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Wang H, Sun H, Huang J, Zhang Z, Cai G, Wang C, Xiao K, Xiong X, Zhang J, Liu P, Lu X, Feng W, Wang J. Therapeutic targeting ERRγ suppresses metastasis via extracellular matrix remodeling in small cell lung cancer. EMBO Mol Med 2024; 16:2043-2059. [PMID: 39085398 PMCID: PMC11393344 DOI: 10.1038/s44321-024-00108-z] [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: 01/26/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 08/02/2024] Open
Abstract
Small-cell lung cancer (SCLC) is the most aggressive and lethal type of lung cancer, characterized by limited treatment options, early and frequent metastasis. However, the determinants of metastasis in SCLC are poorly defined. Here, we show that estrogen-related receptor gamma (ERRγ) is overexpressed in metastatic SCLC tumors, and is positively associated with SCLC progression. ERRγ functions as an essential activator of extracellular matrix (ECM) remodeling and cell adhesion, two critical steps in metastasis, by directly regulating the expression of major genes involved in these processes. Genetic and pharmacological inhibition of ERRγ markedly reduces collagen production, cell-matrix adhesion, microfilament production, and eventually blocks SCLC cell invasion and tumor metastasis. Notably, ERRγ antagonists significantly suppressed tumor growth and metastasis and restored SCLC vulnerability to chemotherapy in multiple cell-derived and patient-derived xenograft models. Taken together, these findings establish ERRγ as an attractive target for metastatic SCLC and provide a potential pharmacological strategy for treating this lethal disease.
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Affiliation(s)
- Hong Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Huizi Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Jie Huang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 510080, Guangzhou, China
| | - Zhenhua Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Guodi Cai
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Chaofan Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, 510632, Guangzhou, China
| | - Kai Xiao
- Precision Medicine Research Center, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, 610041, Chengdu, China
| | - Xiaofeng Xiong
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
| | - Jian Zhang
- Thoracic Surgery Department, The Third Affiliated Hospital of Sun Yat-sen University, No. 600, Tianhe Road, Tianhe District, 510630, Guangzhou, China
| | - Peiqing Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China
- National-Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-sen University, 510006, Guangzhou, Guangdong, PR China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, P.R. China
| | - Xiaoyun Lu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Discovery of Chinese Ministry of Education (MOE), School of Pharmacy, Jinan University, #855 Xingye Avenue, 510632, Guangzhou, China.
| | - Weineng Feng
- Department of Pulmonary Oncology, The First People's Hospital of Foshan, 528000, Foshan, Guangdong, China.
| | - Junjian Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, China.
- National-Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-sen University, 510006, Guangzhou, Guangdong, PR China.
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, 510006, Guangzhou, Guangdong, P.R. China.
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Suhardi VJ, Oktarina A, Hammad M, Niu Y, Li Q, Thomson A, Lopez J, McCormick J, Ayturk UM, Greenblatt MB, Ivashkiv LB, Bostrom MPG, Yang X. Prevention and treatment of peri-implant fibrosis by functionally inhibiting skeletal cells expressing the leptin receptor. Nat Biomed Eng 2024:10.1038/s41551-024-01238-y. [PMID: 39085645 DOI: 10.1038/s41551-024-01238-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
The cellular and molecular mediators of peri-implant fibrosis-a most common reason for implant failure and for surgical revision after the replacement of a prosthetic joint-remain unclear. Here we show that peri-implant fibrotic tissue in mice and humans is largely composed of a specific population of skeletal cells expressing the leptin receptor (LEPR) and that these cells are necessary and sufficient to generate and maintain peri-implant fibrotic tissue. In a mouse model of tibial implantation and osseointegration that mimics partial knee arthroplasty, genetic ablation of LEPR+ cells prevented peri-implant fibrosis and the implantation of LEPR+ cells from peri-implant fibrotic tissue was sufficient to induce fibrosis in secondary hosts. Conditional deletion of the adhesion G-protein-coupled receptor F5 (ADGRF5) in LEPR+ cells attenuated peri-implant fibrosis while augmenting peri-implant bone formation, and ADGRF5 inhibition by the intra-articular or systemic administration of neutralizing anti-ADGRF5 in the mice prevented and reversed peri-implant fibrosis. Pharmaceutical agents that inhibit the ADGRF5 pathway in LEPR+ cells may be used to prevent and treat peri-implant fibrosis.
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Affiliation(s)
- Vincentius Jeremy Suhardi
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | | | - Mohammed Hammad
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Yingzhen Niu
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Joint Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, P. R. China
| | - Qingdian Li
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedics, Guangdong Provincial People's Hospital, Southern Medical University, Guangzhou, P. R. China
| | - Andrew Thomson
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Juan Lopez
- Research Institute, Hospital for Special Surgery, New York, NY, USA
| | - Jason McCormick
- Flow Cytometry Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Ugur M Ayturk
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Matthew B Greenblatt
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Mathias P G Bostrom
- Department of Orthopedic Surgery, Hospital for Special Surgery, New York, NY, USA
- Research Institute, Hospital for Special Surgery, New York, NY, USA
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA
| | - Xu Yang
- Research Institute, Hospital for Special Surgery, New York, NY, USA.
- Department of Orthopedic Surgery, Weill Cornell Medicine, New York, NY, USA.
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Qin P, Pan Z, Zhang W, Wang R, Li X, Lu J, Xu S, Gong X, Ye J, Yan X, Liu Y, Li Y, Zhang Y, Fang F. Integrative proteomic and transcriptomic analysis in the female goat ovary to explore the onset of puberty. J Proteomics 2024; 301:105183. [PMID: 38688390 DOI: 10.1016/j.jprot.2024.105183] [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: 12/10/2023] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/02/2024]
Abstract
Puberty is considered a prerequisite for affecting reproductive performance and productivity. Little was known about molecular changes in pubertal goat ovaries. Therefore, we measured and performed a correlation analysis of the mRNA and proteins changes in the pre-pubertal and pubertal goat ovaries. The results showed that only six differentially expressed genes and differentially abundant proteins out of 18,139 genes and 7550 proteins quantified had significant correlations. CNTN2 and THBS1, discovered in the mRNA-mRNA interaction network, probably participated in pubertal and reproductive regulation by influencing GnRH receptor signals, follicular development, and ovulation. The predicted core transcription factors may either promote or inhibit the expression of reproductive genes and act synergistically to maintain normal reproductive function in animals. The interaction between PKM and TIMP3 with other proteins may impact animal puberty through energy metabolism and ovarian hormone secretion. Pathway enrichment analyses revealed that the co-associated key pathways between ovarian genes and proteins at puberty included calcium signalling pathway and olfactory transduction. These pathways were associated with gonadotropin-releasing hormone synthesis and secretion, signal transmission, and cell proliferation. In summary, these results enriched the potential molecules and signalling pathways that affect puberty and provided new insights for regulating and promoting the onset of puberty. SIGNIFICANCE: This study conducted the first transcriptomic and proteomic correlation analysis of pre-pubertal and pubertal goat ovaries and identified six significantly correlated molecules at both the gene and protein levels. Meanwhile, we were drawn to several molecules and signalling pathways that may play a regulatory role in the onset of puberty and reproduction by influencing reproductive-related gene expression, GnRH receptor signals, energy metabolism, ovarian hormone secretion, follicular development, and ovulation. This information contributed to identify potential biomarkers in pubertal goat ovaries, which was vital for predicting the onset of puberty and improving livestock performance.
