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Trebucq LL, Salvatore N, Wagner PM, Golombek DA, Chiesa JJ. Circadian Clock Gene bmal1 Acts as a Tumor Suppressor Gene in a Mice Model of Human Glioblastoma. Mol Neurobiol 2024; 61:5216-5229. [PMID: 38180613 DOI: 10.1007/s12035-023-03895-7] [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: 07/28/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024]
Abstract
Glioblastomas derived from malignant astrocytes are the most common primary tumors of the central nervous system in humans, exhibiting very bad prognosis. Treatment with surgery, radiotherapy, and chemotherapy (mainly using temozolomide), generates as much one-year survival. The circadian clock controls different aspects of tumor development, and its role in GBM is beginning to be explored. Here, the role of the canonic circadian clock gene bmal1 was studied in vivo in a nude mice model bearing human GBMs from LN229 cells xenografted orthotopically in the dorsal striatum. For that aim, a bmal1 knock-down was generated in LN229 cells by CRISPR/Cas9 gene editing tool, and tumor progression was followed in male mice by measuring survival, tumor growth, cell proliferation and prognosis with CD44 marker, as well as astrocyte activation in the tumor microenvironment with GFAP and nestin markers. Disruption of bmal1 in the tumor decreased survival, increased tumor growth and CD44 expression, worsened motor performance, as well as increased GFAP expression in astrocytes at tumor microenvironment. In addition, survival and tumor progression was not affected in mice bearing LN229 wild type GBM that underwent circadian disruption by constant light, as compared to mice synchronized to 12:12 light-dark cycles. These results consistently demonstrate in an in vivo orthotopic model of human GBM, that bmal1 has a key role as a tumor suppressor gene regulating GBM progression.
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Affiliation(s)
- Laura L Trebucq
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/CONICET, Roque S. Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Nicolas Salvatore
- Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/CONICET, Roque S. Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Paula M Wagner
- CIQUIBIC-CONICET y Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina
| | - Diego A Golombek
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés, B1644BID, Victoria, Buenos Aires, Argentina
| | - Juan J Chiesa
- Laboratorio de Cronobiología, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/CONICET, Roque S. Peña 352, B1876BXD, Bernal, Buenos Aires, Argentina.
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2
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Liu JL, Xu X, Rixiati Y, Wang CY, Ni HL, Chen WS, Gong HM, Zhang ZL, Li S, Shen T, Li JM. Dysfunctional circadian clock accelerates cancer metastasis by intestinal microbiota triggering accumulation of myeloid-derived suppressor cells. Cell Metab 2024; 36:1320-1334.e9. [PMID: 38838643 DOI: 10.1016/j.cmet.2024.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 02/12/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024]
Abstract
Circadian homeostasis in mammals is a key intrinsic mechanism for responding to the external environment. However, the interplay between circadian rhythms and the tumor microenvironment (TME) and its influence on metastasis are still unclear. Here, in patients with colorectal cancer (CRC), disturbances of circadian rhythm and the accumulation of monocytes and granulocytes were closely related to metastasis. Moreover, dysregulation of circadian rhythm promoted lung metastasis of CRC by inducing the accumulation of myeloid-derived suppressor cells (MDSCs) and dysfunctional CD8+ T cells in the lungs of mice. Also, gut microbiota and its derived metabolite taurocholic acid (TCA) contributed to lung metastasis of CRC by triggering the accumulation of MDSCs in mice. Mechanistically, TCA promoted glycolysis of MDSCs epigenetically by enhancing mono-methylation of H3K4 of target genes and inhibited CHIP-mediated ubiquitination of PDL1. Our study links the biological clock with MDSCs in the TME through gut microbiota/metabolites in controlling the metastatic spread of CRC, uncovering a systemic mechanism for cancer metastasis.
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Affiliation(s)
- Jing-Lin Liu
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xu Xu
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China
| | - Youlutuziayi Rixiati
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China
| | - Chu-Yi Wang
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China
| | - Heng-Li Ni
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Wen-Shu Chen
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China
| | - Hui-Min Gong
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China
| | - Zi-Long Zhang
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Shi Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Tong Shen
- Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China.
| | - Jian-Ming Li
- Department of Pathology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Department of Pathology, Soochow Medical College, Soochow University, Suzhou 215123, China; The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Department of Pathology and Institute of Molecular Pathology, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China.
