levels and an increase in adenosine concentration. Furthermore, the mutants exhibited altered spore yield and morphology, fruiting body development, decreased infectivity, reduced resistance to hyperosmotic stress, oxidative conditions, and cell wall inhibitors. These findings suggest that CcRga8 plays a crucial role in the development, stress response, and bioactive compound production of C. cicadae.


Subject(s)
Cordyceps , Cordyceps/metabolism , Cordyceps/genetics , Cordyceps/growth & development , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Fungal Proteins/metabolism , Fungal Proteins/genetics , Adenosine/metabolism , Polysaccharides/metabolism , Fruiting Bodies, Fungal/growth & development , Fruiting Bodies, Fungal/metabolism , Fruiting Bodies, Fungal/genetics
10.
Mol Biol Cell ; 35(8): ar113, 2024 Aug 01.
Article in English | MEDLINE | ID: mdl-38985515

ABSTRACT

Coat protein complex II (COPII) governs the initial steps of biosynthetic secretory protein transport from the endoplasmic reticulum (ER), facilitating the movement of a wide variety of cargoes. Here, we demonstrate that Trk-fused gene (TFG) regulates the rate at which inner COPII coat proteins are concentrated at ER subdomains. Specifically, in cells lacking TFG, the GTPase-activating protein (GAP) Sec23 accumulates more rapidly at budding sites on the ER as compared with control cells, potentially altering the normal timing of GTP hydrolysis on Sar1. Under these conditions, anterograde trafficking of several secretory cargoes is delayed, irrespective of their predicted size. We propose that TFG controls the local, freely available pool of Sec23 during COPII coat formation and limits its capacity to prematurely destabilize COPII complexes on the ER. This function of TFG enables it to act akin to a rheostat, promoting the ordered recruitment of Sec23, which is critical for efficient secretory cargo export.


Subject(s)
COP-Coated Vesicles , Endoplasmic Reticulum , Monomeric GTP-Binding Proteins , Protein Transport , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Vesicular Transport Proteins , COP-Coated Vesicles/metabolism , Endoplasmic Reticulum/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Vesicular Transport Proteins/metabolism , Vesicular Transport Proteins/genetics , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae/genetics , Monomeric GTP-Binding Proteins/metabolism , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Golgi Apparatus/metabolism
11.
Clin Oral Investig ; 28(8): 432, 2024 Jul 18.
Article in English | MEDLINE | ID: mdl-39020145

ABSTRACT

OBJECTIVES: Temporomandibular joint disorder (TMD) is a complex condition with pain and dysfunction in the temporomandibular joint and related muscles. Scientific evidence indicates both genetic and environmental factors play a crucial role in TMD. In this study, we aimed to discover the genetic changes in individuals from 4 generations of an Iranian family with signs and symptoms of TMD and malocclusion Class III. MATERIALS AND METHODS: Whole Exome Sequencing (WES) was performed in 4 patients (IV-8, IV-9, V-4, and V-6) with TMD according to (DC/TMD), along with skeletal Class III malocclusion. Then, PCR sequencing was performed on 23 family members to confirm the WES. RESULTS: In the present study, WES results analysis detected 6 heterozygous non-synonymous Single Nucleotide Variants (SNVs) in 5 genes, including CRLF3, DNAH17, DOCK1, SEPT9, and VWDE. A heterozygous variant, c.2012T > A (p.F671Y), in Exon 20 of the DOCK1 (NM_001290223.2) gene was identified. Then, this variant was investigated in 19 other members of the same family. PCR-Sequencing results showed that 7/19 had heterozygous TA genotype, all of whom were accompanied by malocclusion and TMD symptoms and 12/19 individuals had homozygous TT genotype, 9 of whom had no temporomandibular joint problems or malocclusion. The remaining 3 showed mild TMD clinical symptoms. The 5 other non-synonymous SNVs of CRLF3, DNAH17, SEPT9, and VWDE were not considered plausible candidates for TMD. CONCLUSIONS: The present study identified a heterozygous nonsynonymous c.2012T > A (p.F671Y) variant of the DOCK1 gene is significantly associated with skeletal class III malocclusion, TMD, and its severity in affected individuals in the Iranian pedigree. CLINICAL RELEVANCE: The role of genetic factors in the development of TMD has been described. The present study identified a nonsynonymous variant of the DOCK1 gene as a candidate for TMD and skeletal class III malocclusion in affected individuals in the Iranian pedigree.


