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Erol ÖD, Şenocak Ş, Aerts-Kaya F. The Role of Rab GTPases in the development of genetic and malignant diseases. Mol Cell Biochem 2024; 479:255-281. [PMID: 37060515 DOI: 10.1007/s11010-023-04727-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/01/2023] [Indexed: 04/16/2023]
Abstract
Small GTPases have been shown to play an important role in several cellular functions, including cytoskeletal remodeling, cell polarity, intracellular trafficking, cell-cycle, progression and lipid transformation. The Ras-associated binding (Rab) family of GTPases constitutes the largest family of GTPases and consists of almost 70 known members of small GTPases in humans, which are known to play an important role in the regulation of intracellular membrane trafficking, membrane identity, vesicle budding, uncoating, motility and fusion of membranes. Mutations in Rab genes can cause a wide range of inherited genetic diseases, ranging from neurodegenerative diseases, such as Parkinson's disease (PD) and Alzheimer's disease (AD) to immune dysregulation/deficiency syndromes, like Griscelli Syndrome Type II (GS-II) and hemophagocytic lymphohistiocytosis (HLH), as well as a variety of cancers. Here, we provide an extended overview of human Rabs, discussing their function and diseases related to Rabs and Rab effectors, as well as focusing on effects of (aberrant) Rab expression. We aim to underline their importance in health and the development of genetic and malignant diseases by assessing their role in cellular structure, regulation, function and biology and discuss the possible use of stem cell gene therapy, as well as targeting of Rabs in order to treat malignancies, but also to monitor recurrence of cancer and metastasis through the use of Rabs as biomarkers. Future research should shed further light on the roles of Rabs in the development of multifactorial diseases, such as diabetes and assess Rabs as a possible treatment target.
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Affiliation(s)
- Özgür Doğuş Erol
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Şimal Şenocak
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey
| | - Fatima Aerts-Kaya
- Department of Stem Cell Sciences, Hacettepe University Graduate School of Health Sciences, 06100, Ankara, Turkey.
- Hacettepe University Center for Stem Cell Research and Development, 06100, Ankara, Turkey.
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Pei Y, Lv S, Shi Y, Jia J, Ma M, Han H, Zhang R, Tan J, Zhang X. RAB21 controls autophagy and cellular energy homeostasis by regulating retromer-mediated recycling of SLC2A1/GLUT1. Autophagy 2023; 19:1070-1086. [PMID: 35993307 PMCID: PMC10012929 DOI: 10.1080/15548627.2022.2114271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 12/09/2022] Open
Abstract
The endosomal system maintains cellular homeostasis by coordinating multiple vesicular trafficking events, and the retromer complex plays a critical role in endosomal cargo recognition and sorting. Here, we demonstrate an essential role for the small GTPase RAB21 in regulating retromer-mediated recycling of the glucose transporter SLC2A1/GLUT1 and macroautophagy/autophagy. RAB21 depletion mis-sorts SLC2A1 to lysosomes and affects glucose uptake, thereby activating the AMPK-ULK1 pathway to increase autophagic flux. RAB21 depletion also increases lysosome function. Notably, RAB21 depletion does not overtly affect retrograde transport of IGF2R/CI-M6PR or WLS from endosomes to the trans-Golgi network. We speculate that RAB21 regulates fission of retromer-decorated endosomal tubules, as RAB21 depletion causes accumulation of the SNX27-containing retromer complex on enlarged endosomes at the perinuclear region. Functionally, RAB21 depletion sensitizes cancer cells to energy stress and inhibits tumor growth in vivo, suggesting an oncogenic role for RAB21. Overall, our study illuminates the role of RAB21 in regulating endosomal dynamics and maintaining cellular energy homeostasis and suggests RAB21 as a potential metabolic target for cancer therapy.