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3
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Melocchi V, Cuttano R, Murgo E, Mazzoccoli G, Bianchi F. The circadian clock circuitry deconvolutes colorectal cancer and lung adenocarcinoma heterogeneity in a dynamic time-related framework. Cancer Gene Ther 2023; 30:1323-1329. [PMID: 37479798 DOI: 10.1038/s41417-023-00646-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/19/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
Increasing evidence imputes cancer progression and resistance to therapy to intra-tumor molecular heterogeneity set off by cancer cell plasticity. Re-activation of developmental programs strictly linked to epithelial-to-mesenchymal transition and gaining of stem cells properties are crucial in this setting. Many biological processes involved in cancer onset and progression show rhythmic fluctuations driven by the circadian clock circuitry. Novel cancer patient stratification tools taking into account the temporal dimension of these biological processes are definitely needed. Lung cancer and colorectal cancer (CRC) are the leading causes of cancer death worldwide. Here, by developing an innovative computational approach we named Phase-Finder, we show that the molecular heterogeneity characterizing the two deadliest cancers, CRC and lung adenocarcinoma (LUAD), rather than a merely stochastic event is the readout of specific cancer molecular states which correlate with time-qualified patterns of gene expression. We performed time-course transcriptome analysis of CRC and LUAD cell lines and upon computing circadian genes expression-based correlation matrices we derived pseudo-time points to infer time-qualified patterns in the transcriptomic analysis of real-world data (RWD) from large cohorts of CRC and LUAD patients. Our temporal classification of CRC and LUAD cohorts was able to effectively render time-specific patterns in cancer phenotype switching determining dynamical distribution of molecular subtypes impacting patient prognosis.
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Affiliation(s)
- Valentina Melocchi
- Unit of Cancer Biomarkers, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, FG, Italy
| | - Roberto Cuttano
- Unit of Cancer Biomarkers, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, FG, Italy
| | - Emanuele Murgo
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, FG, Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, FG, Italy.
| | - Fabrizio Bianchi
- Unit of Cancer Biomarkers, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, FG, Italy.
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4
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Petkovic M, Yalçin M, Heese O, Relógio A. Differential expression of the circadian clock network correlates with tumour progression in gliomas. BMC Med Genomics 2023; 16:154. [PMID: 37400829 DOI: 10.1186/s12920-023-01585-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 06/19/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Gliomas are tumours arising mostly from astrocytic or oligodendrocytic precursor cells. These tumours are classified according to the updated WHO classification from 2021 in 4 grades depending on molecular and histopathological criteria. Despite novel multimodal therapeutic approaches, the vast majority of gliomas (WHO grade III and IV) are not curable. The circadian clock is an important regulator of numerous cellular processes and its dysregulation had been found during the progression of many cancers, including gliomas. RESULTS In this study, we explore expression patterns of clock-controlled genes in low-grade glioma (LGG) and glioblastoma multiforme (GBM) and show that a set of 45 clock-controlled genes can be used to distinguish GBM from normal tissue. Subsequent analysis identified 17 clock-controlled genes with a significant association with survival. The results point to a loss of correlation strength within elements of the circadian clock network in GBM compared to LGG. We further explored the progression patterns of mutations in LGG and GBM, and showed that tumour suppressor APC is lost late both in LGG and GBM. Moreover, HIF1A, involved in cellular response to hypoxia, exhibits subclonal losses in LGG, and TERT, involved in the formation of telomerase, is lost late in the GBM progression. By examining multi-sample LGG data, we find that the clock-controlled driver genes APC, HIF1A, TERT and TP53 experience frequent subclonal gains and losses. CONCLUSIONS Our results show a higher level of disrgulation at the gene expression level in GBM compared to LGG, and indicate an association between the differentially expressed clock-regulated genes and patient survival in both LGG and GBM. By reconstructing the patterns of progression in LGG and GBM, our data reveals the relatively late gains and losses of clock-regulated glioma drivers. Our analysis emphasizes the role of clock-regulated genes in glioma development and progression. Yet, further research is needed to asses their value in the development of new treatments.
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Affiliation(s)
- Marina Petkovic
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
| | - Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, 20457, Hamburg, Germany
| | - Oliver Heese
- Department of Neurosurgery and Spinal Surgery, HELIOS Medical Center Schwerin, University Campus of MSH Medical School Hamburg, 20457, Hamburg, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany.
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117, Berlin, Germany.
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, 20457, Hamburg, Germany.
