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Baum E, Huang W, Vincent-Delorme C, Brunelle P, Antebi A, Dafsari HS. Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders. Int J Mol Sci 2024; 25:2053. [PMID: 38396730 PMCID: PMC10889399 DOI: 10.3390/ijms25042053] [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: 12/31/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Heterozygous variants in the Poly(U) Binding Splicing Factor 60kDa gene (PUF60) have been associated with Verheij syndrome, which has the key features of coloboma, short stature, skeletal abnormalities, developmental delay, palatal abnormalities, and congenital heart and kidney defects. Here, we report five novel patients from unrelated families with PUF60-related disorders exhibiting novel genetic and clinical findings with three truncating variants, one splice-site variant with likely reduced protein expression, and one missense variant. Protein modeling of the patient's missense variant in the PUF60 AlphaFold structure revealed a loss of polar bonds to the surrounding residues. Neurodevelopmental disorders were present in all patients, with variability in speech, motor, cognitive, social-emotional and behavioral features. Novel phenotypic expansions included movement disorders as well as immunological findings with recurrent respiratory, urinary and ear infections, atopic diseases, and skin abnormalities. We discuss the role of PUF60 in immunity with and without infection based on recent organismic and cellular studies. As our five patients showed less-severe phenotypes than classical Verheij syndrome, particularly with the absence of key features such as coloboma or palatal abnormalities, we propose a reclassification as PUF60-related neurodevelopmental disorders with multi-system involvement. These findings will aid in the genetic counseling of patients and families.
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Affiliation(s)
- Emily Baum
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Wenming Huang
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | | | - Perrine Brunelle
- Institut de Génétique Médicale, University of Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Adam Antebi
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
- Department of Pediatric Neurology, Evelina’s Children Hospital, Guy’s & St. Thomas’ Hospital NHS Foundation Trust, London SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King’s College London, London WC2R 2LS, UK
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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2
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Zhang C, Ni X, Tao C, Zhou Z, Wang F, Gu F, Cui X, Jiang S, Li Q, Lu H, Li D, Wu Z, Zhang R. Targeting PUF60 prevents tumor progression by retarding mRNA decay of oxidative phosphorylation in ovarian cancer. Cell Oncol (Dordr) 2024; 47:157-174. [PMID: 37632669 PMCID: PMC10899302 DOI: 10.1007/s13402-023-00859-w] [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] [Accepted: 08/04/2023] [Indexed: 08/28/2023] Open
Abstract
PURPOSE Ovarian cancer (OC) is the leading cause of death from gynecological malignancies, and its etiology and pathogenesis are currently unclear. Recent studies have found that PUF60 overexpressed in various cancers. However, the exact function of PUF60 in global RNA processing and its role in OC has been unclear. METHODS The expression of PUF60 and its relationship with clinical characteristics were analyzed by multiple database analysis and immunohistochemistry. Phenotypic effects of PUF60 on ovarian cancer cell proliferation and metastasis were examined by in vitro cell proliferation assay, migration assay, and in vivo xenograft models and lung metastasis models. RNA immunoprecipitation, seahorse analyses, RNA stability assay were used to study the effect of PUF60 on the stability of oxidative phosphorylation (OXPHOS)-related genes in OC. RESULTS We report PUF60 is highly expressed in OC with frequent amplification of up to 33.9% and its upregulation predicts a poor prognosis. PUF60 promotes the proliferation and migration of OC cells both in vitro and in vivo. Mechanistically, we demonstrated that silencing of PUF60 enhanced the stability of mRNA transcripts involved in OXPHOS and decreased the formation of processing bodies (P-bodies), ultimately elevating the OXPHOS level. CONCLUSION Our study unveils a novel function of PUF60 in OC energy metabolism. Thus, PUF60 may serve as a novel target for the treatment of patients with OC.
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Affiliation(s)
- Cancan Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
- Department of Obstetrics and Gynecology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Xiaoge Ni
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Chunlin Tao
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Ziyang Zhou
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Fengmian Wang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Fei Gu
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Xiaoxiao Cui
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Shuheng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China
| | - Qing Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China
| | - Huan Lu
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China
| | - Dongxue Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Zhiyong Wu
- Gynecology Department, Shanghai Obstetrics and Gynecology Hospital of Fudan University, No. 419 Fangxie Road, Shanghai, 200011, China.
| | - Rong Zhang
- Department of Obstetrics and Gynecology, Fengxian Hospital, The Third School of Clinical Medicine, Southern Medical University, 6600 Nanfeng Road, Shanghai, 201499, China.
- Shanghai Geriatric Medical Center, Shanghai, China.
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3
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Grimes H, Ansari M, Ashraf T, Cueto-González AM, Calder A, Day M, Fernandez Alvarez P, Foster A, Lahiri N, Repetto GM, Scurr I, Varghese V, Low KJ. PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants. Am J Med Genet A 2023; 191:2610-2622. [PMID: 37303278 DOI: 10.1002/ajmg.a.63313] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
PUF60-related developmental disorder (also referred to as Verheij syndrome), resulting from haploinsufficiency of PUF60, is associated with multiple congenital anomalies affecting a wide range of body systems. These anomalies include ophthalmic coloboma, and congenital anomalies of the heart, kidney, and musculoskeletal system. Behavioral and intellectual difficulties are also observed. While less common than other features associated with PUF60-related developmental disorder, for instance hearing impairment and short stature, identification of specific anomalies such as ophthalmic coloboma can aid with diagnostic identification given the limited spectrum of genes linked with this feature. We describe 10 patients with PUF60 gene variants, bringing the total number reported in the literature, to varying levels of details, to 56 patients. Patients were recruited both via locally based exome sequencing from international sites and from the DDD study in the United Kingdom. Eight of the variants reported were novel PUF60 variants. The addition of a further patient with a reported c449-457del variant to the existing literature highlights this as a recurrent variant. One variant was inherited from an affected parent. This is the first example in the literature of an inherited variant resulting in PUF60-related developmental disorder. Two patients (20%) were reported to have a renal anomaly consistent with 22% of cases in previously reported literature. Two patients received specialist endocrine treatment. More commonly observed were clinical features such as: cardiac anomalies (40%), ocular abnormalities (70%), intellectual disability (60%), and skeletal abnormalities (80%). Facial features did not demonstrate a recognizable gestalt. Of note, but remaining of unclear causality, we describe a single pediatric patient with pineoblastoma. We recommend that stature and pubertal progress should be monitored in PUF60-related developmental disorder with a low threshold for endocrine investigations as hormone therapy may be indicated. Our study reports an inherited case with PUF60-related developmental disorder which has important genetic counseling implications for families.