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Affiliation(s)
- Yifei Pei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuning Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Shi
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwen Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hailong Han
- Department of Neuroscience, Postdoctoral Station for Basic Medicine, Hengyang School of Medicine, University of South China, Hengyang, China
| | - Rongying Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jieqiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Xinjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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Weng D, He L, Chen X, Lin H, Ji D, Lu S, Ao L, Wang S. Integrated analysis of transcription factor-mRNA-miRNA regulatory network related to immune characteristics in medullary thyroid carcinoma. Front Immunol 2023; 13:1055412. [PMID: 36713370 PMCID: PMC9877459 DOI: 10.3389/fimmu.2022.1055412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/30/2022] [Indexed: 01/15/2023] Open
Abstract
Background Medullary thyroid carcinoma (MTC), a thyroid C cell-derived malignancy, is poorly differentiated and more aggressive than papillary, follicular and oncocytic types of thyroid cancer. The current therapeutic options are limited, with a third of population suffering resistance. The differential gene expression pattern among thyroid cancer subtypes remains unclear. This study intended to explore the exclusive gene profile of MTC and construct a comprehensive regulatory network via integrated analysis, to uncover the potential key biomarkers. Methods Multiple datasets of thyroid and other neuroendocrine tumors were obtained from GEO and TCGA databases. Differentially expressed genes (DEGs) specific in MTC were identified to construct a transcription factor (TF)-mRNA-miRNA network. The impact of the TF-mRNA-miRNA network on tumor immune characteristics and patient survival was further explored by single-sample GSEA (ssGSEA) and ESTIMATE algorithms, as well as univariate combined with multivariate analyses. RT-qPCR, cell viability and apoptosis assays were performed for in vitro validation. Results We identified 81 genes upregulated and 22 downregulated in MTC but not in other types of thyroid tumor compared to the normal thyroid tissue. According to the L1000CDS2 database, potential targeting drugs were found to reverse the expressions of DEGs, with panobinostat (S1030) validated effective for tumor repression in MTC by in vitro experiments. The 103 DEGs exclusively seen in MTC were involved in signal release, muscle contraction, pathways of neurodegeneration diseases, neurotransmitter activity and related amino acid metabolism, and cAMP pathway. Based on the identified 15 hub genes, a TF-mRNA-miRNA linear network, as well as REST-cored coherent feed-forward loop networks, namely REST-KIF5C-miR-223 and REST-CDK5R2-miR-130a were constructed via online prediction and validation by public datasets and our cohort. Hub-gene, TF and miRNA scores in the TF-mRNA-miRNA network were related to immune score, immune cell infiltration and immunotherapeutic molecules in MTC as well as in neuroendocrine tumor of lung and neuroblastoma. Additionally, a high hub-gene score or a low miRNA score indicated good prognoses of neuroendocrine tumors. Conclusion The present study uncovers underlying molecular mechanisms and potential immunotherapy-related targets for the pathogenesis and drug discovery of MTC.
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Affiliation(s)
- Danfeng Weng
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Long He
- Department of Pain, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiangna Chen
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Huangfeng Lin
- Department of Orthopedics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Daihan Ji
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Shuting Lu
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China
| | - Lu Ao
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China,*Correspondence: Shenglin Wang, ; Lu Ao,
| | - Shenglin Wang
- Department of Orthopedics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China,Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou, China,*Correspondence: Shenglin Wang, ; Lu Ao,
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Peng H, Zhu E, Wang J, Du X, Wang C, Yang M, Zhang Y. RAB6B is a potential prognostic marker and correlated with the remolding of tumor immune microenvironment in hepatocellular carcinoma. Front Pharmacol 2022; 13:989655. [PMID: 36120364 PMCID: PMC9478551 DOI: 10.3389/fphar.2022.989655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Backgrounds: Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and the second leading cause of death among all cancers. The Ras-associated binding (Rab) proteins constitute the largest family of the Ras superfamily of small GTPases, which mainly mediate membrane trafficking processes. RAB6B is a member of Rab GTPases, and it has been found to be dysregulated in various tumors. However, the clinical significance, correlations with immune cells, and stroma infiltration of RAB6B in HCC remain unclear.Methods: RAB6B mRNA and protein expression in HCC were examined using the TIMER, HCCDB, UALCAN, and HPA databases. The genetic alterations of RAB6B were analyzed by cBioPortal and COSMIC databases. The correlations between RAB6B and tumor-infiltrating immune cells and cancer-associated fibroblasts were explored by using TIMER, TISIDB, and GEPIA databases. Co-expression networks of RAB6B were investigated based on LinkedOmics. Drug sensitivity was analyzed through the GDSC and CTRP databases. RAB6B was knocked down with siRNA in HCC cell lines. EdU assay was performed to detect the cell proliferation ability, flow cytometry was used to compare the differences in the ability of apoptosis, and MTT was used to evaluate the drug sensitivity in vitro.Results: RAB6B mRNA and protein expression were upregulated in the HCC tissues. Kaplan–Meier and Cox regression analyses suggested that highly expressed RAB6B was an independent prognostic factor for poor survival in HCC patients. Moreover, we found that RAB6B expression was positively correlated with the infiltration of immune cells in HCC, including some immunosuppressive cells, chemokines, and receptors, meanwhile RAB6B expression was associated with CD8+T cells exhaustion, resulting in an immunosuppressive microenvironment. Additionally, functional enrichment analysis indicated that RAB6B may be involved in ECM remodeling in the TME, and RAB6B expression was positively associated with CAFs infiltration. Furthermore, RAB6B presented a positive association with sensitivity to GDSC and CTRP drugs. RAB6B knockdown inhibited the cell proliferation and promoted apoptosis and sensitivity to cisplatin of HCC cells in vitro.Conclusion: Our study revealed that RAB6B is a potential biomarker for poor prognosis in HCC patients and correlates with the formation of the immunosuppressive microenvironment in HCC.
