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Wen X, Li P, Ma Y, Wang D, Jia R, Xia Y, Li W, Li Y, Li G, Sun T, Lu F, Ye J, Ji C. RHOF activation of AKT/β-catenin signaling pathway drives acute myeloid leukemia progression and chemotherapy resistance. iScience 2024; 27:110221. [PMID: 39021805 PMCID: PMC11253531 DOI: 10.1016/j.isci.2024.110221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/29/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Acute myeloid leukemia (AML) is a clonal malignancy originating from leukemia stem cells, characterized by a poor prognosis, underscoring the necessity for novel therapeutic targets and treatment methodologies. This study focuses on Ras homolog family member F, filopodia associated (RHOF), a Rho guanosine triphosphatase (GTPase) family member. We found that RHOF is overexpressed in AML, correlating with an adverse prognosis. Our gain- and loss-of-function experiments revealed that RHOF overexpression enhances proliferation and impedes apoptosis in AML cells in vitro. Conversely, genetic suppression of RHOF markedly reduced the leukemia burden in a human AML xenograft mouse model. Furthermore, we investigated the synergistic effect of RHOF downregulation and chemotherapy, demonstrating significant therapeutic efficacy in vivo. Mechanistically, RHOF activates the AKT/β-catenin signaling pathway, thereby accelerating the progression of AML. Our findings elucidate the pivotal role of RHOF in AML pathogenesis and propose RHOF inhibition as a promising therapeutic approach for AML management.
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Affiliation(s)
- Xin Wen
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Peng Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Yuechan Ma
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Dongmei Wang
- Shandong Key Laboratory of Immunohematology, Qilu Hospital, Shandong University, Jinan 250012, People’s Republic of China
| | - Ruinan Jia
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Yuan Xia
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Wei Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Yongjian Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Guosheng Li
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
- Shandong Key Laboratory of Immunohematology, Qilu Hospital, Shandong University, Jinan 250012, People’s Republic of China
| | - Tao Sun
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
- Shandong Key Laboratory of Immunohematology, Qilu Hospital, Shandong University, Jinan 250012, People’s Republic of China
| | - Fei Lu
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
- Shandong Key Laboratory of Immunohematology, Qilu Hospital, Shandong University, Jinan 250012, People’s Republic of China
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan 250012, People’s Republic of China
- Shandong Key Laboratory of Immunohematology, Qilu Hospital, Shandong University, Jinan 250012, People’s Republic of China
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2
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Huang H, Wang S, Guan Y, Ren J, Liu X. Molecular basis and current insights of atypical Rho small GTPase in cancer. Mol Biol Rep 2024; 51:141. [PMID: 38236467 DOI: 10.1007/s11033-023-09140-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Atypical Rho GTPases are a subtype of the Rho GTPase family that are involved in diverse cellular processes. The typical Rho GTPases, led by RhoA, Rac1 and Cdc42, have been well studied, while relative studies on atypical Rho GTPases are relatively still limited and have great exploration potential. With the increase in studies, current evidence suggests that atypical Rho GTPases regulate multiple biological processes and play important roles in the occurrence and development of human cancers. Therefore, this review mainly discusses the molecular basis of atypical Rho GTPases and their roles in cancer. We summarize the sequence characteristics, subcellular localization and biological functions of each atypical Rho GTPase. Moreover, we review the recent advances and potential mechanisms of atypical Rho GTPases in the development of multiple cancers. A comprehensive understanding and extensive exploration of the biological functions of atypical Rho GTPases and their molecular mechanisms in tumors will provide important insights into the pathophysiology of tumors and the development of cancer therapeutic strategies.
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Affiliation(s)
- Hua Huang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Sijia Wang
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Yifei Guan
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China
| | - Jing Ren
- Department of Plastic and Reconstructive Surgery, The First Medical Center, Chinese PLA (People's Liberation Army) General Hospital, Beijing, 100853, China.
| | - Xinhui Liu
- Center of Excellence for Environmental Safety and Biological Effects, Faculty of Environment and Life, Beijing International Science and Technology Cooperation Base for Antiviral Drugs, Beijing University of Technology, Beijing, 100124, China.
- Faculty of Environment and Life, Beijing University of Technology, Beijing, 100124, China.
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3
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Su Y, Wang F, Lei Z, Li J, Ma M, Yan Y, Zhang W, Chen X, Xu B, Hu T. An Integrated Multi-Omics Analysis Identifying Immune Subtypes of Pancreatic Cancer. Int J Mol Sci 2023; 25:142. [PMID: 38203311 PMCID: PMC10779306 DOI: 10.3390/ijms25010142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Limited studies have explored novel pancreatic cancer (PC) subtypes or prognostic biomarkers based on the altered activity of relevant signaling pathway gene sets. Here, we employed non-negative matrix factorization (NMF) to identify three immune subtypes of PC based on C7 immunologic signature gene set activity in PC and normal samples. Cluster 1, the immune-inflamed subtype, showed a higher response rate to immune checkpoint blockade (ICB) and had the lowest tumor immune dysfunction and exclusion (TIDE) scores. Cluster 2, the immune-excluded subtype, exhibited strong associations with stromal activation, characterized by elevated expression levels of transforming growth factor (TGF)-β, cell adhesion, extracellular matrix remodeling, and epithelial-to-mesenchymal transition (EMT) related genes. Cluster 3, the immune-desert subtype, displayed limited immune activity. For prognostic prediction, we developed an immune-related prognostic risk model (IRPM) based on four immune-related prognostic genes in pancreatic cancer, RHOF, CEP250, TSC1, and KIF20B. The IRPM demonstrated excellent prognostic efficacy and successful validation in an external cohort. Notably, the key gene in the prognostic model, RHOF, exerted significant influence on the proliferation, migration, and invasion of pancreatic cancer cells through in vitro experiments. Furthermore, we conducted a comprehensive analysis of somatic mutational landscapes and immune landscapes in PC patients with different IRPM risk scores. Our findings accurately stratified patients based on their immune microenvironment and predicted immunotherapy responses, offering valuable insights for clinicians in developing more targeted clinical strategies.