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5
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Hesse J, Müller T, Relógio A. An integrative mathematical model for timing treatment toxicity and Zeitgeber impact in colorectal cancer cells. NPJ Syst Biol Appl 2023; 9:27. [PMID: 37353516 DOI: 10.1038/s41540-023-00287-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 06/05/2023] [Indexed: 06/25/2023] Open
Abstract
Increasing evidence points to a role of the circadian clock in the regulation of cancer hallmarks with a strong impact on the understanding and treatment of this disease. Anti-cancer treatment can be personalized considering treatment timing. Here we present a new mathematical model based on data from three colorectal cancer cell lines and core-clock knock-outs, which couples the circadian and drug metabolism network, and that allows to determine toxicity profiles for a given drug and cell type. Moreover, this model integrates external Zeitgebers and thus may be used to fine-tune toxicity by using external factors, such as light, and therefore, to a certain extent, help fitting the endogenous rhythms of the patients to a defined clinic routine facilitating the implementation of time-dependent treatment in clinical practice.
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Affiliation(s)
- Janina Hesse
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Tim Müller
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany
| | - Angela Relógio
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.
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6
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Liu W, Ma R, Sun C, Xu Y, Liu Y, Hu J, Ma Y, Wang D, Wen D, Yu Y. Implications from proteomic studies investigating circadian rhythm disorder-regulated neurodegenerative disease pathology. Sleep Med Rev 2023; 70:101789. [PMID: 37253318 DOI: 10.1016/j.smrv.2023.101789] [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: 10/26/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 06/01/2023]
Abstract
Neurodegenerative diseases (NDs) affect 15% of the world's population and are becoming an increasingly common cause of morbidity and mortality worldwide. Circadian rhythm disorders (CRDs) have been reported to be involved in the pathogenic regulation of various neurologic diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis and amyotrophic lateral sclerosis. Proteomic technology is helpful to explore treatment targets for CRDs in patients with NDs. Here, we review the key differentially expressed (DE) proteins identified in previous proteomic studies investigating NDs, CRDs and associated models and the related pathways identified by enrichment analysis. Furthermore, we summarize the advantages and disadvantages of the above studies and propose new proteomic technologies for the precise study of circadian disorder-mediated regulation of ND pathology. This review provides a theoretical and technical reference for the precise study of circadian disorder-mediated regulation of ND pathology.
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Affiliation(s)
- Weiwei Liu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Ruze Ma
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Gerontology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China
| | - Chen Sun
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, Liaoning, China
| | - Yingxi Xu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Yang Liu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Jiajin Hu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China
| | - Yanan Ma
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China; Department of Epidemiology and Health Statistics, School of Public Health, China Medical University, Shenyang, 110122, Liaoning, China
| | - Difei Wang
- Department of Gerontology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, 110004, China
| | - Deliang Wen
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China.
| | - Yang Yu
- Health Sciences Institute, Key Laboratory of Obesity and Glucose/Lipid Associated Metabolic Diseases, China Medical University, Shenyang 110122, Liaoning, China.
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7
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Martini T, Naef F, Tchorz JS. Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology. ANNUAL REVIEW OF PATHOLOGY 2023; 18:439-466. [PMID: 36693201 DOI: 10.1146/annurev-pathmechdis-031521-024831] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex complementary or opposing multistep processes, similar to distributed tasks at an assembly line. This so-called metabolic zonation has both spatial and temporal components. Spatial distribution of metabolic function in hepatocytes of different lobular zones is necessary to perform complex sequential multistep metabolic processes and to assign metabolic tasks to the right environment. Moreover, temporal control of metabolic processes is critical to align required metabolic processes to the feeding and fasting cycles. Disruption of this complex spatiotemporal hepatic organization impairs key metabolic processes with both local and systemic consequences. Many metabolic diseases, such as nonalcoholic steatohepatitis and diabetes, are associated with impaired metabolic liver zonation. Recent technological advances shed new light on the spatiotemporal gene expression networks controlling liver function and how their deregulation may be involved in a large variety of diseases. We summarize the current knowledge about spatiotemporal metabolic liver zonation and consequences on liver pathobiology.