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Affiliation(s)
- Ping Qin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Zhihao Pan
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Wei Zhang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Rui Wang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xiaoqian Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Juntai Lu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Shuangshuang Xu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xinbao Gong
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Jing Ye
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Xu Yan
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Ya Liu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yunsheng Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Yunhai Zhang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China
| | - Fugui Fang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui 230036, China; Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui 230036, China.
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Maalim AA, Wang Z, Huang Y, Lei T. RACK1 Promotes Meningioma Progression by Activation of NF-κB Pathway via Preventing CSNK2B from Ubiquitination Degradation. Cancers (Basel) 2024; 16:767. [PMID: 38398158 PMCID: PMC10886518 DOI: 10.3390/cancers16040767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Higher-grade meningiomas (WHO grade II and III) are characterized by aggressive invasiveness and high postoperative recurrence rates. The prognosis remains inadequate even with adjuvant radiotherapy and currently there is no definitive pharmacological treatment strategy and target for malignant meningiomas. This study aims to unveil the mechanisms driving the malignant progression of meningiomas and to identify potential inhibitory targets, with significant clinical implications. Implementing techniques such as protein immunoprecipitation, mass spectrometry, RNA interference, and transcriptome sequencing, we investigated the malignancy mechanisms in meningioma cell lines IOMM-LEE and CH157-MN. Additionally, in vivo experiments were carried out on nude mice. We discovered a positive correlation between meningioma malignancy and the levels of the receptor for activated C kinase 1 (RACK1), which interacts with CSNK2B, the β subunit of casein kinase 2 (CK2), inhibiting its ubiquitination and subsequent degradation. This inhibition allows CK2 to activate the NF-κb pathway, which increases the transcription of CDK4 and cyclin D3, resulting in the transition of the cell cycle into the G2/M phase. The RACK1 inhibitor, harringtonolide (HA), significantly suppressed the malignant tendencies of meningioma cells. Our study suggests that RACK1 may play a role in the malignant progression of meningiomas, and therefore, targeting RACK1 could emerge as an effective strategy for reducing the malignancy of these tumors.
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Affiliation(s)
- Ali Abdi Maalim
- Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China; (A.A.M.); (Z.W.)
- Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zihan Wang
- Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China; (A.A.M.); (Z.W.)
- Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yimin Huang
- Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China; (A.A.M.); (Z.W.)
- Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ting Lei
- Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China; (A.A.M.); (Z.W.)
- Sino-German Neuro-Oncology Molecular Laboratory, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430030, China
- Hubei Key Laboratory of Neural Injury and Functional Reconstruction, Huazhong University of Science and Technology, Wuhan 430030, China
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Currie D, Wong N, Zane I, Rix T, Vardakastanis M, Claxton A, Ong KKV, Macmorland W, Poivet A, Brooks A, Niola P, Huntley D, Montano X. A Potential Prognostic Gene Signature Associated with p53-Dependent NTRK1 Activation and Increased Survival of Neuroblastoma Patients. Cancers (Basel) 2024; 16:722. [PMID: 38398114 PMCID: PMC10886603 DOI: 10.3390/cancers16040722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Neuroblastoma is the most common extracranial solid tumour in children, comprising close to 10% of childhood cancer-related deaths. We have demonstrated that activation of NTRK1 by TP53 repression of PTPN6 expression is significantly associated with favourable survival in neuroblastoma. The molecular mechanisms by which this activation elicits cell molecular changes need to be determined. This is critical to identify dependable biomarkers for the early detection and prognosis of tumours, and for the development of personalised treatment. In this investigation we have identified and validated a gene signature for the prognosis of neuroblastoma using genes differentially expressed upon activation of the NTRK1-PTPN6-TP53 module. A random survival forest model was used to construct a gene signature, which was then assessed across validation datasets using Kaplan-Meier analysis and ROC curves. The analysis demonstrated that high BASP1, CD9, DLG2, FNBP1, FRMD3, IL11RA, ISGF10, IQCE, KCNQ3, and TOX2, and low BSG/CD147, CCDC125, GABRB3, GNB2L1/RACK1 HAPLN4, HEBP2, and HSD17B12 expression was significantly associated with favourable patient event-free survival (EFS). The gene signature was associated with favourable tumour histology and NTRK1-PTPN6-TP53 module activation. Importantly, all genes were significantly associated with favourable EFS in an independent manner. Six of the signature genes, BSG/CD147, GNB2L1/RACK1, TXNDC5, FNPB1, B3GAT1, and IGSF10, play a role in cell differentiation. Our findings strongly suggest that the identified gene signature is a potential prognostic biomarker and therapeutic target for neuroblastoma patients and that it is associated with neuroblastoma cell differentiation through the activation of the NTRK1-PTPN6-TP53 module.
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Affiliation(s)
- David Currie
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Nicole Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Isabelle Zane
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Tom Rix
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Marios Vardakastanis
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Amelia Claxton
- Innovation Hub, Comprehensive Cancer Centre, King’s College London, Great Maze Pond, London SE1 9RT, UK; (A.C.); (K.K.V.O.)
| | - Karine K. V. Ong
- Innovation Hub, Comprehensive Cancer Centre, King’s College London, Great Maze Pond, London SE1 9RT, UK; (A.C.); (K.K.V.O.)
| | - William Macmorland
- Tumour Immunology Group, School of Cancer and Pharmaceutical Sciences, King’s College London, London SE1 1UL, UK;
| | - Arthur Poivet
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Anthony Brooks
- Zayed Centre for Research into Rare Disease in Children, UCL Genomics, London WC1N 1DZ, UK;
| | | | - Derek Huntley
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
| | - Ximena Montano
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK; (D.C.); (N.W.); (I.Z.); (T.R.); (M.V.); (A.P.); (D.H.)
- Innovation Hub, Comprehensive Cancer Centre, King’s College London, Great Maze Pond, London SE1 9RT, UK; (A.C.); (K.K.V.O.)