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Affiliation(s)
- Yongcheng Su
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Fen Wang
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Ziyu Lei
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Jiangquan Li
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Miaomiao Ma
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Ying Yan
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Wenqing Zhang
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Xiaolei Chen
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
| | - Beibei Xu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianhui Hu
- Xiamen Key Laboratory for Tumor Metastasis, Cancer Research Center, School of Medicine, Xiamen University, Xiamen 361102, China; (Y.S.); (F.W.)
- Shenzhen Research Institute of Xiamen University, Shenzhen 518057, China
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Tissue and Temperature-Specific RNA-Seq Analysis Reveals Genomic Versatility and Adaptive Potential in Wild Sea Turtle Hatchlings ( Caretta caretta). Animals (Basel) 2021; 11:ani11113013. [PMID: 34827746 PMCID: PMC8614379 DOI: 10.3390/ani11113013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. Our de novo transcriptome assemblies and measurements of tissue- and temperature- specific global gene expression in the loggerhead sea turtle (Caretta caretta) reveal the genomic basis for potential resiliency in this endangered flagship species, and are crucial to future management and conservation strategies with attention to changing climates. We summarize the interactions among differentially expressed genes by producing network visualizations, and highlight the shared biological pathways related to development, migration, immunity, and longevity reported in the avian and reptilian literature. Our original results for loggerhead sea turtles provide a large, new comparative genomic resource for the investigation of genotype–phenotype relationships in amniotes. Abstract Background: Digital transcriptomics is rapidly emerging as a powerful new technology for modelling the environmental dynamics of the adaptive landscape in diverse lineages. This is particularly valuable in taxa such as turtles and tortoises (order Testudines) which contain a large fraction of endangered species at risk due to anthropogenic impacts on the environment, including pollution, overharvest, habitat degradation, and climate change. Sea turtles (family Cheloniidae) in particular invite a genomics-enabled approach to investigating their remarkable portfolio of adaptive evolution. The sex of the endangered loggerhead sea turtle (Caretta caretta) is subject to temperature-dependent sex determination (TSD), a mechanism by which exposure to temperatures during embryonic development irreversibly determines sex. Higher temperatures produce mainly female turtles and lower temperatures produce mainly male turtles. Incubation temperature can have long term effects on the immunity, migratory ability, and ultimately longevity of hatchlings. We perform RNA-seq differential expression analysis to investigate tissue- and temperature-specific gene expression within brain (n = 7) and gonadal (n = 4) tissue of male and female loggerhead hatchlings. Results: We assemble tissue- and temperature-specific transcriptomes and identify differentially expressed genes relevant to sexual development and life history traits of broad adaptive interest to turtles and other amniotic species. We summarize interactions among differentially expressed genes by producing network visualizations, and highlight shared biological pathways related to migration, immunity, and longevity reported in the avian and reptile literature. Conclusions: The measurement of tissue- and temperature-specific global gene expression of an endangered, flagship species such as the loggerhead sea turtle (Caretta caretta) reveals the genomic basis for potential resiliency and is crucial to future management and conservation strategies with attention to changing climates. Brain and gonadal tissue collected from experimentally reared loggerhead male and female hatchlings comprise an exceedingly rare dataset that permits the identification of genes enriched in functions related to sexual development, immunity, longevity, and migratory behavior and will serve as a large, new genomic resource for the investigation of genotype–phenotype relationships in amniotes.
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Hou Y, Zi J, Ge Z. High Expression of RhoF Predicts Worse Overall Survival: A Potential Therapeutic Target for non-M3 Acute Myeloid Leukemia. J Cancer 2021; 12:5530-5542. [PMID: 34405015 PMCID: PMC8364661 DOI: 10.7150/jca.52648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 07/15/2021] [Indexed: 01/11/2023] Open
Abstract
Rho GTPases are involved in multiple human malignancies and diverse biological functions. However, the patterns and prognostic significance of the expression of RhoD subfamily in acute myeloid leukemia (AML) remain unknown. Here, we detected the expressions of RhoD subfamily genes in AML on the basis of several published datasets and analyzed the survival of RhoD subfamily across the TCGA profiles and in a GEO series. We found that the expression of RhoF, but not RhoD, increased in AML patients in TCGA and GEO (all P<0.001); the survival analysis of two independent cohorts demonstrated that higher RhoF expression was significantly associated with poorer overall survival (OS) (P<0.001), whereas RhoD expression had no significant effect on OS in patients with AML (P>0.05); the subgroup analysis showed that high RhoF expression was correlated with poor 1-, 3-, and 5-year OS (P<0.05 for all); upregulated RhoF expression had a more significant prognostic value for OS in the younger patients (age<60), the intensive chemotherapy group, and wild-type groups (IDH1, NRAS, and TP53) (P<0.05 for all). Multivariate analysis indicated high RhoF expression as a strongly independent unfavorable prognostic factor for OS in patients without transplantation (P<0.05). Furthermore, a higher RhoF expression was closely associated with an older age, intermediate-/poor-risk cytogenetics and mutations in IDH1, NRAS, and TP53. RhoF expression was negatively correlated with BM blasts (P=0.020) and WBC (P=0.003). These findings suggest that high RhoF expression is associated with worsening OS in AML patients and is a potential therapeutic target for the treatment of AML.