Subject(s)
Exome Sequencing , Pedigree , Temporomandibular Joint Disorders , Adolescent , Adult , Child , Female , Humans , Male , GTPase-Activating Proteins/genetics , Iran , Malocclusion, Angle Class III/genetics , Polymerase Chain Reaction , Temporomandibular Joint Disorders/genetics
12.
Cell Death Dis ; 15(7): 520, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-39039052

ABSTRACT

Aldehyde dehydrogenases superfamily (ALDHs), which are ubiquitously present in various organisms with diverse subcellular localizations, play a crucial role in regulating malignant tumor progression; Nevertheless, their involvement in clear cell renal cell carcinoma (ccRCC) has not been elucidated. In this study, we performed comprehensive bioinformatics analyses on the 19 ALDHs genes, and identified ALDH9A1 as a key contributor in ccRCC. Expression patterns and clinical relevance of ALDH9A1 were determined using bioinformatics analyses, real-time PCR, western blotting, and immunohistochemistry. To explore the underlying mechanism behind the tumor suppressor role of ALDH9A1, RNA sequencing, methylated RNA immunoprecipitation, luciferase reporter assay, mass spectroscopy, immunoprecipitation, mutational studies and immunofluorescence were employed. The impact of ALDH9A1 in ccRCC progression and metabolic programming was assessed through both in vitro and in vivo. Here, this study revealed ALDH9A1 as a tumor suppressor gene in ccRCC. The fat mass and obesity associated protein (FTO) was identified as a demethylase for ALDH9A1 mRNA, resulting in its reduced stability and expression levels in ccRCC. Functional experiments demonstrated that the deficiency of ALDH9A1 in ccRCC promoted tumor proliferation, invasion, migration and lipid accumulation. Mechanistic insights illustrated that the diminished levels of ALDH9A1 resulted in the failure to sequester nucleophosmin 1 (NPM1) within cytoplasm, thereby suppressing the transcription of IQ motif containing the GTPase-activating protein 2 (IQGAP2), subsequently activating the AKT-mTOR signaling, ultimately fostering tumor progression and lipid accumulation. In conclusion, the present study highlights the robust prognostic significance of ALDH9A1 and delivers a comprehensive understanding of ALDH9A1-NPM1-IQGAP2-AKT axis in ccRCC. These findings established a solid research foundation for novel therapeutic strategies for ccRCC patients.


Subject(s)
Adenosine , Carcinoma, Renal Cell , Kidney Neoplasms , Nucleophosmin , Proto-Oncogene Proteins c-akt , Signal Transduction , Animals , Female , Humans , Male , Mice , Adenosine/analogs & derivatives , Adenosine/metabolism , Carcinoma, Renal Cell/genetics , Carcinoma, Renal Cell/metabolism , Carcinoma, Renal Cell/pathology , Cell Line, Tumor , Cell Proliferation , Disease Progression , Gene Expression Regulation, Neoplastic , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Kidney Neoplasms/genetics , Kidney Neoplasms/metabolism , Kidney Neoplasms/pathology , Mice, Nude , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , Proto-Oncogene Proteins c-akt/metabolism
13.
Cell Mol Life Sci ; 81(1): 291, 2024 Jul 06.
Article in English | MEDLINE | ID: mdl-38970683