- School of Life Sciences, University of Westminster, London W1W 6UW, UK
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Liu H, Tang T. MAPK signaling pathway-based glioma subtypes, machine-learning risk model, and key hub proteins identification. Sci Rep 2023; 13:19055. [PMID: 37925483 PMCID: PMC10625624 DOI: 10.1038/s41598-023-45774-0] [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: 04/24/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023] Open
Abstract
An early diagnosis and precise prognosis are critical for the treatment of glioma. The mitogen‑activated protein kinase (MAPK) signaling pathway potentially affects glioma, but the exploration of the clinical values of the pathway remains lacking. We accessed data from TCGA, GTEx, CGGA, etc. Up-regulated MAPK signaling pathway genes in glioma were identified and used to cluster the glioma subtypes using consensus clustering. The subtype differences in survival, cancer stemness, and the immune microenvironment were analyzed. A prognostic model was trained with the identified genes using the LASSO method and was validated with three external cohorts. The correlations between the risk model and cancer-associated signatures in cancer were analyzed. Key hub genes of the gene set were identified by hub gene analysis and survival analysis. 47% of the MAPK signaling pathway genes were overexpressed in glioma. Subtypes based on these genes were distinguished in survival, cancer stemness, and the immune microenvironment. A risk model was calculated with high confidence in the prediction of overall survival and was correlated with multiple cancer-associated signatures. 12 hub genes were identified and 8 of them were associated with survival. The MAPK signaling pathway was overexpressed in glioma with prognostic value.
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Affiliation(s)
- Hengrui Liu
- Xinkaiyuan Pharmaceuticals, Beijing, China
- Guangzhou Regenerative Medicine Research Center, Future Homo Sapiens Institute of Regenerative Medicine Co., Ltd (FHIR), Guangzhou, China
| | - Tao Tang
- Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China.
- Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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7
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Chvalova V, Venkadasubramanian V, Klimova Z, Vojtova J, Benada O, Vanatko O, Vomastek T, Grousl T. Characterization of RACK1-depleted mammalian cells by a palette of microscopy approaches reveals defects in cell cycle progression and polarity establishment. Exp Cell Res 2023:113695. [PMID: 37393981 DOI: 10.1016/j.yexcr.2023.113695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/08/2023] [Accepted: 06/22/2023] [Indexed: 07/04/2023]
Abstract
The Receptor for Activated C Kinase 1 (RACK1) is an evolutionarily conserved scaffold protein involved in the regulation of numerous cellular processes. Here, we used CRISPR/Cas9 and siRNA to reduce the expression of RACK1 in Madin-Darby Canine Kidney (MDCK) epithelial cells and Rat2 fibroblasts, respectively. RACK1-depleted cells were examined using coherence-controlled holographic microscopy, immunofluorescence, and electron microscopy. RACK1 depletion resulted in decreased cell proliferation, increased cell area and perimeter, and in the appearance of large binucleated cells suggesting a defect in the cell cycle progression. Our results show that the depletion of RACK1 has a pleiotropic effect on both epithelial and mesenchymal cell lines and support its essential role in mammalian cells.
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Affiliation(s)
- Vera Chvalova
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Vignesh Venkadasubramanian
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic; Faculty of Science, Charles University, 128 00, Prague, Czech Republic
| | - Zuzana Klimova
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Jana Vojtova
- Laboratory of Regulation of Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, 142 00, Prague, Czech Republic
| | - Oldrich Benada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology of the Czech Academy of Sciences, 142 00, Prague, Czech Republic
| | - Ondrej Vanatko
- Department of Cellular Neurophysiology, Institute of Experimental Medicine of the Czech Academy of Sciences, 142 00, Prague, Czech Republic; Second Faculty of Medicine, Charles University, 150 06, Prague, Czech Republic
| | - Tomas Vomastek
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic
| | - Tomas Grousl
- Laboratory of Cell Signalling, Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 00, Prague, Czech Republic.
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Ozair A, Bhat V, Alisch RS, Khosla AA, Kotecha RR, Odia Y, McDermott MW, Ahluwalia MS. DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets. Cancers (Basel) 2023; 15:cancers15041342. [PMID: 36831683 PMCID: PMC9954183 DOI: 10.3390/cancers15041342] [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: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.
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Affiliation(s)
- Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Faculty of Medicine, King George’s Medical University, Lucknow 226003, India
| | - Vivek Bhat
- St. John’s Medical College, Bangalore 560034, India
| | - Reid S. Alisch
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Atulya A. Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Rupesh R. Kotecha
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Michael W. McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
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9
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Liu Y, Gao Z, Peng C, Jiang X. Exploration of the heterogeneity and interaction of epithelial cells and NK/T-cells in Laryngeal Squamous Cell Carcinoma based on single-cell RNA sequencing data. Braz J Otorhinolaryngol 2023; 89:393-400. [PMID: 37105033 PMCID: PMC10164759 DOI: 10.1016/j.bjorl.2023.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
OBJECTIVES We aimed to explore the heterogeneity and differentiation trajectories of epithelial cells and NK/T-cells in Laryngeal Squamous Cell Carcinoma (LSCC). METHODS We downloaded the GSE150321 data set containing LSCC01 and LSCC02 samples single cell RNA data from Gene Expression Omnibus. The UMAP analysis was performed to identify the cell subpopulations and cell locations of subpopulations. Seurat package was used to analyze the differential expression of genes. The function of differential expression genes was analyzed using DAVID database. The monocle2 package was used to analyze differentiation trajectories. We used the CellChat package to observe the signaling pathways and ligand-receptor pairs for epithelial cells and NK/T-cells. RESULTS All the LSCC cells were divided into 16 subpopulation that included 7 epithelial cell subsets, 3 T-cell subsets. The function analysis indicated that epithelial cells and NK/T-cells mainly participated in different process, such as cell cycle, immune response, and cell migration. Then, the results of differentiation trajectory indicated that the ability of migration, and the activation of the immune system increases, while the ability of apoptosis, and glucose metabolic process decreases as pseudotime. Migration-related epithelial cells act on all T-cells via the CNTN2-CNTN2 ligand-receptor pair, which suggested that CNTN2 might be an important biomarker for regulating migration of epithelial cells. CONCLUSIONS Our study characterized the heterogeneity of LSCC, which provided novel insights into LSCC and identified a new mechanism and target for clinical LSCC threapies. EVIDENCE IV.
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Affiliation(s)
- Yanan Liu
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Department of Otorhinolaryngology, Harbin, Heilongjiang, PR China
| | - Zhiguang Gao
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Department of Otorhinolaryngology, Harbin, Heilongjiang, PR China
| | - Cheng Peng
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Department of Otorhinolaryngology, Harbin, Heilongjiang, PR China
| | - Xingli Jiang
- Heilongjiang Provincial Hospital Affiliated to Harbin Institute of Technology, Department of Otorhinolaryngology, Harbin, Heilongjiang, PR China.