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Affiliation(s)
- Yue Hou
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University, Nanjing 210009, China
| | - Jie Zi
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University, Nanjing 210009, China
| | - Zheng Ge
- Department of Hematology, Zhongda Hospital, Medical School of Southeast University, Institute of Hematology Southeast University, Nanjing 210009, China
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6
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Schleiss C, Carapito R, Fornecker LM, Muller L, Paul N, Tahar O, Pichot A, Tavian M, Nicolae A, Miguet L, Mauvieux L, Herbrecht R, Cianferani S, Freund JN, Carapito C, Maumy-Bertrand M, Bahram S, Bertrand F, Vallat L. Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia. Leukemia 2021; 35:1463-1474. [PMID: 33833385 PMCID: PMC8102193 DOI: 10.1038/s41375-021-01221-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 02/21/2021] [Accepted: 03/09/2021] [Indexed: 02/02/2023]
Abstract
B-cell receptor (BCR) signaling is crucial for the pathophysiology of most mature B-cell lymphomas/leukemias and has emerged as a therapeutic target whose effectiveness remains limited by the occurrence of mutations. Therefore, deciphering the cellular program activated downstream this pathway has become of paramount importance for the development of innovative therapies. Using an original ex vivo model of BCR-induced proliferation of chronic lymphocytic leukemia cells, we generated 108 temporal transcriptional and proteomic profiles from 1 h up to 4 days after BCR activation. This dataset revealed a structured temporal response composed of 13,065 transcripts and 4027 proteins, comprising a leukemic proliferative signature consisting of 430 genes and 374 proteins. Mathematical modeling of this complex cellular response further highlighted a transcriptional network driven by 14 early genes linked to proteins involved in cell proliferation. This group includes expected genes (EGR1/2, NF-kB) and genes involved in NF-kB signaling modulation (TANK, ROHF) and immune evasion (KMO, IL4I1) that have not yet been associated with leukemic cells proliferation. Our study unveils the BCR-activated proliferative genetic program in primary leukemic cells. This approach combining temporal measurements with modeling allows identifying new putative targets for innovative therapy of lymphoid malignancies and also cancers dependent on ligand-receptor interactions.
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Affiliation(s)
- Cedric Schleiss
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
| | - Raphael Carapito
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Luc-Matthieu Fornecker
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
- Service d'Hématologie, Institut de Cancérologie Strasbourg Europe (ICANS), Strasbourg, France
| | - Leslie Muller
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
| | - Nicodème Paul
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
| | - Ouria Tahar
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Angelique Pichot
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
| | - Manuela Tavian
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
| | - Alina Nicolae
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
| | - Laurent Miguet
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
- Laboratoire d'Hématologie, Pôle de Biologie, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Laurent Mauvieux
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
- Laboratoire d'Hématologie, Pôle de Biologie, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Raoul Herbrecht
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
- Service d'Hématologie, Institut de Cancérologie Strasbourg Europe (ICANS), Strasbourg, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
| | - Jean-Noel Freund
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR 7178, Strasbourg, France
| | - Myriam Maumy-Bertrand
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
- Institut de Recherche Mathématique Avancée, CNRS UMR 7501, LabEx IRMIA, Université de Strasbourg, Strasbourg, France
| | - Seiamak Bahram
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France
| | - Frederic Bertrand
- Institut de Recherche Mathématique Avancée, CNRS UMR 7501, LabEx IRMIA, Université de Strasbourg, Strasbourg, France.
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France.
- Institut Charles Delaunay, ROSAS, M2S, Université de Technologie de Troyes, Troyes, France.
| | - Laurent Vallat
- Laboratoire d'ImmunoRhumatologie Moléculaire, INSERM UMR-S1109, LabEx Transplantex, Plateforme Genomax, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France.
- Fédération Hospitalo-Universitaire (FHU) Omicare, Université de Strasbourg, Strasbourg, France.
- Laboratoire d'Immunologie, Plateau Technique de Biologie, Pôle de Biologie, Nouvel Hôpital Civil, Strasbourg, France.
- Université de Strasbourg, INSERM, IRFAC UMR-S1113, Strasbourg, France.
- Laboratoire d'Hématologie, Pôle de Biologie, Hôpital de Hautepierre, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
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Karstensen KT, Schein A, Petri A, Bøgsted M, Dybkær K, Uchida S, Kauppinen S. Long Non-Coding RNAs in Diffuse Large B-Cell Lymphoma. Noncoding RNA 2020; 7:1. [PMID: 33379241 PMCID: PMC7838888 DOI: 10.3390/ncrna7010001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid malignancy in adults. Although significant progress has been made in recent years to treat DLBCL patients, 30%-40% of the patients eventually relapse or are refractory to first line treatment, calling for better therapeutic strategies for DLBCL. Long non-coding RNAs (lncRNAs) have emerged as a highly diverse group of non-protein coding transcripts with intriguing molecular functions in human disease, including cancer. Here, we review the current understanding of lncRNAs in the pathogenesis and progression of DLBCL to provide an overview of the field. As the current knowledge of lncRNAs in DLBCL is still in its infancy, we provide molecular signatures of lncRNAs in DLBCL cell lines to assist further lncRNA research in DLBCL.
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Affiliation(s)
- Kasper Thystrup Karstensen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (K.T.K.); (A.S.); (A.P.)
| | - Aleks Schein
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (K.T.K.); (A.S.); (A.P.)
| | - Andreas Petri
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (K.T.K.); (A.S.); (A.P.)
| | - Martin Bøgsted
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (M.B.); (K.D.)
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Faculty of Medicine, Aalborg University, DK-9000 Aalborg, Denmark; (M.B.); (K.D.)