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Affiliation(s)
- H Grimes
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - M Ansari
- South East Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - T Ashraf
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Anna Mª Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona, Barcelona, Spain
| | - A Calder
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | - M Day
- Exeter Genetics Laboratory, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - P Fernandez Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - A Foster
- Department of Clinical Genetics, West Midlands Regional Genetics Centre, Birmingham, UK
| | - N Lahiri
- Department of Clinical Genetics, St Georges University Hospital NHS Foundation Trust, London, UK
- Department of Clinical and Molecular Science, St Georges University of London, London, UK
| | - G M Repetto
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - I Scurr
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - V Varghese
- All Wales Medical Genomics Services, University Hospital of Wales, Cardiff, UK
| | - Karen J Low
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
- Centre for Academic Child Health, University of Bristol, Bristol, UK
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4
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Xu N, Ren Y, Bao Y, Shen X, Kang J, Wang N, Wang Z, Han X, Li Z, Zuo J, Wei GH, Wang Z, Zong WX, Liu W, Xie G, Wang Y. PUF60 promotes cell cycle and lung cancer progression by regulating alternative splicing of CDC25C. Cell Rep 2023; 42:113041. [PMID: 37682709 DOI: 10.1016/j.celrep.2023.113041] [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: 11/08/2022] [Revised: 06/27/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Alternative splicing (AS) has been implicated in cell cycle regulation and cancer, but the underlying mechanisms are poorly understood. The poly(U)-binding splicing factor 60 (PUF60) is essential for embryonic development and is overexpressed in multiple types of cancer. Here, we report that PUF60 promotes mitotic cell cycle and lung cancer progression by controlling AS of the cell division cycle 25C (CDC25C). Systematic analysis of splicing factors deregulated in lung adenocarcinoma (LUAD) identifies that elevated copy number and expression of PUF60 correlate with poor prognosis. PUF60 depletion inhibits LUAD cell-cycle G2/M transition, cell proliferation, and tumor development. Mechanistically, PUF60 knockdown leads to exon skipping enriched in mitotic cell cycle genes, including CDC25C. Exon 3 skipping in the full-length CDC25C results in nonsense-mediated mRNA decay and a decrease of CDC25C protein, thereby inhibiting cell proliferation. This study establishes PUF60 as a cell cycle regulator and an oncogenic splicing factor in lung cancer.
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Affiliation(s)
- Nan Xu
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yunpeng Ren
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yufang Bao
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xianfeng Shen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jiahui Kang
- Institute of Reproductive Medicine, Medical School, Nantong University, Qixiu Road 19, Nantong 226001, China
| | - Ning Wang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zixian Wang
- MOE Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinlu Han
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zhen Li
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ji Zuo
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Gong-Hong Wei
- MOE Key Laboratory of Metabolism and Molecular Medicine & Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Fudan University Shanghai Cancer Center, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Zefeng Wang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei-Xing Zong
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers-The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Wen Liu
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Gangcai Xie
- Institute of Reproductive Medicine, Medical School, Nantong University, Qixiu Road 19, Nantong 226001, China.
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China; Minhang Hospital & Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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5
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Identification of Kinase Targets for Enhancing the Antitumor Activity of Eribulin in Triple-Negative Breast Cell Lines. Biomedicines 2023; 11:biomedicines11030735. [PMID: 36979714 PMCID: PMC10045293 DOI: 10.3390/biomedicines11030735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is the most aggressive molecular subtype of breast cancer, and current treatments are only partially effective in disease control. More effective combination approaches are needed to improve the survival of TNBC patients. Eribulin mesylate, a non-taxane microtubule dynamics inhibitor, is approved by the U.S. Food and Drug Administration to treat metastatic breast cancer after at least two previous chemotherapeutic regimens. However, eribulin as a single agent has limited therapeutic efficacy against TNBC. Methods: High-throughput kinome library RNAi screening, Ingenuity Pathway Analysis, and STRING analysis were performed to identify target kinases for combination with eribulin. The identified combinations were validated using in vivo and ex vivo proliferation assays. Results: We identified 135 potential kinase targets whose inhibition enhanced the antiproliferation effect of eribulin in TNBC cells, with the PI3K/Akt/mTOR and the MAPK/JNK pathways emerging as the top candidates. Indeed, copanlisib (pan-class I PI3K inhibitor), everolimus (mTOR inhibitor), trametinib (MEK inhibitor), and JNK-IN-8 (pan-JNK inhibitor) produced strong synergistic antiproliferative effects when combined with eribulin, and the PI3K and mTOR inhibitors had the most potent effects in vitro. Conclusions: Our data suggest a new strategy of combining eribulin with PI3K or mTOR inhibitors to treat TNBC.