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10
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Sumera, Anwer F, Waseem M, Fatima A, Malik N, Ali A, Zahid S. Molecular Docking and Molecular Dynamics Studies Reveal Secretory Proteins as Novel Targets of Temozolomide in Glioblastoma Multiforme. Molecules 2022; 27:7198. [PMID: 36364024 PMCID: PMC9653723 DOI: 10.3390/molecules27217198] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/24/2022] [Accepted: 09/29/2022] [Indexed: 10/13/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a tumor of glial origin and is the most malignant, aggressive and prevalent type, with the highest mortality rate in adult brain cancer. Surgical resection of the tumor followed by Temozolomide (TMZ) therapy is currently available, but the development of resistance to TMZ is a common limiting factor in effective treatment. The present study investigated the potential interactions of TMZ with several secretory proteins involved in various molecular and cellular processes in GBM. Automated docking studies were performed using AutoDock 4.2, which showed an encouraging binding affinity of TMZ towards all targeted proteins, with the strongest interaction and binding affinity with GDF1 and SLIT1, followed by NPTX1, CREG2 and SERPINI, among the selected proteins. Molecular dynamics (MD) simulations of protein-ligand complexes were performed via CABS-flex V2.0 and the iMOD server to evaluate the root-mean-square fluctuations (RMSFs) and measure protein stability, respectively. The results showed that docked models were more flexible and stable with TMZ, suggesting that it may be able to target putative proteins implicated in gliomagenesis that may impact radioresistance. However, additional in vitro and in vivo investigations can ascertain the potential of the selected proteins to serve as novel targets for TMZ for GBM treatment.
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Affiliation(s)
- Sumera
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Farha Anwer
- Integrative Biology Laboratory, Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Maaz Waseem
- Integrative Biology Laboratory, Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Areeba Fatima
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Nishat Malik
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Amjad Ali
- Integrative Biology Laboratory, Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
| | - Saadia Zahid
- Neurobiology Research Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan
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11
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Rose M, Cardon T, Aboulouard S, Hajjaji N, Kobeissy F, Duhamel M, Fournier I, Salzet M. Surfaceome Proteomic of Glioblastoma Revealed Potential Targets for Immunotherapy. Front Immunol 2021; 12:746168. [PMID: 34646273 PMCID: PMC8503648 DOI: 10.3389/fimmu.2021.746168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma (GBM) is the most common and devastating malignant brain tumor in adults. The mortality rate is very high despite different treatments. New therapeutic targets are therefore highly needed. Cell-surface proteins represent attractive targets due to their accessibility, their involvement in essential signaling pathways, and their dysregulated expression in cancer. Moreover, they are potential targets for CAR-based immunotherapy or mRNA vaccine strategies. In this context, we investigated the GBM-associated surfaceome by comparing it to astrocytes cell line surfaceome to identify new specific targets for GBM. For this purpose, biotinylation of cell surface proteins has been carried out in GBM and astrocytes cell lines. Biotinylated proteins were purified on streptavidin beads and analyzed by shotgun proteomics. Cell surface proteins were identified with Cell Surface Proteins Atlas (CSPA) and Gene Ontology enrichment. Among all the surface proteins identified in the different cell lines we have confirmed the expression of 66 of these in patient’s glioblastoma using spatial proteomic guided by MALDI-mass spectrometry. Moreover, 87 surface proteins overexpressed or exclusive in GBM cell lines have been identified. Among these, we found 11 specific potential targets for GBM including 5 mutated proteins such as RELL1, CYBA, EGFR, and MHC I proteins. Matching with drugs and clinical trials databases revealed that 7 proteins were druggable and under evaluation, 3 proteins have no known drug interaction yet and none of them are the mutated form of the identified proteins. Taken together, we discovered potential targets for immune therapy strategies in GBM.
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Affiliation(s)
- Mélanie Rose
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Tristan Cardon
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Soulaimane Aboulouard
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Nawale Hajjaji
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Breast Cancer Unit, Oscar Lambret Center, Lille, France
| | - Firas Kobeissy
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Marie Duhamel
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France
| | - Isabelle Fournier
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
| | - Michel Salzet
- Université Lille, Inserm, CHU Lille, U1192, Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Lille, France.,Institut Universitaire de France, Paris, France
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12
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Liu F, Shao J, Yang H, Yang G, Zhu Q, Wu Y, Zhu L, Wu H. Disruption of rack1 suppresses SHH-type medulloblastoma formation in mice. CNS Neurosci Ther 2021; 27:1518-1530. [PMID: 34480519 PMCID: PMC8611787 DOI: 10.1111/cns.13728] [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: 03/30/2021] [Revised: 08/19/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022] Open
Abstract
Introduction Medulloblastoma (MB) is a malignant pediatric brain tumor that arises in the cerebellar granular neurons. Sonic Hedgehog subtype of MB (SHH‐MB) is one of the major subtypes of MB in the clinic. However, the molecular mechanisms underlying MB tumorigenesis are still not fully understood. Aims Our previous work demonstrated that the receptor for activated C kinase 1 (Rack1) is essential for SHH signaling activation in granule neuron progenitors (GNPs) during cerebellar development. To investigate the potential role of Rack1 in MB development, human MB tissue array and SHH‐MB genetic mouse model were used to study the expression of function of Rack1 in MB pathogenesis. Results We found that the expression of Rack1 was significantly upregulated in the majority of human cerebellar MB tumors. Genetic ablation of Rack1 expression in SHH‐MB tumor mice could significantly inhibit MB proliferation, reduce the tumor size, and prolong the survival of tumor rescue mice. Interestingly, neither apoptosis nor autophagy levels were affected in Rack1‐deletion rescue mice compared to WT mice, but the expression of Gli1 and HDAC2 was significantly decreased suggesting the inactivation of SHH signaling pathway in rescue mice. Conclusion Our results demonstrated that Rack1 may serve as a potential candidate for the diagnostic marker and therapeutic target of MB, including SHH‐MB.
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Affiliation(s)
- Fengjiao Liu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jingyuan Shao
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Haihong Yang
- Department of Anesthesiology, The General Hospital of Western Theater Command, Chengdu, China
| | - Guochao Yang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Qian Zhu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yan Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Lingling Zhu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Haitao Wu
- Department of Neurobiology, Beijing Institute of Basic Medical Sciences, Beijing, China.,Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China.,Chinese Institute for Brain Research, Beijing, China
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13
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Tan Y, Zhang S, Xiao Q, Wang J, Zhao K, Liu W, Huang K, Tian W, Niu H, Lei T, Shu K. Prognostic significance of ARL9 and its methylation in low-grade glioma. Genomics 2020; 112:4808-4816. [PMID: 32882327 PMCID: PMC7462573 DOI: 10.1016/j.ygeno.2020.08.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 12/11/2022]
Abstract
This study aimed to determine the value of ARL9 expression or methylation as a biomarker for LGG survival. We investigated the expression, methylation, prognosis and immune significance of ARL9 through bioinformatics analysis. ARL9 is negatively regulated by ARL9 methylation, leading to its low expression in LGG tissues. Both low ARL9 expression and hypermethylation predicted favorable OS and PFS in LGG patients, according to the TCGA database. Cox regression demonstrated that low ARL9 expression and ARL9 hypermethylation were independent biomarkers for OS. Moreover, three other glioma databases were utilized to verify the prognostic role of ARL9 in LGG, and the similar results were reached. A meta-analysis revealed that low ARL9 expression was closely relevant to better OS. Finally, ARL9 expression exhibited a close correlation with some immune cells, especially CD8+ T cells. ARL9 could constitute a promising prognostic biomarker, and probably plays an important role in immune cell infiltration in LGG. This is the first study to report the clinical and prognostic significance of ARL9, a methylation-driven gene,in LGG. Meta-analysis could be used for bioinformatics analysis to assess the overall effect of the gene from different datasets. ARL9 probably plays a role in the infiltration of immune cells, and acts as a promising prognostic marker in LGG patients.