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Affiliation(s)
- Tomaz Martini
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland;
| | - Jan S Tchorz
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Basel, Switzerland;
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8
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Chronobiology and Nanotechnology for Personalized Cancer Therapy. Cancer Nanotechnol 2023. [DOI: 10.1007/978-3-031-17831-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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9
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Fuhr L, Basti A, Brás TS, Duarte MF, Relógio A. Antiproliferative Effects of Cynara Cardunculus in Colorectal Cancer Cells Are Modulated by the Circadian Clock. Int J Mol Sci 2022; 23:ijms23169130. [PMID: 36012399 PMCID: PMC9409071 DOI: 10.3390/ijms23169130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
The circadian clock generates 24 h rhythms in behavioural, cellular and molecular processes. Malfunctions of the clock are associated with enhanced susceptibility to cancer, worse treatment response and poor prognosis. Clock-controlled genes are involved in cellular processes associated with tumour development and progression including metabolism of drugs and the cell cycle. Cynara cardunculus, a plant of the Asteraceae family, has been reported to have antiproliferative effects on breast cancer cells. Here, we used the human colorectal cancer (CRC) cell line HCT116 and its knockout variants for different core-clock genes (BMAL1, PER2, NR1D1), to investigate the treatment effect of C. cardunculus lipophilic leaf extract under different clock scenarios. Our results show a direct effect of C. cardunculus on the circadian phenotype of the cells, as indicated by alterations in the phase, amplitude, and period length of core-clock gene oscillations. Furthermore, our data indicate a role for the circadian clock in sensitivity to C. cardunculus treatment. In particular, the treatment inhibited proliferation and induced cytotoxicity and apoptosis in a clock knockout-specific manner, in CRC cells. These results point to a potential effect of C. cardunculus lipophilic leaf extracts as a modulator of the circadian clock, in addition to its anti-proliferative properties.
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Affiliation(s)
- Luise Fuhr
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Institute for Theoretical Biology, 10115 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research Center, 13353 Berlin, Germany
| | - Alireza Basti
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Institute for Theoretical Biology, 10115 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research Center, 13353 Berlin, Germany
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg—University of Applied Sciences and Medical University, 20457 Hamburg, Germany
| | - Teresa Silva Brás
- Alentejo Biotechnology Center for Agriculture and Agro-Food (CEBAL) and Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, CEBAL, 7801-908 Beja, Portugal
| | - Maria F. Duarte
- Alentejo Biotechnology Center for Agriculture and Agro-Food (CEBAL) and Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development & CHANGE—Global Change and Sustainability Institute, CEBAL, 7801-908 Beja, Portugal
| | - Angela Relógio
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Institute for Theoretical Biology, 10115 Berlin, Germany
- Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt—Universität zu Berlin, Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research Center, 13353 Berlin, Germany
- Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg—University of Applied Sciences and Medical University, 20457 Hamburg, Germany
- Correspondence:
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10
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Comprehensive analysis of the circadian nuclear and cytoplasmic transcriptome in mouse liver. PLoS Genet 2022; 18:e1009903. [PMID: 35921362 PMCID: PMC9377612 DOI: 10.1371/journal.pgen.1009903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 08/15/2022] [Accepted: 07/06/2022] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, RNA is synthesised in the nucleus, spliced, and exported to the cytoplasm where it is translated and finally degraded. Any of these steps could be subject to temporal regulation during the circadian cycle, resulting in daily fluctuations of RNA accumulation and affecting the distribution of transcripts in different subcellular compartments. Our study analysed the nuclear and cytoplasmic, poly(A) and total transcriptomes of mouse livers collected over the course of a day. These data provide a genome-wide temporal inventory of enrichment in subcellular RNA, and revealed specific signatures of splicing, nuclear export and cytoplasmic mRNA stability related to transcript and gene lengths. Combined with a mathematical model describing rhythmic RNA profiles, we could test the rhythmicity of export rates and cytoplasmic degradation rates of approximately 1400 genes. With nuclear export times usually much shorter than cytoplasmic half-lives, we found that nuclear export contributes to the modulation and generation of rhythmic profiles of 10% of the cycling nuclear mRNAs. This study contributes to a better understanding of the dynamic regulation of the transcriptome during the day-night cycle.