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6
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Paul AM, Amjesh R, George B, Sankaran D, Sandiford OA, Rameshwar P, Pillai MR, Kumar R. The Revelation of Continuously Organized, Co-Overexpressed Protein-Coding Genes with Roles in Cellular Communications in Breast Cancer. Cells 2022; 11:cells11233806. [PMID: 36497066 PMCID: PMC9741223 DOI: 10.3390/cells11233806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/10/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022] Open
Abstract
Many human cancers, including breast cancer, are polygenic and involve the co-dysregulation of multiple regulatory molecules and pathways. Though the overexpression of genes and amplified chromosomal regions have been closely linked in breast cancer, the notion of the co-upregulation of genes at a single locus remains poorly described. Here, we describe the co-overexpression of 34 continuously organized protein-coding genes with diverse functions at 8q.24.3(143437655-144326919) in breast and other cancer types, the CanCord34 genes. In total, 10 out of 34 genes have not been reported to be overexpressed in breast cancer. Interestingly, the overexpression of CanCord34 genes is not necessarily associated with genomic amplification and is independent of hormonal or HER2 status in breast cancer. CanCord34 genes exhibit diverse known and predicted functions, including enzymatic activities, cell viability, multipotency, cancer stem cells, and secretory activities, including extracellular vesicles. The co-overexpression of 33 of the CanCord34 genes in a multivariant analysis was correlated with poor survival among patients with breast cancer. The analysis of the genome-wide RNAi functional screening, cell dependency fitness, and breast cancer stem cell databases indicated that three diverse overexpressed CanCord34 genes, including a component of spliceosome PUF60, a component of exosome complex EXOSC4, and a ribosomal biogenesis factor BOP1, shared roles in cell viability, cell fitness, and stem cell phenotypes. In addition, 17 of the CanCord34 genes were found in the microvesicles (MVs) secreted from the mesenchymal stem cells that were primed with MDA-MB-231 breast cancer cells. Since these MVs were important in the chemoresistance and dedifferentiation of breast cancer cells into cancer stem cells, these findings highlight the significance of the CanCord34 genes in cellular communications. In brief, the persistent co-overexpression of CanCord34 genes with diverse functions can lead to the dysregulation of complementary functions in breast cancer. In brief, the present study provides new insights into the polygenic nature of breast cancer and opens new research avenues for basic, preclinical, and therapeutic studies in human cancer.
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Affiliation(s)
- Aswathy Mary Paul
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- PhD Program, Manipal Academy of Higher Education, Manipal 576104, India
| | - Revikumar Amjesh
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Bijesh George
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- PhD Program, Manipal Academy of Higher Education, Manipal 576104, India
| | - Deivendran Sankaran
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
| | - Oleta A. Sandiford
- Department of Medicine-Hematology and Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Pranela Rameshwar
- Department of Medicine-Hematology and Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Madhavan Radhakrishna Pillai
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- Correspondence: (M.R.P.); (R.K.)
| | - Rakesh Kumar
- Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695014, India
- Department of Medicine-Hematology and Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
- Cancer Research Institute, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Dehradun 248016, India
- Department of Human and Molecular Genetics, School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
- Correspondence: (M.R.P.); (R.K.)
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7
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Huang W, Kew C, Fernandes SDA, Löhrke A, Han L, Demetriades C, Antebi A. Decreased spliceosome fidelity and egl-8 intron retention inhibit mTORC1 signaling to promote longevity. NATURE AGING 2022; 2:796-808. [PMID: 37118503 PMCID: PMC10154236 DOI: 10.1038/s43587-022-00275-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
AbstractChanges in splicing fidelity are associated with loss of homeostasis and aging, yet only a handful of splicing factors have been shown to be causally required to promote longevity, and the underlying mechanisms and downstream targets in these paradigms remain elusive. Surprisingly, we found a hypomorphic mutation within ribonucleoprotein RNP-6/poly(U)-binding factor 60 kDa (PUF60), a spliceosome component promoting weak 3′-splice site recognition, which causes aberrant splicing, elevates stress responses and enhances longevity in Caenorhabditis elegans. Through genetic suppressor screens, we identify a gain-of-function mutation within rbm-39, an RNP-6-interacting splicing factor, which increases nuclear speckle formation, alleviates splicing defects and curtails longevity caused by rnp-6 mutation. By leveraging the splicing changes induced by RNP-6/RBM-39 activities, we uncover intron retention in egl-8/phospholipase C β4 (PLCB4) as a key splicing target prolonging life. Genetic and biochemical evidence show that neuronal RNP-6/EGL-8 downregulates mammalian target of rapamycin complex 1 (mTORC1) signaling to control organismal lifespan. In mammalian cells, PUF60 downregulation also potently and specifically inhibits mTORC1 signaling. Altogether, our results reveal that splicing fidelity modulates lifespan through mTOR signaling.
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8
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Yao L, Tian F. GRWD1 affects the proliferation, apoptosis, invasion and migration of triple negative breast cancer through the Notch signaling pathway. Exp Ther Med 2022; 24:473. [PMID: 35761807 PMCID: PMC9214606 DOI: 10.3892/etm.2022.11400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/08/2022] [Indexed: 11/28/2022] Open
Abstract
Breast cancer is a highly heterogeneous tumor, among which triple negative breast cancer (TNBC) is the most invasive and prone to recurrence and metastasis. The present study aimed to investigate the regulatory mechanisms of glutamate-rich WD-repeat-containing protein 1 (GRWD1) in TNBC cells. The expression of GRWD1 in the normal human breast epithelial cells and human breast cancer cells was detected by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot analysis. The transfection effects of small interfering RNA (siRNA)-GRWD1 and overexpression (Ov)-Notch1 were also confirmed by RT-qPCR and western blotting. The proliferation, apoptosis, invasion and migration of transfected cells were in turn analyzed by Cell Counting Kit-8, 5-Ethynyl-2'-deoxyuridine, Matrigel and wound healing assays. The expression of proteins related to proliferation, apoptosis, metastasis, epithelial-mesenchymal transition and the Notch signaling pathway was detected by western blotting. As a result, GRWD1 expression was upregulated in breast cancer cells and was revealed to be highest in MDA-MB-231 and HCC1937 cells. GRWD1 knockdown suppressed TNBC cell proliferation, invasion and migration and promoted TNBC cell apoptosis. Furthermore, the expression of Notch1 and Notch4 was inhibited by GRWD1 knockdown. The expression of downstream genes of the Notch signaling pathway Hes1, Hes5, Hey1, Hey2, p21, c-Myc, cyclin D1, human epidermal growth factor 2 receptor and NF-κB were all suppressed after siRNA-GRWD1 transfection. However, Notch1 overexpression reversed the effect of GRWD1 knockdown on biological behaviors of TNBC cells. In conclusion, GRWD1 knockdown could suppress the proliferation, invasion and migration and promoted apoptosis of TNBC cells through inhibiting the Notch signaling pathway.