- Department of Haematology, Clinical Cancer Research Center, Aalborg University Hospital, DK-9000 Aalborg, Denmark
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (K.T.K.); (A.S.); (A.P.)
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (K.T.K.); (A.S.); (A.P.)
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8
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Zhang J, Bing Z, Yan P, Tian J, Shi X, Wang Y, Yang K. Identification of 17 mRNAs and a miRNA as an integrated prognostic signature for lung squamous cell carcinoma. J Gene Med 2020; 21:e3105. [PMID: 31215090 DOI: 10.1002/jgm.3105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 05/22/2019] [Accepted: 06/05/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Gene signatures for predicting the outcome of lung squamous cell carcinoma (LUSC) have been employed for many years. However, various signatures have been applied in clinical practice. Therefore, in the present study, we aimed to filter out an effective LUSC prognostic gene signature by simultaneously integrating mRNA and microRNA (miRNA). METHODS First, based on data from the Cancer Genome Atlas (TCGA) (https://www.cancer.gov/tcga), mRNAs and miRNAs that were related to overall survival of LUSC were obtained by the least absolute shrinkage and selection operator method. Subsequently, the predicting effect was tested by time-dependent receiver operating characteristic curve analysis and Kaplan-Meier survival analysis. Next, related clinical indices were added to evaluate the efficiency of the selected gene signatures. Finally, validation and comparison using three independent gene signatures were performed using data from the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo). RESULTS Our data showed that the prognostic index (PI) contained 17 mRNAs and one miRNA. According to the best normalized cut-off of PI (0.0247), the hazard ratio of the PI was 3.40 (95% confidence interval = 2.33-4.96). Moreover, when clinical factors were introduced, the PI was still the most significant index. In addition, only two Gene Ontology terms with p < 0.05 were reported. Furthermore, validation implied that, using our 18-gene signature, only hazard ratio = 1.36 (95% confidence interval = 1.01-1.83) was significant compared to the other three groups of gene biomarkers. CONCLUSIONS The 18-gene signature selected based on data from the TCGA database had an effective prognostic value for LUSC patients.
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Affiliation(s)
- Jingyun Zhang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Zhitong Bing
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Department of Computational Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Peijing Yan
- Institution of Clinical Research and Evidence Based Medicine, Gansu Provincial Hospital, Lanzhou, China
| | - Jinhui Tian
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Xiue Shi
- Gansu Rehabilitation Center Hospital, Lanzhou, China.,Gansu Evidence-Based Rehabilitation Medicine Center, Lanzhou, China
| | - Yongfeng Wang
- Gansu University of Chinese Medicine, Lanzhou, China
| | - Kehu Yang
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Institution of Clinical Research and Evidence Based Medicine, Gansu Provincial Hospital, Lanzhou, China.,Gansu Evidence-Based Rehabilitation Medicine Center, Lanzhou, China
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9
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Yeh SJ, Chen SW, Chen BS. Investigation of the Genome-Wide Genetic and Epigenetic Networks for Drug Discovery Based on Systems Biology Approaches in Colorectal Cancer. Front Genet 2020; 11:117. [PMID: 32211020 PMCID: PMC7068214 DOI: 10.3389/fgene.2020.00117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/31/2020] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed type of cancer worldwide. The mechanisms leading to the progression of CRC are involved in both genetic and epigenetic regulations. In this study, we applied systems biology methods to identify potential biomarkers and conduct drug discovery in a computational approach. Using big database mining, we constructed a candidate protein-protein interaction network and a candidate gene regulatory network, combining them into a genome-wide genetic and epigenetic network (GWGEN). With the assistance of system identification and model selection approaches, we obtain real GWGENs for early-stage, mid-stage, and late-stage CRC. Subsequently, we extracted core GWGENs for each stage of CRC from their real GWGENs through a principal network projection method, and projected them to the Kyoto Encyclopedia of Genes and Genomes pathways for further analysis. Finally, we compared these core pathways resulting in different molecular mechanisms in each stage of CRC and identified carcinogenic biomarkers for the design of multiple-molecule drugs to prevent the progression of CRC. Based on the identified gene expression signatures, we suggested potential compounds combined with known CRC drugs to prevent the progression of CRC with querying Connectivity Map (CMap).
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Affiliation(s)
- Shan-Ju Yeh
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Shuo-Wei Chen
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Automatic Control, Signaling Processing and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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10
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Garcia-Villatoro EL, DeLuca JAA, Callaway ES, Allred KF, Davidson LA, Hensel ME, Menon R, Ivanov I, Safe SH, Jayaraman A, Chapkin RS, Allred CD. Effects of high-fat diet and intestinal aryl hydrocarbon receptor deletion on colon carcinogenesis. Am J Physiol Gastrointest Liver Physiol 2020; 318:G451-G463. [PMID: 31905023 PMCID: PMC7137094 DOI: 10.1152/ajpgi.00268.2019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Consumption of a high-fat diet has been associated with an increased risk of developing colorectal cancer (CRC). However, the effects of the interaction between dietary fat content and the aryl hydrocarbon receptor (AhR) on colorectal carcinogenesis remain unclear. Mainly known for its role in xenobiotic metabolism, AhR has been identified as an important regulator for maintaining intestinal epithelial homeostasis. Although previous research using whole body AhR knockout mice has revealed an increased incidence of colon and cecal tumors, the unique role of AhR activity in intestinal epithelial cells (IECs) and modifying effects of fat content in the diet at different stages of sporadic CRC development are yet to be elucidated. In the present study, we have examined the effects of a high-fat diet on IEC-specific AhR knockout mice in a model of sporadic CRC. Although loss of AhR activity in IECs significantly induced the development of premalignant lesions, in a separate experiment, no significant changes in colon mass incidence were observed. Moreover, consumption of a high-fat diet promoted cell proliferation in crypts at the premalignant colon cancer lesion stage and colon mass multiplicity as well as β-catenin expression and nuclear localization in actively proliferating cells in colon masses. Our data demonstrate the modifying effects of high-fat diet and AhR deletion in IECs on tumor initiation and progression.NEW & NOTEWORTHY Through the use of an intestinal-specific aryl hydrocarbon receptor (AhR) knockout mouse model, this study demonstrates that the expression of AhR in intestinal epithelial cells is required to reduce the formation of premalignant colon cancer lesions. Furthermore, consumption of a high-fat diet and the loss of AhR in intestinal epithelial cells influences the development of colorectal cancer at various stages.