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Affiliation(s)
- Hao Peng
- Medical School, Southeast University, Nanjing, China
| | - Erwei Zhu
- The Second People’s Hospital of Lianyungang (The Oncology Hospital of Lianyungang), Lianyungang, China
| | - Jitao Wang
- Medical School, Southeast University, Nanjing, China
- Xingtai Institute of Cancer Control, Xingtai People’s Hospital, Xingtai, China
| | - Xuanlong Du
- Medical School, Southeast University, Nanjing, China
| | - Chonggao Wang
- Medical School, Southeast University, Nanjing, China
| | - Meng Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Department of Ultrasound, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Meng Yang, ; Yewei Zhang,
| | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- *Correspondence: Meng Yang, ; Yewei Zhang,
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Zhang K, Fang T, Zhao D, Cen F, Yan X, Jin X. Circular RNA Circ_0008043 promotes the proliferation and metastasis of hepatocellular carcinoma cells by regulating the microRNA (miR)-326/RAB21 axis. Bioengineered 2022; 13:6600-6614. [PMID: 35220907 PMCID: PMC8973620 DOI: 10.1080/21655979.2022.2044260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Circular RNAs (circRNAs) are non-coding RNAs with covalently closed structures that modulate the progression of hepatocellular carcinoma (HCC). Here, we explored whether circ_0008043 regulated the biological function of HCC cells. Quantitative real-time polymerase chain reaction (qPCR) was used to detect circ_0008043, microRNA (miR)-326, and RAB21 levels. Expression of E-cadherin, N-cadherin, and vimentin was assessed using qPCR. Cell proliferation, migration, and invasion were evaluated using 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, colony formation, and transwell assays. Xenograft tumors were used to evaluate cell growth in vivo. The interaction between miR-326 and circ_0008043 or RAB21 was assessed using dual-luciferase reporter analysis and RNA pull-down analysis. The data illustrated that circ_0008043 and RAB21 were highly expressed, while miR-326 was expressed at less levels in HCC tissues and cells. Interfering with circ_0008043 suppressed cellular proliferation, migration, invasion, and cell growth. Circ_0008043 was confirmed to be an miR-326 sponge that targets RAB21. Rescue experiments showed that inhibiting miR-326 abrogated the effect induced by knockdown of circ_0008043, and overexpressed RAB21 abolished the effect induced by miR-326 overexpression. In summary, silencing of circ_0008043 impeded HCC progression by regulating the miR-326/RAB21 axis. These data suggest that circ_0008043 may have clinical value in the treatment of HCC.