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Affiliation(s)
- Yutang Tan
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Suojun Zhang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qungen Xiao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Junwen Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kai Zhao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weihua Liu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kuan Huang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Weidong Tian
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Department of Neurosurgery, First Affiliated Hospital of Medical College, Shihezi University, Xinjiang 832000, China
| | - Hongquan Niu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ting Lei
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Kai Shu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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14
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Kalafatakis I, Kalafatakis K, Tsimpolis A, Giannakeas N, Tsipouras M, Tzallas A, Karagogeos D. Using the Allen gene expression atlas of the adult mouse brain to gain further insight into the physiological significance of TAG-1/Contactin-2. Brain Struct Funct 2020; 225:2045-2056. [PMID: 32601750 DOI: 10.1007/s00429-020-02108-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 06/21/2020] [Indexed: 12/11/2022]
Abstract
The anatomic gene expression atlas (AGEA) of the adult mouse brain of the Allen Institute for Brain Science is a transcriptome-based atlas of the adult C57Bl/6 J mouse brain, based on the extensive in situ hybridization dataset of the Institute. This spatial mapping of the gene expression levels of mice under baseline conditions could assist in the formation of new, reasonable transcriptome-derived hypotheses on brain structure and underlying biochemistry, which could also have functional implications. The aim of this work is to use the data of the AGEA (in combination with Tabula Muris, a compendium of single cell transcriptome data collected from mice, enabling direct and controlled comparison of gene expression among cell types) to provide further insights into the physiology of TAG-1/Contactin-2 and its interactions, by presenting the expression of the corresponding gene across the adult mouse brain under baseline conditions and to investigate any spatial genomic correlations between TAG-1/Contactin-2 and its interacting proteins and markers of mature and immature oligodendrocytes, based on the pre-existing experimental or bibliographical evidence. The across-brain correlation analysis on the gene expression intensities showed a positive spatial correlation of TAG-1/Contactin-2 with the gene expression of Plp1, Myrf, Mbp, Mog, Cldn11, Bace1, Kcna1, Kcna2, App and Nfasc and a negative spatial correlation with the gene expression of Cspg4, Pdgfra, L1cam, Ncam1, Ncam2 and Ptprz1. Spatially correlated genes are mainly expressed by mature oligodendrocytes (like Cntn2), while spatially anticorrelated genes are mainly expressed by oligodendrocyte precursor cells. According to the data presented in this work, we propose that even though Contactin-2 expression during development correlates with high plasticity events, such as neuritogenesis, in adulthood it correlates with pathways characterized by low plasticity.
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Affiliation(s)
- Ilias Kalafatakis
- Faculty of Medicine, University of Crete & Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas, Heraklion, Crete, Greece.
| | - Konstantinos Kalafatakis
- Faculty of Medicine, University of Crete & Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, Arta, Greece
| | - Alexandros Tsimpolis
- Faculty of Medicine, University of Crete & Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas, Heraklion, Crete, Greece
| | - Nikos Giannakeas
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, Arta, Greece
| | - Markos Tsipouras
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, Arta, Greece
| | - Alexandros Tzallas
- Department of Informatics and Telecommunications, School of Informatics and Telecommunications, University of Ioannina, Arta, Greece
| | - Domna Karagogeos
- Faculty of Medicine, University of Crete & Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology Hellas, Heraklion, Crete, Greece
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15
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Liu Z, Zhang R, Sun Z, Yao J, Yao P, Chen X, Wang X, Gao M, Wan J, Du Y, Zhao S. Identification of hub genes and small-molecule compounds in medulloblastoma by integrated bioinformatic analyses. PeerJ 2020; 8:e8670. [PMID: 32328342 PMCID: PMC7164431 DOI: 10.7717/peerj.8670] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/30/2020] [Indexed: 01/03/2023] Open
Abstract
Background Medulloblastoma (MB) is the most common intracranial malignant tumor in children. The genes and pathways involved in the pathogenesis of MB are relatively unknown. We aimed to identify potential biomarkers and small-molecule drugs for MB. Methods Gene expression profile data sets were obtained from the Gene Expression Omnibus (GEO) database and the differentially expressed genes (DEGs) were identified using the Limma package in R. Functional annotation, and cell signaling pathway analysis of DEGs was carried out using DAVID and Kobas. A protein-protein interaction network was generated using STRING. Potential small-molecule drugs were identified using CMap. Result We identified 104 DEGs (29 upregulated; 75 downregulated). Gene ontology analysis showed enrichment in the mitotic cell cycle, cell cycle, spindle, and DNA binding. Cell signaling pathway analysis identified cell cycle, HIF-1 signaling pathway, and phospholipase D signaling pathway as key pathways. SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were the prominent hub genes and their expression level were verified by RT-qPCR. Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB. The five hub genes may be targets for diagnosis and treatment of MB, and the small-molecule compounds are promising drugs for effective treatment of MB. Conclusion In this study we obtained five hub genes of MB, SYN1, CNTN2, FAIM2, MT3, and SH3GL2 were confirmed as hub genes. Meanwhile, Vorinostat, resveratrol, trichostatin A, pyrvinium, and prochlorperazine were identified as potential drugs for MB.
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Affiliation(s)
- Zhendong Liu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Ruotian Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhenying Sun
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jiawei Yao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Penglei Yao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Xin Chen
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Xinzhuang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Ming Gao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Jinzhao Wan
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yiming Du
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Shiguang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China.,Institute of Brain Science, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
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16
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Donovan MKR, D'Antonio-Chronowska A, D'Antonio M, Frazer KA. Cellular deconvolution of GTEx tissues powers discovery of disease and cell-type associated regulatory variants. Nat Commun 2020; 11:955. [PMID: 32075962 PMCID: PMC7031340 DOI: 10.1038/s41467-020-14561-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/17/2020] [Indexed: 12/31/2022] Open
Abstract
The Genotype-Tissue Expression (GTEx) resource has provided insights into the regulatory impact of genetic variation on gene expression across human tissues; however, thus far has not considered how variation acts at the resolution of the different cell types. Here, using gene expression signatures obtained from mouse cell types, we deconvolute bulk RNA-seq samples from 28 GTEx tissues to quantify cellular composition, which reveals striking heterogeneity across these samples. Conducting eQTL analyses for GTEx liver and skin samples using cell composition estimates as interaction terms, we identify thousands of genetic associations that are cell-type-associated. The skin cell-type associated eQTLs colocalize with skin diseases, indicating that variants which influence gene expression in distinct skin cell types play important roles in traits and disease. Our study provides a framework to estimate the cellular composition of GTEx tissues enabling the functional characterization of human genetic variation that impacts gene expression in cell-type-specific manners.