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11
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Core-Clock Genes Regulate Proliferation and Invasion via a Reciprocal Interplay with MACC1 in Colorectal Cancer Cells. Cancers (Basel) 2022; 14:cancers14143458. [PMID: 35884519 PMCID: PMC9319284 DOI: 10.3390/cancers14143458] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/26/2022] [Accepted: 07/12/2022] [Indexed: 12/20/2022] Open
Abstract
The circadian clock coordinates the timing of several cellular processes including transcription, the cell cycle, and metabolism. Disruptions in the clock machinery trigger the abnormal regulation of cancer hallmarks, impair cellular homeostasis, and stimulate tumourigenesis. Here we investigated the role of a disrupted clock by knocking out or knocking down the core-clock (CC) genes ARNTL, PER2 or NR1D1 in cancer progression (e.g., cell proliferation and invasion) using colorectal cancer (CRC) cell lines HCT116, SW480 and SW620, from different progression stages with distinct clock phenotypes, and identified mechanistic links from the clock to altered cancer-promoting cellular properties. We identified MACC1 (metastasis-associated in colon cancer 1), a known driver for metastasis and an EMT (epithelial-to-mesenchymal transition)-related gene, to be significantly differentially expressed in CC manipulated cells and analysed the effect of MACC1 manipulation (knockout or overexpression) in terms of circadian clock phenotype as well as cancer progression. Our data points to a bi-directional MACC1-circadian clock interplay in CRC, via CC genes. In particular, knocking out MACC1 reduced the period of oscillations, while its overexpression increased it. Interestingly, we found the MACC1 protein to be circadian expressed in HCT116 WT cells, which was disrupted after the knockout of CC genes, and identified a MACC1-NR1D1 protein-protein interaction. In addition, MACC1 manipulation and CC knockout altered cell invasion properties of HCT116 cells, pointing to a regulation of clock and cancer progression in CRC, possibly via the interaction of MACC1 with core-clock genes.
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12
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Yalçin M, Mundorf A, Thiel F, Amatriain-Fernández S, Kalthoff IS, Beucke JC, Budde H, Garthus-Niegel S, Peterburs J, Relógio A. It's About Time: The Circadian Network as Time-Keeper for Cognitive Functioning, Locomotor Activity and Mental Health. Front Physiol 2022; 13:873237. [PMID: 35547585 PMCID: PMC9081535 DOI: 10.3389/fphys.2022.873237] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 03/08/2022] [Indexed: 12/24/2022] Open
Abstract
A variety of organisms including mammals have evolved a 24h, self-sustained timekeeping machinery known as the circadian clock (biological clock), which enables to anticipate, respond, and adapt to environmental influences such as the daily light and dark cycles. Proper functioning of the clock plays a pivotal role in the temporal regulation of a wide range of cellular, physiological, and behavioural processes. The disruption of circadian rhythms was found to be associated with the onset and progression of several pathologies including sleep and mental disorders, cancer, and neurodegeneration. Thus, the role of the circadian clock in health and disease, and its clinical applications, have gained increasing attention, but the exact mechanisms underlying temporal regulation require further work and the integration of evidence from different research fields. In this review, we address the current knowledge regarding the functioning of molecular circuits as generators of circadian rhythms and the essential role of circadian synchrony in a healthy organism. In particular, we discuss the role of circadian regulation in the context of behaviour and cognitive functioning, delineating how the loss of this tight interplay is linked to pathological development with a focus on mental disorders and neurodegeneration. We further describe emerging new aspects on the link between the circadian clock and physical exercise-induced cognitive functioning, and its current usage as circadian activator with a positive impact in delaying the progression of certain pathologies including neurodegeneration and brain-related disorders. Finally, we discuss recent epidemiological evidence pointing to an important role of the circadian clock in mental health.
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Affiliation(s)
- Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Annakarina Mundorf
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | - Freya Thiel
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany.,Institute and Policlinic of Occupational and Social Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Sandra Amatriain-Fernández
- Institute for Systems Medicine and Faculty of Human Sciences, MSH Medical School Hamburg, Hamburg, Germany
| | - Ida Schulze Kalthoff
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | - Jan-Carl Beucke
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany.,Department of Psychology, Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Henning Budde
- Institute for Systems Medicine and Faculty of Human Sciences, MSH Medical School Hamburg, Hamburg, Germany
| | - Susan Garthus-Niegel
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany.,Institute and Policlinic of Occupational and Social Medicine, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Jutta Peterburs
- Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Institute for Systems Medicine and Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, Germany
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13
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Malhan D, Basti A, Relógio A. Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes. NPJ Syst Biol Appl 2022; 8:17. [PMID: 35552415 PMCID: PMC9098426 DOI: 10.1038/s41540-022-00225-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/04/2022] [Indexed: 12/13/2022] Open
Abstract
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin’s lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTLKO), SNW1 (in NR1D1KO), and HNRNPC (in PER2KO), which led to a differential pattern of KO-specific AS events. All HCT116KO cells showed a rhythmicity loss of a crucial spliceosome gene U2AF1, which was also not rhythmic in higher progression stage CRC and HL cancer cells. AS analysis revealed an increase in alternative first exon events specific to PER2 and NR1D1 KO in HCT116 cells, and a KO-specific change in expression and rhythmicity pattern of AS transcripts related to cancer hallmarks genes including FGFR2 in HCT116_ARNTLKO, CD44 in HCT116_NR1D1KO, and MET in HCT116_PER2KO. KO-specific changes in rhythmic properties of known spliced variants of these genes (e.g. FGFR2 IIIb/FGFR2 IIIc) correlated with epithelial-mesenchymal-transition signalling. Altogether, our bioinformatic analysis highlights a role for the circadian clock in the regulation of AS, and reveals a potential impact of clock disruption in aberrant splicing in cancer hallmark genes.