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Affiliation(s)
- Liang Yao
- Department of Breast Surgery, Shanxi Provincial Tumor Hospital and Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
| | - Fuguo Tian
- Department of Breast Surgery, Shanxi Provincial Tumor Hospital and Affiliated Tumor Hospital of Shanxi Medical University, Taiyuan, Shanxi 030013, P.R. China
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9
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Xu L, Lin J, Liu Y, Hua B, Cheng Q, Lin C, Yan Z, Wang Y, Sun N, Qian R, Lu C. CLOCK regulates Drp1 mRNA stability and mitochondrial homeostasis by interacting with PUF60. Cell Rep 2022; 39:110635. [PMID: 35417690 DOI: 10.1016/j.celrep.2022.110635] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 01/26/2022] [Accepted: 03/16/2022] [Indexed: 12/16/2022] Open
Abstract
Circadian genes such as Clock, Bmal1, Cryptochrome1/2, and Period1/2/3 constitute the precise circadian system. ClockΔ19 is a commonly used mouse model harboring a circadian clock gene mutation, which lacks the EXON-19-encoded 51 amino acids. Previous reports have shown that ClockΔ19 mice have severe metabolic abnormalities. Here, we report that the mitochondria of ClockΔ19 mice exhibit excessive fission and dysfunction. We also demonstrate that CLOCK binds to the RNA-binding protein PUF60 through its EXON 19. Further, we find that PUF60 directly maintains mitochondrial homeostasis through regulating Drp1 mRNA stability, while the association with CLOCK can competitively inhibit this function. In ClockΔ19 mice, CLOCKΔ19 releases PUF60, leading to enhanced Drp1 mRNA stability and persistent mitochondrial fission. Our results reveal a direct post-transcriptional role of CLOCK in regulating mitochondrial homeostasis via Drp1 mRNA stability and that the loss of EXON 19 of CLOCK in ClockΔ19 mice leads to severe mitochondrial homeostasis disorders.
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Affiliation(s)
- Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jiaxin Lin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yutong Liu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Bingxuan Hua
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qianyun Cheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Changpo Lin
- Institute of Vascular Surgery, Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zuoqin Yan
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yaping Wang
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Ning Sun
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214122, China.
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
| | - Chao Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China.
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10
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Chowdhury SG, Ray R, Bhattacharya D, Karmakar P. DNA damage induced cellular senescence and it’s PTEN-armed exosomes—the warriors against prostate carcinoma cells. Med Oncol 2022; 39:34. [DOI: 10.1007/s12032-021-01614-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/19/2021] [Indexed: 11/27/2022]
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11
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Zhang Y, Wang J, Ruan Y, Yang Y, Cheng Y, Wang F, Zhang C, Xu Y, Liu L, Yu M, Ren B, Wang J, Zhao B, Yang R, Xiong J, Wang J, Zhang J, Jian R, Liu Y, Tian Y. Genome-wide CRISPR screen identifies Puf60 as a novel stemness gene of mouse Embryonic Stem Cells. Stem Cells Dev 2022; 31:132-142. [PMID: 35019759 DOI: 10.1089/scd.2021.0309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The mechanisms underlying self-renewal of embryonic stem cells (ESCs) hold great value in the clinical translation of stem cell biology and regenerative medicine research. To study the mechanisms in ESC self-renewal, screening and identification of key genes maintaining ESC self-renewal were performed by a genome-wide CRISPR-Cas9 knockout virus library. The mouse ESC R1 were infected with CRISPR-Cas9 knockout virus library and cultured for 14 days. The variation of sgRNA ratio was analyzed by high-throughput sequencing, followed by bioinformatics analysis to profile the altered genes. Our results showed 1375 genes with increased sgRNA ratio were found to be mainly involved in signal transduction, cell differentiation and cell apoptosis; 2929 genes with decreased sgRNA ratio were mainly involved in cell cycle regulation, RNA splicing, and biological metabolic processes. We further confirmed our screen specificity by confirming Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal. Meanwhile, further analysis showed the relevance between Puf60 expression and tumor. In conclusion, our study screened key genes maintaining ESC self-renewal and successful identified Puf60, U2af2, Wdr75 and Usp16 as novel positive regulators in mESC self-renewal, which provided theoretical basis and research clues for a better understanding of ESC self-renewal regulation.
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Affiliation(s)
- Yue Zhang
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, 30# Gaotanyan St., Shapingba District, Chongqing 400038, China, Chongqing, China, 400038;
| | - Jiaqi Wang
- Army Medical University, 12525, Institude of Immunulogy PLA & Department of Immunology, Army Medical University, Chongqing 400038, China, Chongqing, China;
| | - Yan Ruan
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yi Yang
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Yuda Cheng
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Fengsheng Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Chen Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Yixiao Xu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Lianlian Liu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Meng Yu
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Bangqi Ren
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Chongqing, China;
| | - Jiangjun Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Binyu Zhao
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Ran Yang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Chongqing, China;
| | - Jiaxiang Xiong
- Army Medical University, 12525, Experimental Center of Basic Medicine, College of Basic Medical Sciences, Chongqing, China;
| | - Jiali Wang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Junlei Zhang
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, Army Medical University, Chongqing, China;
| | - Rui Jian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
| | - Yong Liu
- Army Medical University, 12525, Southwest Hospital/Southwest Eye Hospital, Chongqing, China;
| | - Yanping Tian
- Army Medical University, 12525, Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology,, Chongqing, China;
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12
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Role of PTEN, PI3K, and mTOR in Triple-Negative Breast Cancer. Life (Basel) 2021; 11:life11111247. [PMID: 34833123 PMCID: PMC8621563 DOI: 10.3390/life11111247] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 12/21/2022] Open
Abstract
Breast cancer is the most commonly occurring malignancy and the leading cause of cancer-related death in women. Triple-negative breast cancer (TNBC) is the most aggressive subtype and is associated with high recurrence rates, high incidence of distant metastases, and poor overall survival. The aim of this study was to investigate the PI3K/PTEN/Akt/mTOR pathway as one of the most frequently deregulated pathways in cancer. We aimed to explore the impact of PI3K and mTOR oncogenes as well as the PTEN tumor suppressor on TNBC clinical behavior, prognosis, and multidrug resistance (MDR), using immunohistochemistry and copy number analysis by quantitative real-time PCR. Our results revealed that loss of PTEN and high expression of PI3K and mTOR proteins are associated with poor outcome of TNBC patients. PTEN deletions appeared as a major cause of reduced or absent PTEN expression in TNBC. Importantly, homozygous deletions of PTEN (and not hemizygous deletions) are a potential molecular marker of metastasis formation and good predictors of TNBC outcome. In conclusion, we believe that concurrent examination of PTEN/PI3K/mTOR protein expression may be more useful in predicting TNBC clinical course than the analysis of single protein expression. Specifically, our results showed that PTEN-reduced/PI3K-high/mTOR-high expression constitutes a ‘high risk’ profile of TNBC.