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Affiliation(s)
- Kangjun Zhang
- Hepatic Surgery Department, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Taishi Fang
- Hepatic Surgery Department, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Dong Zhao
- Hepatic Surgery Department, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Fulan Cen
- Department of Intensive Care Unit, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Xu Yan
- Hepatic Surgery Department, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
| | - Xin Jin
- Hepatic Surgery Department, The Third People’s Hospital of Shenzhen, Shenzhen, Guangdong Province, China
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Jiang X, Yang L, Gao Q, Liu Y, Feng X, Ye S, Yang Z. The Role of RAB GTPases and Its Potential in Predicting Immunotherapy Response and Prognosis in Colorectal Cancer. Front Genet 2022; 13:828373. [PMID: 35154286 PMCID: PMC8833848 DOI: 10.3389/fgene.2022.828373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/10/2022] [Indexed: 12/29/2022] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common cancer worldwide, in which aberrant activation of the RAS signaling pathway appears frequently. RAB proteins (RABs) are the largest Ras small GTPases superfamily that regulates intracellular membrane trafficking pathways. The dysregulation of RABs have been found in various diseases including cancers. Compared with other members of Ras families, the roles of RABs in colorectal cancer are less well understood. Methods: We analyzed the differential expression and clinicopathological association of RABs in CRC using RNA sequencing and genotyping datasets from TCGA samples. Moreover, the biological function of RAB17 and RAB34 were investigated in CRC cell lines and patient samples. Results: Of the 62 RABs we analyzed in CRC, seven (RAB10, RAB11A, RAB15, RAB17, RAB19, RAB20, and RAB25) were significantly upregulated, while six (RAB6B, RAB9B, RAB12, RAB23, RAB31, and RAB34) were significantly downregulated in tumor tissues as compared to normal. We found that the upregulated-RABs, which were highly expressed in metabolic activated CRC subtype (CMS3), are associated with cell cycle related pathways enrichment and positively correlated with the mismatch repair (MMR) genes in CRC, implying their role in regulating cell metabolism and tumor growth. While, high expression of the downregulated-RABs were significantly associated with poor prognostic CRC mesenchymal subtypes (CMS4), immune checkpoint genes, and tumor infiltrating immune cells, indicating their role in predicting prognosis and immunotherapy efficacy. Interestingly, though RAB34 mRNA is downregulated in CRC, its high expression is significantly associated with poor prognosis. In vitro experiments showed that RAB17 overexpression can promote cell proliferation via cell cycle regulation. While, RAB34 overexpression can promote cell migration and invasion and is associated with PD-L1/PD-L2 expression increase in CRC cells. Conclusions: Our study showed that RABs may play important roles in regulating cell cycle and immune-related pathways, therefore might be potential biomarkers in predicting prognosis and immunotherapy response in CRC.
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Zhou M, Chen X, Bai H, Sun Y, Zhang Z, Li S, Wang X, Zeng M. RABL2A-CCDC34 Axis Promotes Sorafenib Resistance in Hepatocellular Carcinoma. DNA Cell Biol 2021; 40:1418-1427. [PMID: 34767735 DOI: 10.1089/dna.2021.0473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In this study, we examined the regulatory role of CCDC34 in the sorafenib sensitivity of hepatocellular carcinoma (HCC) and its functional partners. Wide-type Huh7 and Hep3B and induced sorafenib-resistant (SR) Huh7/SR and Hep3B/SR cells were used as in vitro cell models. Immunofluorescent staining and coimmunoprecipitation were performed to check protein-protein interaction. Cell Counting Kit-8 (CCK-8), terminal deoxynucleotidyl transferase-mediated nick end labeling (TUNEL), PI/Annexin V staining, and western blot analysis were performed to assess cell response to sorafenib. The results showed that CCDC34 upregulation in HCC was associated with poor survival. Huh7/SR and Hep3B/SR cells had significantly higher CCDC34 expression than the parental cell lines. RABL2A expression was significantly upregulated in SR HCC cells and interacted with CCDC34 in its GTP-bound state in Huh7/SR and Hep3B/SR cells. RABL2A depletion sensitized Huh7/SR and Hep3B/SR cells to sorafenib. RABL2A Q80L mutant (GTP-bound state locked), but not S35N mutant (GDP-bound state locked) overexpression increased sorafenib IC50 of Huh7 and Hep3B cells. CCDC34 depletion nearly abrogated the protective effects of RABL2A Q80L overexpression both in vitro and in vivo. RABL2A Q80L overexpression significantly increased the expression of p-p38 and p-JNK, the effects of which were significantly attenuated by CCDC34 depletion. In summary, we infer that the RABL2A-CCDC34 axis plays an important role in mediating p38/MAPK and JNK/MAPK signaling, thereby contributing to acquired sorafenib resistance in HCC.