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Affiliation(s)
| | - Jennifer A. A. DeLuca
- 1Department of Nutrition and Food Science, Texas A&M University, College Station, Texas
| | - Evelyn S. Callaway
- 2Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kimberly F. Allred
- 1Department of Nutrition and Food Science, Texas A&M University, College Station, Texas
| | - Laurie A. Davidson
- 1Department of Nutrition and Food Science, Texas A&M University, College Station, Texas,3Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, Texas
| | - Martha E. Hensel
- 4Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas
| | - Rani Menon
- 2Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ivan Ivanov
- 5Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas
| | - Stephen H. Safe
- 5Department of Veterinary Physiology and Pharmacology, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- 2Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Robert S. Chapkin
- 1Department of Nutrition and Food Science, Texas A&M University, College Station, Texas,3Program in Integrative Nutrition & Complex Diseases, Texas A&M University, College Station, Texas
| | - Clinton D. Allred
- 1Department of Nutrition and Food Science, Texas A&M University, College Station, Texas
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11
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Abstract
The Rho GTPases were discovered more than 30 years ago, and they were for a long time considered to follow simple cycling between GDP-bound and GTP-bound conformations, as for the Ras subfamily of small GTPases. The Rho GTPases consist of 20 members, but at least 10 of these do not follow this classical GTPase cycle. Thus, based on their kinetic properties, these Rho GTPases can instead be classified as atypical. Some of these atypical Rho GTPases do not hydrolyze GTP, and some have significantly increased intrinsic GDP/GTP exchange activity. This review focuses on this latter category of atypical Rho GTPases, the so-called 'fast-cycling' Rho GTPases. The different members of these fast-cycling atypical Rho GTPases are described in more detail here, along with their potential regulatory mechanisms. Finally, some insights are provided into the involvement of the atypical Rho GTPases in human pathologies.
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Affiliation(s)
- Pontus Aspenström
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16 , Box 280, SE, Stockholm, Sweden
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12
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Yang RM, Zhan M, Xu SW, Long MM, Yang LH, Chen W, Huang S, Liu Q, Zhou J, Zhu J, Wang J. miR-3656 expression enhances the chemosensitivity of pancreatic cancer to gemcitabine through modulation of the RHOF/EMT axis. Cell Death Dis 2017; 8:e3129. [PMID: 29048402 PMCID: PMC5682692 DOI: 10.1038/cddis.2017.530] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/29/2017] [Accepted: 09/07/2017] [Indexed: 02/08/2023]
Abstract
The highly refractory nature of pancreatic cancer (PC) to chemotherapeutic drugs is one of the key reasons contributing to the poor prognosis of this disease. MicroRNAs (miRNAs) are key regulators of gene expression and have been implicated in a variety of processes from cancer development through to drug resistance. Herein, through miRNA profiling of gemcitabine-resistant (GR) and parental PANC-1 cell lines, we found a consistent reduction of miR-3656 in GR PANC-1 cells. miR-3656 overexpression enhanced the antitumor effect of gemcitabine, whereas silencing of miR-3656 resulted in the opposite effect. By performing mechanistic studies using both in vitro and in vivo models, we found that miR-3656 could target RHOF, a member of the Rho subfamily of small GTPases, and regulate the EMT process. Moreover, enforced EMT progression via TWIST1 overexpression compromised the chemotherapy-enhancing effects of miR-3656. Finally, we found significantly lower levels of miR-3656 and higher levels of RHOF in PC tissues compared with adjacent noncancerous pancreatic tissues, and this was also associated with poor PC patients’ prognosis. Taken together, our results suggest that the miR-3656/RHOF/EMT axis is an important factor involved in regulating GR in PC, and highlights the potential of novel miR-3656-based clinical modalities as a therapeutic approach in PC patients.
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Affiliation(s)
- Rui-Meng Yang
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ming Zhan
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Sun-Wang Xu
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Man-Mei Long
- Department of Pathology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lin-Hua Yang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Chen
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuai Huang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Liu
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Zhou
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Zhu
- CNRS-LIA Hematology and Cancer, Sino-French Research Center for Life Sciences and Genomics, State Key Laboratory of Medical Genomics, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Université de Paris 7/INSERM/CNRS UMR 944/7212, Equipe Labellisée No. 11 Ligue Nationale Contre le Cancer, Hôpital St. Louis, Paris, France
| | - Jian Wang
- Department of Biliary-Pancreatic Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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13
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Tian X, Yan H, Li J, Wu S, Wang J, Fan L. Neurotrophin Promotes Neurite Outgrowth by Inhibiting Rif GTPase Activation Downstream of MAPKs and PI3K Signaling. Int J Mol Sci 2017; 18:E148. [PMID: 28098758 PMCID: PMC5297781 DOI: 10.3390/ijms18010148] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/01/2017] [Accepted: 01/06/2017] [Indexed: 12/16/2022] Open
Abstract
Members of the well-known semaphorin family of proteins can induce both repulsive and attractive signaling in neural network formation and their cytoskeletal effects are mediated in part by small guanosine 5'-triphosphatase (GTPases). The aim of this study was to investigate the cellular role of Rif GTPase in the neurotrophin-induced neurite outgrowth. By using PC12 cells which are known to cease dividing and begin to show neurite outgrowth responding to nerve growth factor (NGF), we found that semaphorin 6A was as effective as nerve growth factor at stimulating neurite outgrowth in PC12 cells, and that its neurotrophic effect was transmitted through signaling by mitogen-activated protein kinases (MAPKs) and phosphatidylinositol-3-kinase (PI3K). We further found that neurotrophin-induced neurite formation in PC12 cells could be partially mediated by inhibition of Rif GTPase activity downstream of MAPKs and PI3K signaling. In conclusion, we newly identified Rif as a regulator of the cytoskeletal rearrangement mediated by semaphorins.