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Affiliation(s)
- Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany.,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany. .,Institute for Systems Medicine, Faculty of Human Medicine, MSH Medical School Hamburg, Hamburg, 20457, Germany.
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14
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Liu S, Cheng Y, Wang S, Liu H. Circadian Clock Genes Modulate Immune, Cell Cycle and Apoptosis in the Diagnosis and Prognosis of Pan-Renal Cell Carcinoma. Front Mol Biosci 2022; 8:747629. [PMID: 34977153 PMCID: PMC8717949 DOI: 10.3389/fmolb.2021.747629] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/10/2021] [Indexed: 01/20/2023] Open
Abstract
Background: Pan-renal cell carcinoma (pan-RCC) is mainly divided into renal clear cell carcinoma (KIRC), renal papillary cell carcinoma (KIRP), and chromophobe cell carcinoma (KICH). Pan-RCC is a common malignant neoplasm with a high incidence and poor prognosis. Several studies have demonstrated a close association between cancer development and circadian rhythms; however, the clinical significance and molecular mechanism of the clock gene remain unclear in pan-RCC. Methods: In this study, we systematically characterized the alterations of 15 well-known clock genes of three types of kidney cancer. Bioinformatics methods, including differential expression analysis, survival analysis, signing pathway analysis, co-expression network analysis, and drug sensitivity analysis were used to study the diagnosis, prognostic role, and mechanism of clock genes. Results: Thirteen rhythmic genes fluctuated in circadian rhythm in the kidney tissue of mice, and the opposite trend of these rhythm phases was also found in baboons. There are twelve clock genes that were differentially expressed in at least two types of RCC, of which NR1D1, DBP, BHLHE40, CRY1, and CLOCK had the same trend in RCC. Changes in clock control genes may be regulated through methylation, copy number, and mutations. Five rhythmic genes, including PER2, DBP, PER3, CRY2, and RORA, have significant prognostic role in patient survival in at least two types of kidney cancer. Immune infiltration analysis showed that the expression of these rhythmic genes related to prognosis was positively correlated with the infiltration levels of CD4 and CD8 T cells. Pathway analysis suggests that the clock genes is widely related to cancer-related signaling pathways, such as apoptosis, cell cycle, and other pathways. The PPI network showed that circadian genes are closely linked to cancer-related genes such as HIF-1A, TP53, and ERBB2. Moreover, clock gene expression is correlated with the sensitivity of anticancer drugs such as bleomycin and methotrexate in pan-RCC. Conclusion: Taken together, the abnormal expression of biological clock genes plays an important role in the clinical prognosis of RCC through immunity, cell cycle, and apoptosis. These findings provide a reliable basis for the diagnosis, prognosis, and drug guidance for RCC.
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Affiliation(s)
- Shuwen Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory for Functional Substances in Medicinal Edible Resources and Healthcare Products, School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, China
| | - Yongxian Cheng
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China.,Guangdong Key Laboratory for Functional Substances in Medicinal Edible Resources and Healthcare Products, School of Life Sciences and Food Engineering, Hanshan Normal University, Chaozhou, China
| | - Shaoxiang Wang
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Huiyu Liu
- Institute for Inheritance-Based Innovation of Chinese Medicine, School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
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15
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Hesse J, Martinelli J, Aboumanify O, Ballesta A, Relógio A. A mathematical model of the circadian clock and drug pharmacology to optimize irinotecan administration timing in colorectal cancer. Comput Struct Biotechnol J 2021; 19:5170-5183. [PMID: 34630937 PMCID: PMC8477139 DOI: 10.1016/j.csbj.2021.08.051] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 12/21/2022] Open
Abstract
Scheduling anticancer drug administration over 24 h may critically impact treatment success in a patient-specific manner. Here, we address personalization of treatment timing using a novel mathematical model of irinotecan cellular pharmacokinetics and -dynamics linked to a representation of the core clock and predict treatment toxicity in a colorectal cancer (CRC) cellular model. The mathematical model is fitted to three different scenarios: mouse liver, where the drug metabolism mainly occurs, and two human colorectal cancer cell lines representing an in vitro experimental system for human colorectal cancer progression. Our model successfully recapitulates quantitative circadian datasets of mRNA and protein expression together with timing-dependent irinotecan cytotoxicity data. The model also discriminates time-dependent toxicity between the different cells, suggesting that treatment can be optimized according to their cellular clock. Our results show that the time-dependent degradation of the protein mediating irinotecan activation, as well as an oscillation in the death rate may play an important role in the circadian variations of drug toxicity. In the future, this model can be used to support personalized treatment scheduling by predicting optimal drug timing based on the patient's gene expression profile.