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Affiliation(s)
- Margaret K R Donovan
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Matteo D'Antonio
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Kelly A Frazer
- Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, La Jolla, CA, 92093, USA.
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
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17
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Shen C, Hua H, Gu L, Cao S, Cai H, Yao X, Chen X. Overexpression of RACK1 Predicts Poor Prognosis in Melanoma. J Cancer 2020; 11:795-803. [PMID: 31949482 PMCID: PMC6959021 DOI: 10.7150/jca.36905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/22/2019] [Indexed: 12/13/2022] Open
Abstract
Melanoma is a highly malignant skin cancer with limited treatment options, the mechanism of the occurrence and development of melanoma is still unclear till now. Receptor for activated C kinase 1 (RACK1) is a scaffolding protein that mediates multiple signaling pathways; it interconnects distinct signaling pathways to control essential cellular processes. RACK1 was reported as an oncogene in human tumorigenesis, but little is known about its role in melanoma. This study aimed to investigate the expression of RACK1 in patients with melanoma and to reveal its possible functions in melanoma cells. The expression profiles of RACK1 detected in tumor tissues from melanoma patients showed that RACK1 was higher in tumor tissues, and its expression level was well associated with the clinical progression of melanoma (TNM stage, P=0.009). Furthermore, RNA interfering (RNAi) knockdown of RACK1 could efficiently suppress the proliferation, migration and invasion of A375 and A875 cells and promote their apoptosis. Taken together, these results suggest that RACK1 may be a poor prognostic factor in human melanoma, and it may be a new therapeutic target for melanoma treatment.
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Affiliation(s)
- Congcong Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
| | - Hui Hua
- Department of Dermatology, The Third People's Hospital of Nantong, Nantong, 226001, P.R. China
| | - Lixiong Gu
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
| | - Shuanglin Cao
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
| | - Hengji Cai
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
| | - Xiaodong Yao
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
| | - Xiaodong Chen
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, 226001, P.R. China
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18
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Liu W, Long H, Zhang M, Wang Y, Lu Q, Yuan H, Qu Q, Qu J. Glutathione S-transferase genes variants and glioma risk: A case-control and meta-analysis study. J Cancer 2019; 10:4679-4688. [PMID: 31528233 PMCID: PMC6746118 DOI: 10.7150/jca.29398] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 06/23/2019] [Indexed: 01/17/2023] Open
Abstract
Background: The glutathione S-transferase (GST) genes encode enzymes that metabolize carcinogenic compounds, and their variants, GSTP1 (Ile105Val and Ala114Val), GSTT1 (null/present), and GSTM1 (null/present), reduce enzyme activity that may affect the risk of developing cerebral glioma. This study undertook a case-control study and a meta-analysis to evaluate associations between these GST gene variants and the risk of glioma. Methods: The study enrolled 384 glioma patients (194 men and 190 women; mean age, 48.3 ± 9.2 years) and 340 healthy controls (174 men and 166 women; mean age, 46.5 ± 9.8 years). The amplification refractory mutation system assay was performed to identify GST gene variants of all 724 subjects. A meta-analysis enrolled 15 studies (including our case-control results) was performed. Results: Our case-control study found that the frequency of GSTP1 Ile105Val Val/Val genotype was significantly higher in the glioma group than that in the healthy controls (11.7% vs. 6.4%) (OR=1.50; 95% CI=1.05-2.04; P=0.01); the frequency of the Val/Ile + Ile/Ile genotypes was different from glioma patients and controls (88.3% vs. 93.6%) (OR=1.47(1.04-2.10); P=0.015); there were no associations between GSTP1 Ala114Val, GSTT1 (null/present) and GSTM1 (null/present) variants and glioma risk. Our meta-analysis confirmed that the GSTP1 Ile105Val variant was associated with an overall increased glioma risk. Moreover, our meta-analysis also confirmed the GSTP1 Ala114Val and GSTT1 null/present variants were associated with an increased glioma risk in the Caucasian population, rather than the Asian population. Conclusions: This study showed that GST gene variants were associated with an increased risk of glioma with ethnic differences. Future large-scale, multi center, controlled, prospective studies are required to support these findings and to determine how these GST gene variants may affect the pathogenesis of glioma.
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Affiliation(s)
- Weiping Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Mengqi Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Yanjing Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, People's Republic of China
| | - Haiyan Yuan
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, Changsha 410011, People's Republic of China
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19
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Zhu L, Chen W, Li G, Chen H, Liao W, Zhang L, Xiao X. Upregulated RACK1 attenuates gastric cancer cell growth and epithelial-mesenchymal transition via suppressing Wnt/β-catenin signaling. Onco Targets Ther 2019; 12:4795-4805. [PMID: 31417279 PMCID: PMC6592218 DOI: 10.2147/ott.s205869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose: As there have been few studies on the effects of the receptor for activated C kinase 1 (RACK1) on gastric cancer (GC), we aimed to explore such effects and the mechanism that may be involved. Patients and methods: Normal gastric epithelial cells and six GC cell lines were used to detect the mRNA expression of RACK1. Overexpressing RACK1 was transfected in HGC27 and MGC803 cells. The effects of overexpressing RACK1 on cell viability, migration, and invasion were determined by cell counting kit-8, wound scratch, and Transwell assay, respectively. The expressions of epithelial–mesenchymal transition (EMT) and Wnt/β-catenin signaling related genes were detected using quantitative real-time PCR or Western blot. Wnt pathway agonist LiCl was added into RACK1 overexpressing GC cells, and then cell viability, migration, and invasion were also detected. Results: RACK1 was downregulated in GC cell lines. Under the circumstance that overexpressing RACK1 was successfully transfected in the two lowest RACK1-expressing GC cells, significant inhibition of cell viability, migration, and invasion, promotion to the mRNA and protein expression of E-cadherin, as well as a decrease in the N-cadherin and Snail expressions could be observed. Overexpressing RACK1 also enhanced the protein level of phosphorylation-β-catenin/β-catenin and attenuated c-Jun protein expression. Additionally, LiCl could partially reverse the inhibitory effects of cell viability, migration and invasion by overexpressing RACK. Conclusion: We found RACK1 possibly inhibited epithelial–mesenchymal transition of GC cells through limitation of the Wnt/β-catenin pathway, thereby suppressing cell migration and invasion; RACK1 could also suppress cell growth.