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Affiliation(s)
- Mingxiu Zhou
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xue Chen
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Hansong Bai
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuemei Sun
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China
| | - Zican Zhang
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China
| | - Simin Li
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China
| | - Xiaoshan Wang
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China
| | - Ming Zeng
- Cancer Center, Hospital of University of Electronic Science and Technology of China and Sichuan Provincial People's Hospital, Chengdu, China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Cancer Center, Chengdu BOE Hospital, Chengdu, China
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Bianchetti E, Bates SJ, Nguyen TTT, Siegelin MD, Roth KA. RAB38 Facilitates Energy Metabolism and Counteracts Cell Death in Glioblastoma Cells. Cells 2021; 10:cells10071643. [PMID: 34209035 PMCID: PMC8306361 DOI: 10.3390/cells10071643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma is a high-grade glial neoplasm with a patient survival of 12–18 months. Therefore, the identification of novel therapeutic targets is an urgent need. RAB38 is a GTPase protein implicated in regulating cell proliferation and survival in tumors. The role of RAB38 in glioblastoma is relatively unexplored. Here, we test the hypothesis that RAB38 regulates glioblastoma growth using human glioblastoma cell lines. We found that genetic interference of RAB38 resulted in a decrease in glioblastoma growth through inhibition of proliferation and cell death induction. Transcriptome analysis showed that RAB38 silencing leads to changes in genes related to mitochondrial metabolism and intrinsic apoptosis (e.g., Bcl-xL). Consistently, rescue experiments demonstrated that loss of RAB38 causes a reduction in glioblastoma viability through downregulation of Bcl-xL. Moreover, RAB38 knockdown inhibited both glycolysis and oxidative phosphorylation. Interference with RAB38 enhanced cell death induced by BH3-mimetics. RAB38 antagonists are under development, but not yet clinically available. We found that FDA-approved statins caused a rapid reduction in RAB38 protein levels, increased cell death, and phenocopied some of the molecular changes elicited by loss of RAB38. In summary, our findings suggest that RAB38 is a potential therapeutic target for glioblastoma treatment.
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Jin H, Tang Y, Yang L, Peng X, Li B, Fan Q, Wei S, Yang S, Li X, Wu B, Huang M, Tang S, Liu J, Li H. Rab GTPases: Central Coordinators of Membrane Trafficking in Cancer. Front Cell Dev Biol 2021; 9:648384. [PMID: 34141705 PMCID: PMC8204108 DOI: 10.3389/fcell.2021.648384] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor progression involves invasion, migration, metabolism, autophagy, exosome secretion, and drug resistance. Cargos transported by membrane vesicle trafficking underlie all of these processes. Rab GTPases, which, through coordinated and dynamic intracellular membrane trafficking alongside cytoskeletal pathways, determine the maintenance of homeostasis and a series of cellular functions. The mechanism of vesicle movement regulated by Rab GTPases plays essential roles in cancers. Therefore, targeting Rab GTPases to adjust membrane trafficking has the potential to become a novel way to adjust cancer treatment. In this review, we describe the characteristics of Rab GTPases; in particular, we discuss the role of their activation in the regulation of membrane transport and provide examples of Rab GTPases regulating membrane transport in tumor progression. Finally, we discuss the clinical implications and the potential as a cancer therapeutic target of Rab GTPases.