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Affiliation(s)
- Xiaoxia Tian
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Huijuan Yan
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Jiayi Li
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Shuang Wu
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Junyu Wang
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
| | - Lifei Fan
- School of Life Sciences, Inner Mongolia University, Hohhot 010021, China.
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14
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Melloni GEM, de Pretis S, Riva L, Pelizzola M, Céol A, Costanza J, Müller H, Zammataro L. LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. BMC Bioinformatics 2016; 17:80. [PMID: 26860319 PMCID: PMC4748640 DOI: 10.1186/s12859-016-0935-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 02/05/2016] [Indexed: 01/18/2023] Open
Abstract
Background The increasing availability of resequencing data has led to a better understanding of the most important genes in cancer development. Nevertheless, the mutational landscape of many tumor types is heterogeneous and encompasses a long tail of potential driver genes that are systematically excluded by currently available methods due to the low frequency of their mutations. We developed LowMACA (Low frequency Mutations Analysis via Consensus Alignment), a method that combines the mutations of various proteins sharing the same functional domains to identify conserved residues that harbor clustered mutations in multiple sequence alignments. LowMACA is designed to visualize and statistically assess potential driver genes through the identification of their mutational hotspots. Results We analyzed the Ras superfamily exploiting the known driver mutations of the trio K-N-HRAS, identifying new putative driver mutations and genes belonging to less known members of the Rho, Rab and Rheb subfamilies. Furthermore, we applied the same concept to a list of known and candidate driver genes, and observed that low confidence genes show similar patterns of mutation compared to high confidence genes of the same protein family. Conclusions LowMACA is a software for the identification of gain-of-function mutations in putative oncogenic families, increasing the amount of information on functional domains and their possible role in cancer. In this context LowMACA emphasizes the role of genes mutated at low frequency otherwise undetectable by classical single gene analysis. LowMACA is an R package available at http://www.bioconductor.org/packages/release/bioc/html/LowMACA.html. It is also available as a GUI standalone downloadable at: https://cgsb.genomics.iit.it/wiki/projects/LowMACA Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0935-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Giorgio E M Melloni
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Stefano de Pretis
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Mattia Pelizzola
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Arnaud Céol
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Jole Costanza
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Heiko Müller
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
| | - Luca Zammataro
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Via Adamello 16, 20139, Milan, Italy.
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15
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Yin CP, Guan SH, Zhang B, Wang XX, Yue SW. Upregulation of HIF-1α protects neuroblastoma cells from hypoxia-induced apoptosis in a RhoA-dependent manner. Mol Med Rep 2015; 12:7123-31. [PMID: 26323527 DOI: 10.3892/mmr.2015.4267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/29/2015] [Indexed: 11/06/2022] Open
Abstract
Hypoxic conditions regulate several metabolic enzymes and transcription factors that are involved in cancer, ischemia and pulmonary diseases. The Ras homolog (Rho) family, including Rho member A (RhoA), is involved in reorganization of the actin cytoskeleton, cell migration and in the regulation of apoptosis and gene transcription. The aim of the present study was to investigate the expression of hypoxia‑inducible factor (HIF)‑α and the activity of RhoA in PC12 neuroblastoma cells under hypoxic conditions. The upregulation of HIF‑α and RhoA by hypoxia was determined using reverse transcription‑quantitative polymerase chain reaction and western blot assays, cell apoptosis was analyzed using flow cytometry, and the activity of caspase 3 was examined using a western blot assay and caspase 3 activity assay kit. The PC12 cells were induced to apoptosis following exposure to hypoxia, and exhibited increased expression of HIF‑α and increased mRNA and protein expression levels of RhoA. The overexpression of HIF‑α attenuated the hypoxia‑induced apoptosis of the PC12 cells. In addition, RhoA knockdown using small interfering RNA abrogated the antagonism of HIF‑1α towards hypoxia‑induced apoptosis. The results of the present study confirmed the protective role of HIF‑1α and RhoA in hypoxia‑induced PC12 cell apoptosis, and that the upregulation of HIF‑1α by hypoxia is RhoA‑dependent.