ABSTRACT

Plakophilin 4 (PKP4) is a component of cell-cell junctions that regulates intercellular adhesion and Rho-signaling during cytokinesis with an unknown function during epidermal differentiation. Here we show that keratinocytes lacking PKP4 fail to develop a cortical actin ring, preventing adherens junction maturation and generation of tissue tension. Instead, PKP4-depleted cells display increased stress fibers. PKP4-dependent RhoA localization at AJs was required to activate a RhoA-ROCK2-MLCK-MLC2 axis and organize actin into a cortical ring. AJ-associated PKP4 provided a scaffold for the Rho activator ARHGEF2 and the RhoA effectors MLCK and MLC2, facilitating the spatio-temporal activation of RhoA signaling at cell junctions to allow cortical ring formation and actomyosin contraction. In contrast, association of PKP4 with the Rho suppressor ARHGAP23 reduced ARHGAP23 binding to RhoA which prevented RhoA activation in the cytoplasm and stress fiber formation. These data identify PKP4 as an AJ component that transduces mechanical signals into cytoskeletal organization.


Subject(s)
Actins , Adherens Junctions , Plakophilins , rhoA GTP-Binding Protein , Plakophilins/metabolism , Plakophilins/genetics , rhoA GTP-Binding Protein/metabolism , Adherens Junctions/metabolism , Humans , Actins/metabolism , Keratinocytes/metabolism , Keratinocytes/cytology , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , rho-Associated Kinases/metabolism , rho-Associated Kinases/genetics , Signal Transduction , Stress Fibers/metabolism , Cells, Cultured , Animals
14.
Int Immunopharmacol ; 139: 112783, 2024 Sep 30.
Article in English | MEDLINE | ID: mdl-39068752

ABSTRACT

BACKGROUND: This study performs a detailed bioinformatics and machine learning analysis to investigate the genetic foundations of membranous nephropathy (MN) in lung adenocarcinoma (LUAD). METHODS: In this study, the gene expression profiles of MN microarray datasets (GSE99339) and LUAD dataset (GSE43767) were downloaded from the Gene Expression Omnibus database, common differentially expressed genes (DEGs) were obtained using the limma R package. The biological functions were analyzed with R Cluster Profiler package according to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. Machine learning algorithms, including LASSO regression, support vector machine (SVM), Random Forest, and Boruta analysis, were applied to identify hubgenes linked to LUAD-associated MN. These genes' prognostic values were evaluated in the TCGA-LUAD cohort and validated through immunohistochemistry on renal biopsy specimens. RESULTS: A total of 36 DEGs in common were identified for downstream analyses. Functional enrichment analysis highlighted the involvement of the Toll-like receptor 4 pathway and several immune recognition pathways in LUAD-associated MN. COL3A1, PSENEN, RACGAP1, and TNFRSF10B were identified as hub genes in LUAD-associated MN using machine learning algorithms. ROC analysis demonstrated their effective discrimination of MN with high accuracy. Survival analysis showed that lung adenocarcinoma patients with higher expression of these genes had significantly reduced overall survival. In patients with lung adenocarcinoma-associated MN, RACGAP1, COL3A1, PSENEN, and TNFRSF10B were higher expressed in the glomerular, especially RACGAP1, indicating an important role in the pathogenesis of LUAD-associated membranous nephropathy. CONCLUSIONS: Our study underscores the critical role of RACGAP1, COL3A1, PSENEN, and TNFRSF10B in the development of LUAD-associated MN, providing important insights for future research and the development of potential therapeutic strategies.


Subject(s)
Adenocarcinoma of Lung , Computational Biology , Glomerulonephritis, Membranous , Lung Neoplasms , Machine Learning , Humans , Glomerulonephritis, Membranous/genetics , Glomerulonephritis, Membranous/immunology , Adenocarcinoma of Lung/genetics , Computational Biology/methods , Lung Neoplasms/genetics , GTPase-Activating Proteins/genetics , Gene Expression Regulation, Neoplastic , Prognosis , Male , Female , Gene Expression Profiling , Databases, Genetic , Middle Aged , Collagen Type III
15.
BMC Med Genomics ; 17(1): 175, 2024 Jul 02.
Article in English | MEDLINE | ID: mdl-38956616