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Affiliation(s)
- Hongyuan Jin
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuanxin Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Bowen Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Qin Fan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shibo Wei
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shuo Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Bo Wu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Mingyao Huang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Shilei Tang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Jingang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Hangyu Li
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
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Comprehensive Analysis of Prognostic and Genetic Signatures for General Transcription Factor III (GTF3) in Clinical Colorectal Cancer Patients Using Bioinformatics Approaches. Curr Issues Mol Biol 2021; 43:cimb43010002. [PMID: 33925358 PMCID: PMC8935981 DOI: 10.3390/cimb43010002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) has the fourth-highest incidence of all cancer types, and its incidence has steadily increased in the last decade. The general transcription factor III (GTF3) family, comprising GTF3A, GTF3B, GTF3C1, and GTFC2, were stated to be linked with the expansion of different types of cancers; however, their messenger (m)RNA expressions and prognostic values in colorectal cancer need to be further investigated. To study the transcriptomic expression levels of GTF3 gene members in colorectal cancer in both cancerous tissues and cell lines, we first performed high-throughput screening using the Oncomine, GEPIA, and CCLE databases. We then applied the Prognoscan database to query correlations of their mRNA expressions with the disease-specific survival (DSS), overall survival (OS), and disease-free survival (DFS) status of the colorectal cancer patient. Furthermore, proteomics expressions of GTF3 family members in clinical colorectal cancer specimens were also examined using the Human Protein Atlas. Finally, genomic alterations of GTF3 family gene expressions in colorectal cancer and their signal transduction pathways were studied using cBioPortal, ClueGO, CluePedia, and MetaCore platform. Our findings revealed that GTF3 family members' expressions were significantly correlated with the cell cycle, oxidative stress, WNT/β-catenin signaling, Rho GTPases, and G-protein-coupled receptors (GPCRs). Clinically, high GTF3A and GTF3B expressions were significantly correlated with poor prognoses in colorectal cancer patients. Collectively, our study declares that GTF3A was overexpressed in cancer tissues and cell lines, particularly colorectal cancer, and it could possibly step in as a potential prognostic biomarker.
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Du Y, Fan K, Lu X, Wu C. Integrating Multi–Omics Data for Gene-Environment Interactions. BIOTECH 2021; 10:biotech10010003. [PMID: 35822775 PMCID: PMC9245467 DOI: 10.3390/biotech10010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Gene-environment (G×E) interaction is critical for understanding the genetic basis of complex disease beyond genetic and environment main effects. In addition to existing tools for interaction studies, penalized variable selection emerges as a promising alternative for dissecting G×E interactions. Despite the success, variable selection is limited in terms of accounting for multidimensional measurements. Published variable selection methods cannot accommodate structured sparsity in the framework of integrating multiomics data for disease outcomes. In this paper, we have developed a novel variable selection method in order to integrate multi-omics measurements in G×E interaction studies. Extensive studies have already revealed that analyzing omics data across multi-platforms is not only sensible biologically, but also resulting in improved identification and prediction performance. Our integrative model can efficiently pinpoint important regulators of gene expressions through sparse dimensionality reduction, and link the disease outcomes to multiple effects in the integrative G×E studies through accommodating a sparse bi-level structure. The simulation studies show the integrative model leads to better identification of G×E interactions and regulators than alternative methods. In two G×E lung cancer studies with high dimensional multi-omics data, the integrative model leads to an improved prediction and findings with important biological implications.
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Xiong Y, Si Y, Feng Y, Zhuo S, Cui B, Zhang Z. Prognostic value of lipid metabolism-related genes in head and neck squamous cell carcinoma. IMMUNITY INFLAMMATION AND DISEASE 2020; 9:196-209. [PMID: 33277966 PMCID: PMC7860527 DOI: 10.1002/iid3.379] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Altered lipid metabolism is involved in the development of many tumors. However, the role of dissimilar lipid metabolism in head and neck squamous cell carcinoma (HNSCC) is not fully established. AIMS Here, we sought to determine the prognostic value of lipid metabolism-related genes in HNSCC. METHODS RNA-seq data and clinical features of 545 HNSCC cases were obtained from The Cancer Genome Atlas database. A regulatory network of transcription factors-lipid metabolism genes and a risk prognostic model of lipid metabolism-related genes was developed using bioinformatics and Cox regression modeling. We used tumor immune estimation resource to analyze immune cell infiltration in patients with HNSCC based on the prognostic index (PI) of lipid metabolism-related genes. RESULTS A total of 136 differentially expressed lipid metabolism genes were identified. Of these, 23 are related to prognosis. In addition to predicting HNSCC prognosis, 11 lipid metabolism-related genes (ARSI, CYP27B1, CYP2D6, DGKG, DHCR7, LPIN1, PHYH, PIP5K1B, PLA2G2D, RDH16, and TRIB3) also affect HNSCC clinical features (stage, gender, and pathological stage). The PI of lipid metabolism-related genes embodied the state of HNSCC tumor immune microenvironment.
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Affiliation(s)
- Ying Xiong
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Si
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yisi Feng
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shipei Zhuo
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bozhen Cui
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhigang Zhang
- Department of Otolaryngology Head and Neck Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.,Institute of Hearing and Speech-Language Science, Sun Yat-sen University, Guangzhou, Guangdong, China
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