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Affiliation(s)
- Cui-Ping Yin
- Department of Physical Medicine and Rehabilitation, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Shang-Hui Guan
- Department of Radiation Oncology, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Bo Zhang
- Department of Physical Medicine and Rehabilitation, Dongying People's Hospital, Dongying, Shandong 257091, P.R. China
| | - Xue-Xin Wang
- Department of Physical Medicine and Rehabilitation, Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Shou-Wei Yue
- Department of Physical Medicine and Rehabilitation, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
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16
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Abstract
Rho GTPases are critical for platelet function. Although the roles of RhoA, Rac and Cdc42 are characterized, platelets express other Rho GTPases, whose activities are less well understood. This review summarizes our understanding of the roles of platelet Rho GTPases and focuses particularly on the functions of Rif and RhoG. In human platelets, Rif interacts with cytoskeleton regulators including formins mDia1 and mDia3, whereas RhoG binds SNARE-complex proteins and cytoskeletal regulators ELMO and DOCK1. Knockout mouse studies suggest that Rif plays no critical functions in platelets, likely due to functional overlap with other Rho GTPases. In contrast, RhoG is essential for normal granule secretion downstream of the collagen receptor GPVI. The central defect in RhoG-/- platelets is reduced dense granule secretion, which impedes integrin activation and aggregation and limits platelet recruitment to growing thrombi under shear, translating into reduced thrombus formation in vivo. Potential avenues for future work on Rho GTPases in platelets are also highlighted, including identification of the key regulator for platelet filopodia formation and investigation of the role of the many Rho GTPase regulators in platelet function in both health and disease.
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17
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Yeganeh B, Wiechec E, Ande SR, Sharma P, Moghadam AR, Post M, Freed DH, Hashemi M, Shojaei S, Zeki AA, Ghavami S. Targeting the mevalonate cascade as a new therapeutic approach in heart disease, cancer and pulmonary disease. Pharmacol Ther 2014; 143:87-110. [PMID: 24582968 DOI: 10.1016/j.pharmthera.2014.02.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/04/2014] [Indexed: 12/21/2022]
Abstract
The cholesterol biosynthesis pathway, also known as the mevalonate (MVA) pathway, is an essential cellular pathway that is involved in diverse cell functions. The enzyme 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase (HMGCR) is the rate-limiting step in cholesterol biosynthesis and catalyzes the conversion of HMG-CoA to MVA. Given its role in cholesterol and isoprenoid biosynthesis, the regulation of HMGCR has been intensely investigated. Because all cells require a steady supply of MVA, both the sterol (i.e. cholesterol) and non-sterol (i.e. isoprenoid) products of MVA metabolism exert coordinated feedback regulation on HMGCR through different mechanisms. The proper functioning of HMGCR as the proximal enzyme in the MVA pathway is essential under both normal physiologic conditions and in many diseases given its role in cell cycle pathways and cell proliferation, cholesterol biosynthesis and metabolism, cell cytoskeletal dynamics and stability, cell membrane structure and fluidity, mitochondrial function, proliferation, and cell fate. The blockbuster statin drugs ('statins') directly bind to and inhibit HMGCR, and their use for the past thirty years has revolutionized the treatment of hypercholesterolemia and cardiovascular diseases, in particular coronary heart disease. Initially thought to exert their effects through cholesterol reduction, recent evidence indicates that statins also have pleiotropic immunomodulatory properties independent of cholesterol lowering. In this review we will focus on the therapeutic applications and mechanisms involved in the MVA cascade including Rho GTPase and Rho kinase (ROCK) signaling, statin inhibition of HMGCR, geranylgeranyltransferase (GGTase) inhibition, and farnesyltransferase (FTase) inhibition in cardiovascular disease, pulmonary diseases (e.g. asthma and chronic obstructive pulmonary disease (COPD)), and cancer.
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Affiliation(s)
- Behzad Yeganeh
- Hospital for Sick Children Research Institute, Department of Physiology & Experimental Medicine, University of Toronto, Toronto, Canada
| | - Emilia Wiechec
- Dept. Clinical & Experimental Medicine, Division of Cell Biology & Integrative Regenerative Med. Center (IGEN), Linköping University, Sweden
| | - Sudharsana R Ande
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Pawan Sharma
- Department of Physiology & Pharmacology, Snyder Institute for Chronic Diseases, Faculty of Medicine, University of Calgary, 4C46 HRIC, 3280 Hospital Drive NW, Calgary, Alberta, Canada
| | - Adel Rezaei Moghadam
- Scientific Association of Veterinary Medicine, Faculty of Veterinary Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran; Young Researchers and Elite Club, Ardabil Branch, Islamic Azad University, Ardabil, Iran
| | - Martin Post
- Hospital for Sick Children Research Institute, Department of Physiology & Experimental Medicine, University of Toronto, Toronto, Canada
| | - Darren H Freed
- Department of Physiology, St. Boniface Research Centre, University of Manitoba, Winnipeg, Canada
| | - Mohammad Hashemi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shahla Shojaei
- Department of Biochemistry, Recombinant Protein Laboratory, Medical School, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir A Zeki
- U.C. Davis, School of Medicine, U.C. Davis Medical Center, Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, Center for Comparative Respiratory Biology & Medicine, Davis, CA, USA.
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, St. Boniface Research Centre, Manitoba Institute of Child Health, Biology of Breathing Theme, University of Manitoba, Winnipeg, Canada.
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18
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Abstract
The Rho family of GTPases (members of the Ras superfamily) are best known for their roles in regulating cytoskeletal dynamics. It is also well established that misregulation of Rho proteins contributes to tumorigenesis and metastasis. Unlike Ras proteins, which are frequently mutated in cancer (around 30%), Rho proteins themselves are generally not found to be mutated in cancer. Rather, misregulation of Rho activity in cancer was thought to occur by overexpression of these proteins or by misregulation of molecules that control Rho activity, such as activation or overexpression of GEFs and inactivation or loss of GAPs or GDIs. Recent studies, enabled by next-generation tumor exome sequencing, report activating point mutations in Rho GTPases as driver mutations in melanoma, as well as breast, and head and neck cancers. The Rac1(P29L) mutation identified in these tumor studies was previously identified by our lab as an activating Rac mutation in C. elegans neuronal development, highlighting the conserved nature of this mutation. Furthermore, this finding supports the relevance of studying Rho GTPases in model organisms such as C. elegans to study the mechanisms that underlie carcinogenesis. This review will describe the recent findings that report activating Rho mutations in various cancer types, moving Rho GTPases from molecules misregulated in cancer to mutagenic targets that drive tumorigenesis.