ABSTRACT

This research analyzes the clinical data, whole-exome sequencing results, and in vitro minigene functional experiments of a child with developmental delay and intellectual disability. The male patient, aged 4, began experiencing epileptic seizures at 3 months post-birth and has shown developmental delay. Rehabilitation training was administered between the ages of one and two. There were no other significant family medical histories. Through comprehensive family exome genetic testing, a hemizygous variant in the 11th exon of the OPHN1 gene was identified in the affected child: c.1025 + 1G > A. Family segregation analysis confirmed the presence of this variant in the patient's mother, which had not been previously reported. According to the ACMG guidelines, this variant was classified as a likely pathogenic variant. In response to this variant, an in vitro minigene functional experiment was designed and conducted, confirming that the mutation affects the normal splicing of the gene's mRNA, resulting in a 56 bp retention on the left side of Intron 11. It was confirmed that OPHN1: c.1025 + 1G > A is the pathogenic cause of X-linked intellectual disabilities in the child, with clinical phenotypes including developmental delay and seizures.


Subject(s)
Intellectual Disability , Nuclear Proteins , RNA Splicing , Humans , Male , Child, Preschool , Intellectual Disability/genetics , Nuclear Proteins/genetics , Cytoskeletal Proteins/genetics , GTPase-Activating Proteins/genetics , Developmental Disabilities/genetics , Pedigree , Mutation , Exome Sequencing
16.
J Cell Mol Med ; 28(14): e18555, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39075640

ABSTRACT

ARHGAP family genes are often used as glioma oncogenic factors, and their mechanism of action remains unexplained. Our research entailed a thorough examination of the immune microenvironment and enrichment pathways across various glioma subtypes. A distinctive 6-gene signature was developed employing the CGGA cohort, leading to insights into the disparities in clinical characteristics, mutation patterns, and immune cell infiltration among distinct risk categories. Additionally, a unique nomogram was established, grounded on ARHGAPs, with DCA curves illustrating the model's prospective clinical utility in guiding therapeutic strategies. Emphasizing the role of ARHGAP30, integral to our model, its impact on glioma severity and the credibility of our risk assessment model were substantiated through RT-qPCR, Western blot analysis, and cellular functional assays. We identified 6 ARHGAP family genes associated with glioma prognosis. Analysis using the Kaplan-Meier method indicated a correlation between elevated risk levels and adverse outcomes in glioma patients. The risk score, linked with tumour staging and IDH mutation status, emerged as an independent factor predicting prognosis. Patients in the high-risk category exhibited increased immune cell infiltration, enhanced tumour mutational burden, more pronounced expression of immune checkpoint genes, and a better response to ICB therapy. A nomogram, integrating the risk score with the pathological features of glioma patients, was developed. DCA analysis and cellular studies confirmed the model's potential to improve clinical treatment outcomes for patients. A novel ARHGAP family gene signature reveals the prognosis of glioma.


Subject(s)
Brain Neoplasms , GTPase-Activating Proteins , Gene Expression Regulation, Neoplastic , Glioma , Nomograms , Humans , Glioma/genetics , Glioma/pathology , Glioma/mortality , GTPase-Activating Proteins/genetics , Prognosis , Brain Neoplasms/genetics , Brain Neoplasms/mortality , Brain Neoplasms/pathology , Biomarkers, Tumor/genetics , Female , Mutation/genetics , Tumor Microenvironment/genetics , Tumor Microenvironment/immunology , Male , Gene Expression Profiling , Transcriptome , Kaplan-Meier Estimate , Middle Aged
17.
Int J Dev Biol ; 68(2): 79-83, 2024 Jun 11.
Article in English | MEDLINE | ID: mdl-38869222