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Affiliation(s)
- Janina Hesse
- Institute for Systems Medicine, Department of Human Medicine, MSH Medical School Hamburg - University of Applied Sciences and Medical University, Hamburg 20457, Germany.,Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Julien Martinelli
- INSERM U900, Saint-Cloud, France, Institut Curie, Saint Cloud, France, Paris Saclay University, France, MINES ParisTech, CBIO - Centre for Computational Biology, PSL Research University, Paris, France.,UPR 'Chronotherapy, Cancers and Transplantation', Faculty of Medicine, Paris Saclay University, Campus CNRS, 7 rue Guy Moquet, 94800 Villejuif, France.,Lifeware Group, Inria Saclay Ile-de-France, Palaiseau 91120, France
| | - Ouda Aboumanify
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin
| | - Annabelle Ballesta
- INSERM U900, Saint-Cloud, France, Institut Curie, Saint Cloud, France, Paris Saclay University, France, MINES ParisTech, CBIO - Centre for Computational Biology, PSL Research University, Paris, France.,UPR 'Chronotherapy, Cancers and Transplantation', Faculty of Medicine, Paris Saclay University, Campus CNRS, 7 rue Guy Moquet, 94800 Villejuif, France
| | - Angela Relógio
- Institute for Systems Medicine, Department of Human Medicine, MSH Medical School Hamburg - University of Applied Sciences and Medical University, Hamburg 20457, Germany.,Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt - Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.,Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumor Immunology, Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin
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16
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Vadlamudi Y, Dey DK, Kang SC. Emerging Multi-cancer Regulatory Role of ESRP1: Orchestration of Alternative Splicing to Control EMT. Curr Cancer Drug Targets 2021; 20:654-665. [PMID: 32564755 DOI: 10.2174/1568009620666200621153831] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/06/2023]
Abstract
RNA binding proteins (RBPs) associate with nascent and mature RNAs to perform biological functions such as alternative splicing and RNA stability. Having unique RNA recognition binding motifs, RBPs form complexes with RNA in a sequence- and structure-based manner. Aberrant expressions of several RBPs have been identified in tumorigenesis and cancer progression. These uncontrolled RBPs affect several mechanisms, including cell proliferation, tumor growth, invasion, metastasis and chemoresistance. Epithelial splicing regulatory protein 1 (ESRP1) is a member of the hnRNP family of proteins that play a crucial role in regulating numerous cellular processes, including alternative splicing and translation of multiple genes during organogenesis. Abnormal expression of ESRP1 alters the cell morphology, and leads to cell proliferation and tumor growth during cancer progression. ESRP1 mediated alternative splicing of target genes, including CD44, FGFR, PTBP1, LYN, ENAH, SPAG1 and ZMYND8, results in cancer progression. In addition, ESRP1 also regulates circularization and biogenesis of circular RNAs such as circUHRF1, circNOL10 and circANKS1B, whose expressions have been identified as key factors in various cancers. This multi-functional protein is also involved in imposing stability of target mRNAs such as cyclin A2, and thereby cell cycle regulation. The scope of this review is to examine recent scientific data, outcomes of the up- and down-regulated proteins, and the role of ESRP1 in various cancers. We conclude by summarizing ESRP1 dysregulation and its consequences on target genes in various human cancers. Collectively, the consequences of ESRP1 mediated splicing in cancer cells suggest the role of ESRP1 in cell proliferation and chemoresistance via apoptosis and autophagy modulation, which could, therefore, be potential targets for cancer therapeutics.