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13
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Zhang H, Han B, Han X, Zhu Y, Liu H, Wang Z, Cui Y, Tian R, Gao Z, Tian R, Ren S, Zuo X, Tian J, Zhang F, Niu R. Comprehensive Analysis of Splicing Factor and Alternative Splicing Event to Construct Subtype-Specific Prognosis-Predicting Models for Breast Cancer. Front Genet 2021; 12:736423. [PMID: 34630526 PMCID: PMC8497829 DOI: 10.3389/fgene.2021.736423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/08/2021] [Indexed: 11/27/2022] Open
Abstract
Recent evidence suggests that splicing factors (SFs) and alternative splicing (AS) play important roles in cancer progression. We constructed four SF-risk-models using 12 survival-related SFs. In Luminal-A, Luminal-B, Her-2, and Basal-Like BRCA, SF-risk-models for three genes (PAXBP1, NKAP, and NCBP2), four genes (RBM15B, PNN, ACIN1, and SRSF8), three genes (LSM3, SNRNP200, and SNU13), and three genes (SRPK3, PUF60, and PNN) were constructed. These models have a promising prognosis-predicting power. The co-expression and protein-protein interaction analysis suggest that the 12 SFs are highly functional-connected. Pathway analysis and gene set enrichment analysis suggests that the functional role of the selected 12 SFs is highly context-dependent among different BRCA subtypes. We further constructed four AS-risk-models with good prognosis predicting ability in four BRCA subtypes by integrating the four SF-risk-models and 21 survival-related AS-events. This study proposed that SFs and ASs were potential multidimensional biomarkers for the diagnosis, prognosis, and treatment of BRCA.
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Affiliation(s)
- He Zhang
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Baoai Han
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Xingxing Han
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Yuying Zhu
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Hui Liu
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Zhiyong Wang
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Yanfen Cui
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Ran Tian
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Zicong Gao
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Ruinan Tian
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Sixin Ren
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Xiaoyan Zuo
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Jianfei Tian
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Fei Zhang
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
| | - Ruifang Niu
- Public Laboratory, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Key Laboratory of Cancer Prevention and Therapy, Tianjin, China.,Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Key Laboratory of Breast Cancer Prevention and Therapy, Ministry of Education, Tianjin, China
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14
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Schuster A, Klein E, Neirinckx V, Knudsen AM, Fabian C, Hau AC, Dieterle M, Oudin A, Nazarov PV, Golebiewska A, Muller A, Perez-Hernandez D, Rodius S, Dittmar G, Bjerkvig R, Herold-Mende C, Klink B, Kristensen BW, Niclou SP. AN1-type zinc finger protein 3 (ZFAND3) is a transcriptional regulator that drives Glioblastoma invasion. Nat Commun 2020; 11:6366. [PMID: 33311477 PMCID: PMC7732990 DOI: 10.1038/s41467-020-20029-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 11/04/2020] [Indexed: 01/12/2023] Open
Abstract
The infiltrative nature of Glioblastoma (GBM), the most aggressive primary brain tumor, critically prevents complete surgical resection and masks tumor cells behind the blood brain barrier reducing the efficacy of systemic treatment. Here, we use a genome-wide interference screen to determine invasion-essential genes and identify the AN1/A20 zinc finger domain containing protein 3 (ZFAND3) as a crucial driver of GBM invasion. Using patient-derived cellular models, we show that loss of ZFAND3 hampers the invasive capacity of GBM, whereas ZFAND3 overexpression increases motility in cells that were initially not invasive. At the mechanistic level, we find that ZFAND3 activity requires nuclear localization and integral zinc-finger domains. Our findings indicate that ZFAND3 acts within a nuclear protein complex to activate gene transcription and regulates the promoter of invasion-related genes such as COL6A2, FN1, and NRCAM. Further investigation in ZFAND3 function in GBM and other invasive cancers is warranted. Glioblastomas (GBMs) are highly invasive brain tumours, but the underlying mechanisms of GBM invasion are unclear. Here, the authors perform an RNA interference screen and identify AN1-Type Zinc Finger protein 3 (ZFAND3) as a regulator of GBM invasion, and find that it acts through the transcriptional regulation of invasion-related genes.
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Affiliation(s)
- Anne Schuster
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Eliane Klein
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Virginie Neirinckx
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnon Møldrup Knudsen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Carina Fabian
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Ann-Christin Hau
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Monika Dieterle
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anais Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Arnaud Muller
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | - Sophie Rodius
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Rolf Bjerkvig
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg.,Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University of Heidelberg, Heidelberg, Germany
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg.,Functional Tumor Genetics, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Bjarne Winther Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg. .,Department of Biomedicine, University of Bergen, Bergen, Norway.