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Affiliation(s)
- Lihui Zhu
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Wen Chen
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Guoqing Li
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Honghui Chen
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Wenqiu Liao
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Li Zhang
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
| | - Xiaoli Xiao
- Department of Gastroenterology, The Second Hospital Affiliated to the University of South China, Hengyang, Hunan Province, People's Republic of China
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20
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Flowers E, Flentje A, Levine J, Olshen A, Hammer M, Paul S, Conley Y, Miaskowski C, Kober KM. A Pilot Study Using a Multistaged Integrated Analysis of Gene Expression and Methylation to Evaluate Mechanisms for Evening Fatigue in Women Who Received Chemotherapy for Breast Cancer. Biol Res Nurs 2019; 21:142-156. [PMID: 30701989 PMCID: PMC6700896 DOI: 10.1177/1099800418823286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CONTEXT Fatigue is the most common symptom associated with cancer and its treatment. Investigation of molecular mechanisms associated with fatigue may identify new therapeutic targets. OBJECTIVE The objective of this pilot study was to evaluate the relationships between gene expression and methylation status and evening fatigue severity in women with breast cancer who received chemotherapy. METHODS Latent class analysis (LCA) was used to identify evening fatigue phenotypes. In this analysis, the lowest (i.e., moderate, n = 7) and highest (i.e., very high, n = 29) fatigue-severity classes identified using LCA were analyzed via two stages. First, a total of 32,609 transcripts from whole blood were evaluated for differences in expression levels between the classes. Next, 637 methylation sites located within the putative transcription factor binding sites for those genes demonstrating differential expression were evaluated for differential methylation state between the classes. RESULTS A total of 89 transcripts in 75 unique genes were differentially expressed between the moderate (the lowest fatigue-severity class identified) and very high evening fatigue classes. In addition, 23 differentially methylated probes and three differentially methylated regions were found between the moderate and very high evening fatigue classes. CONCLUSIONS Using a multistaged integrated analysis of gene expression and methylation, differential methylation was identified in the regulatory regions of genes associated with previously hypothesized mechanisms for fatigue, including inflammation, immune function, neurotransmission, circadian rhythm, skeletal muscle energy, carbohydrate metabolism, and renal function as well as core biological processes including gene transcription and the cell-cycle regulation.
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Affiliation(s)
- Elena Flowers
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Annesa Flentje
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Jon Levine
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Adam Olshen
- 2 School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Marilyn Hammer
- 3 Department of Nursing, Mount Sinai Hospital, New York, NY, USA
| | - Steven Paul
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Yvette Conley
- 4 School of Nursing, University of Pittsburg, Pittsburg, PA, USA
| | - Christine Miaskowski
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
| | - Kord M Kober
- 1 School of Nursing, University of California, San Francisco, San Francisco, CA, USA
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21
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He W, Ju D, Jie Z, Zhang A, Xing X, Yang Q. Aberrant CpG-methylation affects genes expression predicting survival in lung adenocarcinoma. Cancer Med 2018; 7:5716-5726. [PMID: 30353687 PMCID: PMC6246931 DOI: 10.1002/cam4.1834] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/09/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a common diagnosed disease with high-mortality rate, and its prognostic implications are under discovered. DNA methylation aberrations are not only an important event for dysregulation of gene expression during tumorigenesis but also a revolution in epigenetics by identifying key prognostic biomarkers for multiple cancers. In this study, we analyzed methylation status of 485 578 CpG sites and RNA-seq transcriptomes of 20 532 genes for 1095 LUAD samples in TCGA database. The association between DNA methylation and the prognostic value of the corresponding gene expression was identified as well. In total, ten aberrantly methylated and dysregulated genes (AURKA, BLK, CNTN2, HMGA1, PTTG1, TNS4, DAPK2, MFSD2A, THSD1, and WNT7A) were highlighted which were significantly correlated with overall survival of 492 LUAD patients, which were all reported as tumor-associated genes in other various cancers and worthy of further investigated and might be used as therapeutic targets for LUAD. Together, methylation aberrances regulate gene expression level during tumorigenesis and influence prognosis of LUAD patients. Integrating knowledge of epigenetics and expression of genes can be useful for an in-depth understanding of cancer mechanism and for the eventual purpose of precisely prognostic and therapeutic target verification.
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Affiliation(s)
- Wei He
- Department of Respiratory Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Dandan Ju
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhijun Jie
- Department of Respiratory Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Ai Zhang
- The People's Hospital of Shanghai Pudong District, Shanghai, China
| | - Xin Xing
- Department of Obstetrics and Gynecology, Fengxian Hospital, Shanghai, China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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22
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Zhang L, Xu Y, Wang L, Liu H. Role of RACK1 on cell proliferation, adhesion, and bortezomib-induced apoptosis in multiple myeloma. Int J Biol Macromol 2018; 121:1077-1085. [PMID: 30315883 DOI: 10.1016/j.ijbiomac.2018.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 09/16/2018] [Accepted: 10/09/2018] [Indexed: 12/30/2022]
Abstract
Receptor for activated C kinase 1 (RACK1), a scaffold protein, plays a crucial role in the progression of various cancers. However, the biological function and underlying mechanism of RACK1 in multiple myeloma (MM) cells remain unclear. The present study aimed to explore the function of RACK1 on the cell proliferation, adhesion, and bortezomib-induced apoptosis in MM. We found that RACK1 was significantly overexpressed in myeloma cell lines and primary myeloma cells compared with normal bone marrow plasma cells. Moreover, immunofluorescence revealed that RACK1 was primarily expressed in the cytoplasm of MM cells. Knockdown of RACK1 impaired growth of MM cells, blocked entry into the S-phase of the cell cycle, and resulted in reduced cell adhesion rates. More importantly, knockdown of RACK1 decreased the proliferation of MM cells by activating P-P38 and P-ERK in the MAPK/ERK signaling pathway. We also found that altered expression of RACK1 is associated with bortezomib-mediated MM cell apoptosis. In summary, these results may provide a possible target for therapy in MM.
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Affiliation(s)
- Linlin Zhang
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong, People's Republic of China
| | - Ya Xu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong, People's Republic of China
| | - Li Wang
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong, People's Republic of China
| | - Hong Liu
- Department of Hematology, Affiliated Hospital of Nantong University, Nantong University, Nantong, People's Republic of China.