ABSTRACT

Mutations in the gene encoding Tre2/Bub2/Cdc16 (TBC)1 domain family member 24 (TBC1D24) protein are associated with a variety of neurological disorders, ranging from non-syndromic hearing loss to drug-resistant lethal epileptic encephalopathy and DOORS syndrome [Deafness, Onychodystrophy, Osteodystrophy, intellectual disability (formerly referred to as mental Retardation), and Seizures]. TBC1D24 is a vesicle-associated protein involved in neural crest cell and neuronal migration, maturation, and neurotransmission. In the cochlea, TBC1D24 has been detected in auditory neurons, but few reliable and convergent data exist about the sensory epithelium. Here, the expression of TBC1D24 has been characterized via immunolabelling throughout the postnatal maturation of the mouse cochlear sensory epithelium. TBC1D24 was detected in glia-like non-sensory epithelial cells during early developmental stages. In contrast, TBC1D24 was virtually absent in adjacent sensory hair cells. This expression distinguishing non-sensory from sensory epithelial cells almost disappears around the onset of hearing. Until now, TBC1D24 was mainly described as a neuronal protein either in the brain or in the cochlea. The present observations suggest that TBC1D24 could also regulate vesicle trafficking in cochlear glia-like non-sensory epithelial cells. For a long time, research about epilepsy has been mainly neurocentric. However, there is now evidence proving that glial cell dysregulation contribute to pathogenesis of epilepsy and neurodevelopmental disorders. As a consequence, exploring the possibility that TBC1D24 could also have a role in glial cells of the central nervous system could help to gain insight into TBC1D24-related neurological pathogenesis.


Subject(s)
Cochlea , GTPase-Activating Proteins , Neuroglia , Animals , Mice , Cochlea/metabolism , Neuroglia/metabolism , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Epithelial Cells/metabolism , Nerve Tissue Proteins/metabolism , Nerve Tissue Proteins/genetics , Hair Cells, Auditory/metabolism
18.
J Alzheimers Dis ; 100(1): 279-296, 2024.
Article in English | MEDLINE | ID: mdl-38848175

ABSTRACT

Background: Mitochondrial dysfunction exists in Alzheimer's disease (AD) brain, and damaged mitochondria need to be removed by mitophagy. Small GTPase Rab7 regulates the fusion of mitochondria and lysosome, while TBC1D5 inhibits Rab7 activation. However, it is not clear whether the regulation of Rab7 activity by TBC1D5 can improve mitophagy and inhibit AD progression. Objective: To investigate the role of TBC1D5 in mitophagy and its regulatory mechanism for Rab7, and whether activation of mitophagy can inhibit the progression of AD. Methods: Mitophagy was determined by western blot and immunofluorescence. The morphology and quantity of mitochondria were tracked by TEM. pCMV-Mito-AT1.03 was employed to detect the cellular ATP. Amyloid-ß secreted by AD cells was detected by ELISA. Co-immunoprecipitation was used to investigate the binding partner of the target protein. Golgi-cox staining was applied to observe neuronal morphology of mice. The Morris water maze test and Y-maze were performed to assess spatial learning and memory, and the open field test was measured to evaluate motor function and anxiety-like phenotype of experimental animals. Results: Mitochondrial morphology was impaired in AD models, and TBC1D5 was highly expressed. Knocking down TBC1D5 increased the expression of active Rab7, promoted the fusion of lysosome and autophagosome, thus improving mitophagy, and improved the morphology of hippocampal neurons and the impaired behavior in AD mice. Conclusions: Knocking down TBC1D5 increased Rab7 activity and promoted the fusion of autophagosome and lysosome. Our study provided insights into the mechanisms that bring new possibilities for AD therapy targeting mitophagy.