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15
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Guo Y, Liu J, Luo J, You X, Weng H, Wang M, Ouyang T, Li X, Liao X, Wang M, Lan Z, Shi Y, Chen S. Molecular Profiling Reveals Common and Specific Development Processes in Different Types of Gynecologic Cancers. Front Oncol 2020; 10:584793. [PMID: 33194730 PMCID: PMC7658613 DOI: 10.3389/fonc.2020.584793] [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: 07/30/2020] [Accepted: 09/21/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Gynecologic cancers have become a major threat to women's health. The molecular biology of gynecologic cancers is not as well understood as that of breast cancer, and precision targeting is still new. Although viewed collectively as a group of cancers within the female reproductive system, they are more often studied separately. A comprehensive within-group comparison on molecular profiles is lacking. METHODS We conducted a whole-exome sequencing study of cervical/endometrial/ovarian cancer samples from 209 Chinese patients. We combined our data with genomic and transcriptomic data from relevant TCGA cohorts to identify and verify common/exclusive molecular changes in cervical/endometrial/ovarian cancer. RESULTS We identified shared molecular features including a COSMIC signature of deficient mismatch repair (dMMR), four recurrent copy-number variation (CNV) events, and extensive alterations in PI3K-Akt-mTOR signaling and cilium component genes; we also identified transcription factors and pathways that are exclusively altered in cervical/endometrial/ovarian cancer. The functions of the commonly/exclusively altered genomic circuits suggest (1) a common reprogramming process during early tumor initiation, which involves PI3K activation, defects in mismatch repair and cilium organization, as well as disruption in interferon signaling and immune recognition; (2) a cell-type specific program at late-stage tumor development that eventually lead to tumor proliferation and migration. CONCLUSION This study describes, from a molecular point of view, how similar and how different gynecologic cancers are, and it provides a hypothesis about the causes of the observed similarities and differences.
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Affiliation(s)
- Yuanli Guo
- Department of Gynaecology and Obstetrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junfeng Liu
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaqi Luo
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Xiaobin You
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Hui Weng
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Minyi Wang
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Ting Ouyang
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Xiao Li
- Department of Gynaecology and Obstetrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoming Liao
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Maocai Wang
- Department of Gynaecology and Obstetrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhaoji Lan
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Yujian Shi
- Department of Research, Top Gene Tech (Guangzhou) Co., Ltd., Guangzhou, China
| | - Shan Chen
- Department of Gynaecology and Obstetrics, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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16
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Long Q, Hua Y, He L, Zhang C, Sui S, Li Y, Qiu H, Tian T, An X, Luo G, Yan Y, Zhao A, Shi D, Xie F, Chen M, Zheng F, Deng W. Poly(U) binding splicing factor 60 promotes renal cell carcinoma growth by transcriptionally upregulating telomerase reverse transcriptase. Int J Biol Sci 2020; 16:3002-3017. [PMID: 33061812 PMCID: PMC7545719 DOI: 10.7150/ijbs.45115] [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: 02/22/2020] [Accepted: 09/10/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Abnormal transcriptional upregulation of telomerase reverse transcriptase (TERT) plays a dominant role in telomerase activation in various cancers. TERT promoter mutations (TPMs) have been identified as a key mechanism in TERT upregulation. However, the mechanism of TERT upregulation in cancers with low frequency of TPMs are not fully elucidated so far. Methods: The expression of PUF60 and TERT was detected by real-time PCR, western blot and immunohistochemistry. TERT promoter binding proteins were identified by streptavidin-agarose pulldown assay and mass spectrum (MS) analysis. The role of PUF60/TERT in renal cancer was evaluated on cell growth in vitro and in vivo. Results: In this study, we identify the regulation mechanism of TERT in renal cell carcinoma (RCC) cells which have rare TPMs but exert significant upregulation of TERT. We found that TERT was highly expressed in RCC tumor tissues, and elevated TERT expression was associated with poor prognosis for patients. We also detected the relatively rare TPM status in both RCC tumor tissues and RCC cell lines. Mechanistically, PUF60, a RNA binding protein, was identified as a novel TERT regulator which bound to the TERT and transcriptionally upregulated TERT expression in RCC cells. The in vitro and in vivo experiments also demonstrated that PUF60 could promote RCC cell growth through activation of TERT expression in a TPM status independent way. Furthermore, we showed that there was a strong correlation of the expression of PUF60 and TERT in RCC tumor tissues and RCC cell lines, and the patients with high expression of PUF60 and TERT had significantly shorter survival. Conclusions: Collectively, these results indicated that PUF60 transcriptionally upregulated TERT expression to promote RCC growth and progression in a TPM status independent way, suggesting that the PUF60/TERT signaling pathway may serve as potential prognostic biomarkers and therapeutic targets for RCC.
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Affiliation(s)
- Qian Long
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yijun Hua
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Liru He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Changlin Zhang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Silei Sui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yixin Li
- Department of Clinical Oncology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Huijuan Qiu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Tian Tian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Xin An
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Guangyu Luo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Yue Yan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Anshi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Dingbo Shi
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fangyun Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Fufu Zheng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
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17
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Long Q, An X, Chen M, Wang N, Sui S, Li Y, Zhang C, Lee K, Wang X, Tian T, Pan Y, Qiu H, Xie F, Deng W, Zheng F, He L. PUF60/AURKA Axis Contributes to Tumor Progression and Malignant Phenotypes in Bladder Cancer. Front Oncol 2020; 10:568015. [PMID: 33117697 PMCID: PMC7576680 DOI: 10.3389/fonc.2020.568015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 09/04/2020] [Indexed: 12/17/2022] Open
Abstract
Abnormal expression or mutation of RNA splicing proteins are widely observed in human cancers. Here, we identified poly(U) binding splicing factor 60 (PUF60) as one of the most differentially expressed genes out of 97 RNA splicing proteins between normal and bladder cancer tissues by bioinformatics analysis of TCGA bladder cancer expression data. The expression of PUF60 was significantly higher in tumor tissues, while high PUF60 expression was associated with malignant phenotypes of bladder cancer and shorter survival time. Moreover, we identified aurora kinase A (AURKA) as a new downstream target of PUF60 in bladder cancer cells. PUF60 knockdown significantly inhibited cell viability and colony formation capacity in bladder cancer cells, whereas AURKA overexpression reversed this inhibition effect. Overexpression of PUF60 significantly promoted cell viability and colony formation in bladder cancer cells, while treatment with AURKA specific inhibitor reversed this promotive effect. Mechanistically, PUF60 specifically bound to the AURKA promoter, thereby activating its transcription and expression. Furthermore, we showed that there was a significant positive correlation between PUF60 and AURKA expression in bladder cancer tissues, and PUF60 and AURKA expression contributed to tumor progression and malignant phenotypes in the patients with bladder cancer. Collectively, these results indicate that the PUF60/AURKA axis plays a key role in regulating tumorigenesis and progression of bladder cancer, and may be a potential prognostic biomarker and therapeutic target for bladder cancer patients.