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23
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Xu J, He J, Huang H, Peng R, Xi J. MicroRNA-423-3p promotes glioma growth by targeting PANX2. Oncol Lett 2018; 16:179-188. [PMID: 29928399 PMCID: PMC6006452 DOI: 10.3892/ol.2018.8636] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 03/15/2018] [Indexed: 01/08/2023] Open
Abstract
Previously, a number of microRNAs (miRs) have been identified to participate in the development and progression of glioma via the regulation of their target genes. However, the molecular mechanisms underlying the effect of miR-423-3p in glioma growth remain unclear. In the present study, the reverse transcription-quantitative polymerase chain reaction and western blotting were used to assess the mRNA and protein expression levels of miR-423-3p, respectively. An MTT assay and flow cytometry were performed to determine cell proliferation and apoptosis, respectively. A luciferase reporter gene assay was performed to determine the target association between pannexin 2 (PANX2) and miR-423-3p. It was revealed that miR-423-3p was significantly upregulated in glioma tissues compared with normal brain tissues, and the increased expression of miR-423-3p was significantly associated with an advanced grade as well as a poorer prognosis of patients with glioma. Inhibition of miR-423-3p using an miR-423-3p inhibitor resulted in the decreased proliferation of glioma U251 and U87MG Uppsala cells, and the induction of apoptosis. PANX2 was identified as a novel target gene of miR-423-3p, and the expression of PANX2 was revealed to be increased in U251 and U87MG Uppsala cells when miR-423-3p was inhibited. Knockdown of PANX2 attenuated the effects of miR-423-3p inhibition on glioma cell proliferation and apoptosis. Furthermore, PANX2 was significantly downregulated in glioma tissues compared with normal brain tissues, and its levels were markedly lower in World Health Organization (WHO) stage III–IV gliomas compared with WHO stage I–II gliomas. Additionally, the expression levels of PANX2 were identified to be inversely correlated with miR-423-3p expression levels in glioma tissues. Consequently, targeting miR-423-3p may inhibit glioma growth via the upregulation of PANX2.
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Affiliation(s)
- Jing Xu
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jian He
- Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - He Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Renjun Peng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Jian Xi
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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Abstract
Contactin-2/transiently expressed axonal surface glycoprotein-1 (TAG-1) is a cell adhesion molecule belonging to the immunoglobulin superfamily (IgSF). It has six immunoglobulin-like extracellular domains and four fibronectin III-like ones, with anchoring to the cell membrane through glycosylphosphatidyl inositol. Contactin-2/TAG-1 is expressed in specific neurons transiently on the axonal surface during the fetal period. In postnatal stages, Contactin-2/TAG-1 is expressed in cerebellar granule cells, hippocampal pyramidal cells, and the juxtaparanodal regions of myelinated nerve fibers. In the embryonic nervous system, Contactin-2/TAG-1 plays important roles in axonal elongation, axonal guidance, and cellular migration. In the postnatal nervous system, it also plays an essential role in the formation of myelinated nerve fibers. Moreover, Contactin-2/TAG-1 has been linked to autoimmune diseases of the human nervous system. Taken together, Contactin-2/TAG-1 plays a central role in a variety of functions from development to disease.
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Affiliation(s)
- Tomoyuki Masuda
- a Doctoral and Master's Programs in Kansei, Behavioral and Brain Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba , Ibaraki , Japan.,b Department of Neurology , Faculty of Medicine, University of Tsukuba , Ibaraki , Japan.,c Department of Neurobiology , Faculty of Medicine, University of Tsukuba , Ibaraki , Japan
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25
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Zhou Y, Peng Y, Liu M, Jiang Y. MicroRNA-181b Inhibits Cellular Proliferation and Invasion of Glioma Cells via Targeting Sal-Like Protein 4. Oncol Res 2016; 25:947-957. [PMID: 27938503 PMCID: PMC7841051 DOI: 10.3727/096504016x14791732531006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRs), a class of noncoding RNAs that are 18-25 nucleotides in length, are able to suppress gene expression by targeting complementary regions of mRNAs and inhibiting protein translation. Recently, miR-181b was found to play a suppressive role in glioma, but the regulatory mechanism of miR-181b in the malignant phenotypes of glioma cells remains largely unclear. In this study, we found that miR-181b was significantly downregulated in glioma tissues when compared with normal brain tissues, and decreased miR-181b levels were significantly associated with high-grade pathology and a poor prognosis for patients with glioma. Moreover, miR-181b was downregulated in glioma cell lines (U87, SHG44, U373, and U251) compared to normal astrocytes. Overexpression of miR-181b significantly decreased the proliferation, migration, and invasion of glioma U251 cells. Sal-like protein 4 (SALL4) was identified as a novel target gene of miR-181b in U251 cells. The expression of SALL4 was significantly upregulated in glioma tissues and cell lines, and an inverse correlation was observed between the miR-181b and SALL4 expression levels in glioma. Further investigation showed that the protein expression of SALL4 was negatively regulated by miR-181b in U251 cells. Knockdown of SALL4 significantly inhibited the proliferation, migration, and invasion of U251 cells, while overexpression of SALL4 effectively reversed the suppressive effects of miR-181b on these malignant phenotypes of U251 cells. In conclusion, our study demonstrates that miR-181b has a suppressive effect on the malignant phenotypes of glioma cells, at least partly, by directly targeting SALL4. Therefore, the miR-181b/SALL4 axis may become a potential therapeutic target for glioma.
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Dai Z, Wu J, Chen F, Cheng Q, Zhang M, Wang Y, Guo Y, Song T. CXCL5 promotes the proliferation and migration of glioma cells in autocrine- and paracrine-dependent manners. Oncol Rep 2016; 36:3303-3310. [PMID: 27748886 DOI: 10.3892/or.2016.5155] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 06/21/2016] [Indexed: 12/16/2022] Open
Abstract
CXCL5 and its receptor CXCR2 have been found to be involved in tumorigenesis and cancer progression. Recent studies have shown that CXCR2 is upregulated in glioma tissues, and associated with poor prognosis and recurrence. However, the role of CXCL5/CXCR2 signaling in mediating the malignant phenotypes of glioma cells, as well as the underlying mechanism, still remains unclear. In the present study, we found that CXCL5 was upregulated in glioma tissues compared to that noted in normal brain tissues. High CXCL5 levels were significantly associated with higher tumor grade, advanced clinical stage, and shorter survival time of glioma patients. In vitro studies indicated that the protein expression levels of CXCL5 and CXCR2 were markedly higher in human glioma cell lines (U87, U251, U373 and A172), when compared with those in normal human gliocyte HEB cells. Overexpression of CXLC5 significantly promoted the proliferation and migration of U87 cells, while knockdown of CXCL5 by small interfering RNA markedly inhibited U87 cell proliferation and migration. Moreover, both exogenous CXCL5 treatment and the conditioned medium of CXCL5-overexpressing HEB cells also enhanced the proliferation and migration of U87 cells. Molecular mechanism investigation revealed that CXLC5 activated the ERK, JNK, p38 MAPK signaling pathways, which play key roles in tumor growth and metastasis. According to these data, our study suggests that CXCL5 plays a promoting role in glioma in autocrine- and paracrine-dependent manners.
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Affiliation(s)
- Zhijie Dai
- Institute of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Jun Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Fenghua Chen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Mingyu Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Ying Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Yong Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
| | - Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan 410008, P.R. China
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