Subject(s)
Alzheimer Disease , Disease Models, Animal , GTPase-Activating Proteins , Mitochondria , Mitophagy , rab GTP-Binding Proteins , rab7 GTP-Binding Proteins , Animals , Alzheimer Disease/metabolism , Alzheimer Disease/pathology , Alzheimer Disease/genetics , Mitophagy/physiology , rab GTP-Binding Proteins/metabolism , rab GTP-Binding Proteins/genetics , Mice , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Humans , Mitochondria/metabolism , Male , Mice, Transgenic , Amyloid beta-Peptides/metabolism , Neurons/metabolism , Neurons/pathology
19.
Cancer Genomics Proteomics ; 21(4): 368-379, 2024.
Article in English | MEDLINE | ID: mdl-38944420

ABSTRACT

BACKGROUND/AIM: Aggressive breast cancer (BC) cells show high expression of Rho GTPase activating protein 29 (ARHGAP29), a negative regulator of RhoA. In breast cancer cells in which mesenchymal transformation was induced, ARHGAP29 was the only one of 32 GTPase-activating enzymes whose expression increased significantly. Therefore, we investigated whether there is a correlation between expression of ARHGAP29 and tumor progression in BC. Since tamoxifen-resistant BC cells exhibit increased mesenchymal properties and invasiveness, we additionally investigated the relationship between ARHGAP29 and increased invasion rate in tamoxifen resistance. The question arises as to whether ARHGAP29 is a suitable prognostic marker for the progression of BC. MATERIALS AND METHODS: Tissue microarrays were used to investigate expression of ARHGAP29 in BC and adjacent normal breast tissues. Knockdown experiments using siRNA were performed to investigate the influence of ARHGAP29 and the possible downstream actors RhoC and pAKT1 on invasive growth of tamoxifen-resistant BC spheroids in vitro. RESULTS: Expression of ARHGAP29 was frequently increased in BC tissues compared to adjacent normal breast tissues. In addition, there was evidence of a correlation between high ARHGAP29 expression and advanced clinical tumor stage. Tamoxifen-resistant BC cells show a significantly higher expression of ARHGAP29 compared to their parental wild-type cells. After knockdown of ARHGAP29 in tamoxifen-resistant BC cells, expression of RhoC was significantly reduced. Further, expression of pAKT1 decreased significantly. Invasive growth of three-dimensional tamoxifen-resistant BC spheroids was reduced after knockdown of ARHGAP29. This could be partially reversed by AKT1 activator SC79. CONCLUSION: Expression of ARHGAP29 correlates with the clinical tumor parameters of BC patients. In addition, ARHGAP29 is involved in increased invasiveness of tamoxifen-resistant BC cells. ARHGAP29 alone or in combination with its downstream partners RhoC and pAKT1 could be suitable prognostic markers for BC progression.


Subject(s)
Breast Neoplasms , Drug Resistance, Neoplasm , GTPase-Activating Proteins , Neoplasm Invasiveness , Tamoxifen , Humans , Tamoxifen/pharmacology , Tamoxifen/therapeutic use , Breast Neoplasms/pathology , Breast Neoplasms/genetics , Breast Neoplasms/drug therapy , Breast Neoplasms/metabolism , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/genetics , Female , Middle Aged , Gene Expression Regulation, Neoplastic/drug effects , Prognosis , Antineoplastic Agents, Hormonal/pharmacology , Antineoplastic Agents, Hormonal/therapeutic use , Biomarkers, Tumor/metabolism , Biomarkers, Tumor/genetics , Cell Line, Tumor , rhoC GTP-Binding Protein/metabolism , rhoC GTP-Binding Protein/genetics
20.
J Biol Chem ; 300(7): 107459, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38857861

ABSTRACT

The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 phosphatidylinositol (3,4,5)-trisphosphate binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex.


Subject(s)
Adaptor Proteins, Signal Transducing , Guanine Nucleotide Exchange Factors , rac1 GTP-Binding Protein , Humans , Adaptor Proteins, Signal Transducing/metabolism , Adaptor Proteins, Signal Transducing/chemistry , GTPase-Activating Proteins/metabolism , GTPase-Activating Proteins/chemistry , GTPase-Activating Proteins/genetics , Guanine Nucleotide Exchange Factors/metabolism , Guanine Nucleotide Exchange Factors/chemistry , Protein Binding , Protein Conformation , rac1 GTP-Binding Protein/metabolism , rac1 GTP-Binding Protein/chemistry , rho GTP-Binding Proteins/metabolism , rho GTP-Binding Proteins/chemistry
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