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Affiliation(s)
- Qian Long
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xin An
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Miao Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Nan Wang
- College of Life Science, Jiaying University, Meizhou, China
| | - Silei Sui
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yixin Li
- The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Changlin Zhang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Kaping Lee
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiaonan Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Tian Tian
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yangxun Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Huijuan Qiu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,College of Life Science, Jiaying University, Meizhou, China.,Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.,The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China.,The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China.,The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Fangyun Xie
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wuguo Deng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Fufu Zheng
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Liru He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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18
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An J, Luo Z, An W, Cao D, Ma J, Liu Z. Identification of spliceosome components pivotal to breast cancer survival. RNA Biol 2020; 18:833-842. [PMID: 32965163 DOI: 10.1080/15476286.2020.1822636] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Cancer cells employ alternative splicing (AS) to acquire splicing isoforms favouring their survival. However, the causes of aberrant AS in breast cancer are poorly understood. In this study, the METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) data were analysed with univariate feature selection. Of 122 analysed spliceosome components, U2SURP, PUF60, DDX41, HNRNPAB, EIF4A3, and PPIL3 were significantly associated with breast cancer survival. The top 4 four genes, U2SURP, PUF60, DDX41, and HNRNPAB, were chosen for further analyses. Their expression was significantly associated with cancer molecular subtype, tumour stage, tumour grade, overall survival (OS), and cancer-specific survival in the METABRIC data. These results were verifiable using other cohorts. The Cancer Genome Atlas data unveiled the elevated expression of PUF60, DDX41, and HNRNPAB in tumours compared with the normal tissue and confirmed the differential expression of the four genes among cancer molecular subtypes, as well as the associations of U2SURP, PUF60, and DDX41 expression with tumour stage. A meta-analysis data verified the associations of U2SURP, PUF60, and HNRNPAB expression with tumour grade, the associations of PUF60, DDX41, and HNRNPAB expression with OS and distant metastasis-free survival, and the associations of U2SURP and HNRNPAB expression with relapse-free survival. Experimentally, we demonstrated that inhibiting the expression of the four genes separately suppressed cell colony formation and slowed down cell growth considerably in breast cancer cells, but not in immortal breast epithelial cells. In conclusion, we have identified U2SURP, PUF60, DDX41, and HNRNPAB are spliceosome-related genes pivotal for breast cancer survival.
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Affiliation(s)
- Jing An
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China.,Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, China
| | - Zhehui Luo
- Department of Epidemiology and Biostatistics, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Weiwei An
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China.,Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, China
| | - Difei Cao
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China.,Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, China.,Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, China
| | - Jianli Ma
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Zhaoliang Liu
- Institute of Cancer Prevention and Treatment, Harbin Medical University, Harbin, China.,Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, China
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19
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Five-mRNA Signature for the Prognosis of Breast Cancer Based on the ceRNA Network. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9081852. [PMID: 32964046 PMCID: PMC7486635 DOI: 10.1155/2020/9081852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 12/29/2022]
Abstract
Background The purpose of this study was to investigate the regulatory mechanisms of ceRNAs in breast cancer (BC) and construct a new five-mRNA prognostic signature. Methods The ceRNA network was constructed by different RNAs screened by the edgeR package. The BC prognostic signature was built based on the Cox regression analysis. The log-rank method was used to analyse the survival rate of BC patients with different risk scores. The expression of the 5 genes was verified by the GSE81540 dataset and CPTAC database. Results A total of 41 BC-adjacent tissues and 473 BC tissues were included in this study. A total of 2,966 differentially expressed lncRNAs, 5,370 differentially expressed mRNAs, and 359 differentially expressed miRNAs were screened. The ceRNA network was constructed using 13 lncRNAs, 267 mRNAs, and 35 miRNAs. Kaplan-Meier (K-M) methods showed that two lncRNAs (AC037487.1 and MIR22HG) are related to prognosis. Five mRNAs (VPS28, COL17A1, HSF1, PUF60, and SMOC1) in the ceRNA network were used to establish a prognostic signature. Survival analysis showed that the prognosis of patients in the low-risk group was significantly better than that in the high-risk group (p = 0.0022). ROC analysis showed that this signature has a good diagnostic ability (AUC = 0.77). Compared with clinical features, this signature was also an independent prognostic factor (HR: 1.206, 95% CI 1.108−1.311; p < 0.001). External verification results showed that the expression of the 5 mRNAs differed between the normal and tumour groups at the chip and protein levels (p < 0.001). Conclusions These ceRNAs may play a key role in the development of BC, and the new 5-mRNA prognostic signature can improve the prediction of survival for BC patients.
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20
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Gu X, Wan G, Yang Y, Liu Y, Yang X, Zheng Y, Jiang L, Zhang P, Liu D, Zhao W, Huang G, Lu C. SLFN5 influences proliferation and apoptosis by upregulating PTEN transcription via ZEB1 and inhibits the purine metabolic pathway in breast cancer. Am J Cancer Res 2020; 10:2832-2850. [PMID: 33042620 PMCID: PMC7539779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/14/2020] [Indexed: 06/11/2023] Open
Abstract
Human Schlafen-5 (SLFN5) is aberrantly involved in tumorigenesis in several types of cancer. However, its implications in breast cancer (BRCA) are unknown. Herein, we demonstrated that SLFN5 expression is negatively associated with the tumour growth of human BRCA using GEO database analysis and clinical sample immunostaining. Lentiviral overexpression of SLFN5 in BRCA cell lines suppressed tumourigenicity in nude mice. Knockdown and overexpression of SLFN5 in BRCA cell lines proved that SLFN5 can inhibit cell proliferation and colony formation and promote apoptosis by upregulating the transcription of a known cancer suppressor gene (the phosphatase and tensin homologue on chromosome 10, PTEN), resulting in molecular changes in the downstream AKT pathway and in proliferation/apoptosis. Lentiviral knockdown and overexpression of ZEB1 blocked the changes in the PTEN and AKT pathways and in the colony formation ability caused by SLFN5 knockdown and overexpression, respectively. Luciferase reporter assays demonstrated that ZEB1 can inhibit the PTEN promoter activity in MCF7 cells by binding to a motif in the PTEN promoter. Metabonomics analysis showed that SLFN5 influences many metabolic pathways and especially decreases purine metabolites, including inosine, xanthine, and hypoxanthine. In conclusion, our findings suggest that SLFN5 may be an important protective factor against BRCA, as it regulates PTEN transcription, the AKT pathway, and proliferation/apoptosis via ZEB1 mediation and inhibits the purine metabolic pathway. Thus, SLFN5 may be a potential therapeutic target for BRCA.