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Affiliation(s)
- Jamie K Alan
- Central Michigan University College of Medicine; Mt. Pleasant, MI USA
| | - Erik A Lundquist
- Department of Molecular Biosciences; University of Kansas; Lawrence, KS USA
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19
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Abstract
The Rif GTPase is a recent addition to small Rho GTPase family; it shares low homology with other members in the family and evolutionarily parallels with the development of vertebrates. Rif has the conserved Rho GTPase domain structures and cycles between a GDP-bound inactive form and a GTP-bound active form. In its active form, Rif signals through multiple downstream effectors. In the present review, our aim is to summarize the current information about the Rif effectors and how Rif remodels actin cytoskeleton in many aspects.
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20
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Gad AK, Aspenström P. Rif proteins take to the RhoD: Rho GTPases at the crossroads of actin dynamics and membrane trafficking. Cell Signal 2010; 22:183-9. [DOI: 10.1016/j.cellsig.2009.10.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 10/01/2009] [Indexed: 01/03/2023]
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Carbone A, Bernardini L, Valenzano F, Bottillo I, De Simone C, Capizzi R, Capalbo A, Romano F, Novelli A, Dallapiccola B, Amerio P. Array-based comparative genomic hybridization in early-stage mycosis fungoides: recurrent deletion of tumor suppressor genes BCL7A, SMAC/DIABLO, and RHOF. Genes Chromosomes Cancer 2008; 47:1067-75. [PMID: 18663754 DOI: 10.1002/gcc.20601] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The etiology of mycosis fungoides (MF), the most frequent form of cutaneous T cell lymphoma (CTCL), is poorly understood. No specific genetic aberration has been detected, especially in early-stage disease, possibly due to the clinical and histological heterogeneity of patient series and to the different sources of malignant cells (skin, blood, or lymph node) included in most studies. Frozen skin biopsies from 16 patients with early-stage MF were studied using array-based comparative genomic hybridization. A DNA pool from healthy donors was used as the reference. Results demonstrated recurrent loss of 19, 7p22.1-p22.3, 7q11.1-q11.23, 9q34.12, 12q24.31, and 16q22.3-q23.1, and gain of 8q22.3-q23.1 and 21q22.12. The 12q24.31 region was recurrently deleted in 7/16 patients. Real-time PCR investigation for deletion of genes BCL7A, SMAC/DIABLO, and RHOF-three tumor suppressor genes with a putative role in hematological malignancies-demonstrated that they were deleted in 9, 10, and 13 cases, respectively. The identified genomic alterations and individual genes could yield important insights into the early steps of MF pathogenesis.
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Affiliation(s)
- Angelo Carbone
- Department of Dermatology, Catholic University of the Sacred Heart, Rome, Italy.
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Identifying subset of genes that have influential impacts on cancer progression: a new approach to analyze cancer microarray data. Funct Integr Genomics 2008; 8:361-73. [DOI: 10.1007/s10142-008-0084-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 04/10/2008] [Accepted: 04/20/2008] [Indexed: 01/30/2023]
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Vega FM, Ridley AJ. Rho GTPases in cancer cell biology. FEBS Lett 2008; 582:2093-101. [PMID: 18460342 DOI: 10.1016/j.febslet.2008.04.039] [Citation(s) in RCA: 597] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Accepted: 04/22/2008] [Indexed: 12/18/2022]
Abstract
Rho GTPases contribute to multiple cellular processes that could affect cancer progression, including cytoskeletal dynamics, cell cycle progression, transcriptional regulation, cell survival and vesicle trafficking. In vitro several Rho GTPases have oncogenic activity and/or can promote cancer cell invasion, and this correlates with increased expression and activity in a variety of cancers. Conversely, other family members appear to act as tumour suppressors and are deleted, mutated or downregulated in some cancers. Genetic models are starting to provide new information on how Rho GTPases affect cancer development and progression. Here, we discuss how Rho GTPases could contribute to different steps of cancer progression, including proliferation, survival, invasion and metastasis.
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Affiliation(s)
- Francisco M Vega
- Randall Division of Cell and Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London SE1 1UL, UK.
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Crockett DK, Lin Z, Vaughn CP, Lim MS, Elenitoba-Johnson KSJ. Identification of proteins from formalin-fixed paraffin-embedded cells by LC-MS/MS. J Transl Med 2005; 85:1405-15. [PMID: 16155593 DOI: 10.1038/labinvest.3700343] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
There exists a need for robust approaches for tandem mass spectrometry (MS/MS)-based identification of proteins in formalin-fixed paraffin-embedded (FFPE) material. We demonstrate herein the identification of proteins in FFPE material using enzymatic cleavage for extraction of peptides from the FFPE specimen and liquid chromatography (LC) followed by MS/MS. We identified 324 proteins from a 3-year-old FFPE cell-block of a human lymphoma cell line. The identified proteins were assigned to the membrane, cytosol and nucleus, with diverse cellular functions. The results were comparable to those obtained with lysates from a fresh specimen of the lymphoma cell line. Western blotting analysis and immunofluorescence microscopy confirmed the expression of selected proteins. The functional significance of one protein (PKC eta) was validated using a PKC inhibitory peptide which resulted in lymphoma cell death in vitro. The ability to identify proteins from FFPE specimens has significant implications for MS/MS-based proteomics of vast repositories of archival primary tissue samples for disease-related discovery research.
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Affiliation(s)
- David K Crockett
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT 84132, USA
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