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Affiliation(s)
- Xuefeng Gu
- Shanghai University of Medicine & Health Science Affiliated Zhoupu HospitalShanghai, P. R. China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
- School of Pharmacy, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Guoqing Wan
- Shanghai University of Medicine & Health Science Affiliated Zhoupu HospitalShanghai, P. R. China
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
- School of Pharmacy, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Yue Yang
- Department of Pathology, Mudanjiang Medical UniversityMudanjiang, P. R. China
| | - Yihao Liu
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, CAMS&PUMCBeijing, P. R. China
- Beijing Engineering Research Center for Experimental Animal Models of Human Critical DiseasesBeijing, P. R. China
| | - Xintong Yang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Yanjun Zheng
- Shanghai University of Medicine & Health Science Affiliated Zhoupu HospitalShanghai, P. R. China
| | - Liying Jiang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Peng Zhang
- School of Clinical Medicine, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Dingsheng Liu
- Shanghai University of Medicine & Health Science Affiliated Zhoupu HospitalShanghai, P. R. China
| | | | - Gang Huang
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
| | - Changlian Lu
- Shanghai Key Laboratory of Molecular Imaging, Shanghai University of Medicine & Health SciencesShanghai, P. R. China
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21
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Kew C, Huang W, Fischer J, Ganesan R, Robinson N, Antebi A. Evolutionarily conserved regulation of immunity by the splicing factor RNP-6/PUF60. eLife 2020; 9:57591. [PMID: 32538777 PMCID: PMC7332298 DOI: 10.7554/elife.57591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/14/2020] [Indexed: 12/25/2022] Open
Abstract
Splicing is a vital cellular process that modulates important aspects of animal physiology, yet roles in regulating innate immunity are relatively unexplored. From genetic screens in C. elegans, we identified splicing factor RNP-6/PUF60 whose activity suppresses immunity, but promotes longevity, suggesting a tradeoff between these processes. Bacterial pathogen exposure affects gene expression and splicing in a rnp-6 dependent manner, and rnp-6 gain and loss-of-function activities reveal an active role in immune regulation. Another longevity promoting splicing factor, SFA-1, similarly exerts an immuno-suppressive effect, working downstream or parallel to RNP-6. RNP-6 acts through TIR-1/PMK-1/MAPK signaling to modulate immunity. The mammalian homolog, PUF60, also displays anti-inflammatory properties, and its levels swiftly decrease after bacterial infection in mammalian cells, implying a role in the host response. Altogether our findings demonstrate an evolutionarily conserved modulation of immunity by specific components of the splicing machinery.
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Affiliation(s)
- Chun Kew
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Wenming Huang
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Julia Fischer
- Department I of Internal Medicine, University of Cologne, Cologne, Germany.,Division of Infectious Diseases, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Raja Ganesan
- Cellular-Stress and Immune Response Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Nirmal Robinson
- Cellular-Stress and Immune Response Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide, Australia
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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22
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Guo D, Wang H, Sun L, Liu S, Du S, Qiao W, Wang W, Hou G, Zhang K, Li C, Teng Q. Identification of key gene modules and hub genes of human mantle cell lymphoma by coexpression network analysis. PeerJ 2020; 8:e8843. [PMID: 32219041 PMCID: PMC7087492 DOI: 10.7717/peerj.8843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Purpose Mantle cell lymphoma (MCL) is a rare and aggressive subtype of non-Hodgkin lymphoma that is incurable with standard therapies. The use of gene expression analysis has been of interest, recently, to detect biomarkers for cancer. There is a great need for systemic coexpression network analysis of MCL and this study aims to establish a gene coexpression network to forecast key genes related to the pathogenesis and prognosis of MCL. Methods The microarray dataset GSE93291 was downloaded from the Gene Expression Omnibus database. We systematically identified coexpression modules using the weighted gene coexpression network analysis method (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were performed on the modules deemed important. The protein-protein interaction networks were constructed and visualized using Cytoscape software on the basis of the STRING website; the hub genes in the top weighted network were identified. Survival data were analyzed using the Kaplan-Meier method and were compared using the log-rank test. Results Seven coexpression modules consisting of different genes were applied to 5,000 genes in the 121 human MCL samples using WGCNA software. GO and KEGG enrichment analysis identified the blue module as one of the most important modules; the most critical pathways identified were the ribosome, oxidative phosphorylation and proteasome pathways. The hub genes in the top weighted network were regarded as real hub genes (IL2RB, CD3D, RPL26L1, POLR2K, KIF11, CDC20, CCNB1, CCNA2, PUF60, SNRNP70, AKT1 and PRPF40A). Survival analysis revealed that seven genes (KIF11, CDC20, CCNB1, CCNA2, PRPF40A, CD3D and PUF60) were associated with overall survival time (p < 0.05). Conclusions The blue module may play a vital role in the pathogenesis of MCL. Five real hub genes (KIF11, CDC20, CCNB1, CCNA2 and PUF60) were identified as potential prognostic biomarkers as well as therapeutic targets with clinical utility for MCL.
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Affiliation(s)
- Dongmei Guo
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Hongchun Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Li Sun
- Department of Occupational Disease, Taian City Central Hospital Branch, Taian, Shandong, China
| | - Shuang Liu
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Shujing Du
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Wenjing Qiao
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Weiyan Wang
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
| | - Gang Hou
- Department of Pathology, Taian City Central Hospital, Taian, Shandong, China
| | - Kaigang Zhang
- Department of Orthopedics, Taian City Central Hospital, Taian, Shandong, China
| | - Chunpu Li
- Department of Orthopedics, Taian City Central Hospital, Taian, Shandong, China.,Department of Orthopedics, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Qingliang Teng
- Department of Hematology, Taian City Central Hospital, Taian, Shandong, China
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