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Affiliation(s)
| | - Debasish K Dey
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk-38453, Korea
| | - Sun C Kang
- Department of Biotechnology, Daegu University, Gyeongsan, Gyeongbuk-38453, Korea
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17
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Alternative splicing of mRNA in colorectal cancer: new strategies for tumor diagnosis and treatment. Cell Death Dis 2021; 12:752. [PMID: 34330892 PMCID: PMC8324868 DOI: 10.1038/s41419-021-04031-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) is an important event that contributes to posttranscriptional gene regulation. This process leads to several mature transcript variants with diverse physiological functions. Indeed, disruption of various aspects of this multistep process, such as cis- or trans- factor alteration, promotes the progression of colorectal cancer. Therefore, targeting some specific processes of AS may be an effective therapeutic strategy for treating cancer. Here, we provide an overview of the AS events related to colorectal cancer based on research done in the past 5 years. We focus on the mechanisms and functions of variant products of AS that are relevant to malignant hallmarks, with an emphasis on variants with clinical significance. In addition, novel strategies for exploiting the therapeutic value of AS events are discussed.
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18
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Zhang Y, Devocelle A, Desterke C, de Souza LEB, Hadadi É, Acloque H, Foudi A, Xiang Y, Ballesta A, Chang Y, Giron-Michel J. BMAL1 Knockdown Leans Epithelial-Mesenchymal Balance toward Epithelial Properties and Decreases the Chemoresistance of Colon Carcinoma Cells. Int J Mol Sci 2021; 22:5247. [PMID: 34065633 PMCID: PMC8157026 DOI: 10.3390/ijms22105247] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
The circadian clock coordinates biological and physiological functions to day/night cycles. The perturbation of the circadian clock increases cancer risk and affects cancer progression. Here, we studied how BMAL1 knockdown (BMAL1-KD) by shRNA affects the epithelial-mesenchymal transition (EMT), a critical early event in the invasion and metastasis of colorectal carcinoma (CRC). In corresponding to a gene set enrichment analysis, which showed a significant enrichment of EMT and invasive signatures in BMAL1_high CRC patients as compared to BMAL1_low CRC patients, our results revealed that BMAL1 is implicated in keeping the epithelial-mesenchymal equilibrium of CRC cells and influences their capacity of adhesion, migration, invasion, and chemoresistance. Firstly, BMAL1-KD increased the expression of epithelial markers (E-cadherin, CK-20, and EpCAM) but decreased the expression of Twist and mesenchymal markers (N-cadherin and vimentin) in CRC cell lines. Finally, the molecular alterations after BMAL1-KD promoted mesenchymal-to-epithelial transition-like changes mostly appeared in two primary CRC cell lines (i.e., HCT116 and SW480) compared to the metastatic cell line SW620. As a consequence, migration/invasion and drug resistance capacities decreased in HCT116 and SW480 BMAL1-KD cells. Together, BMAL1-KD alerts the delicate equilibrium between epithelial and mesenchymal properties of CRC cell lines, which revealed the crucial role of BMAL1 in EMT-related CRC metastasis and chemoresistance.
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Affiliation(s)
- Yuan Zhang
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- Institute of Life Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Aurore Devocelle
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- INSERM UMR-S-MD 1197/Ministry of the Armed Forces, Biomedical Research Institute of the Armed Forces (IRBA), Paul-Brousse Hospital Villejuif and CTSA Clamart, 94807 Villejuif, France
| | - Christophe Desterke
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Lucas Eduardo Botelho de Souza
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Éva Hadadi
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Hervé Acloque
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Adlen Foudi
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
| | - Yao Xiang
- INSERM UMR-S 1151, Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), Paris Descartes University, CNRS UMR 8253, 75730 Paris, France;
| | - Annabelle Ballesta
- INSERM UMR-S 900, Institut Curie, MINES ParisTech CBIO, PSL Research University, 92210 Saint-Cloud, France;
| | - Yunhua Chang
- INSERM UMR-S 935, CNRS Campus, 94801 Villejuif, France; (Y.Z.); (C.D.); (L.E.B.d.S.); (É.H.); (H.A.); (A.F.); (Y.C.)
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- INSERM UMR-S 1151, Department of Immunology, Infectiology and Hematology, Institut Necker-Enfants Malades (INEM), Paris Descartes University, CNRS UMR 8253, 75730 Paris, France;
| | - Julien Giron-Michel
- Orsay-Vallée Campus, Paris-Saclay University, 91190 Gif-sur-Yvette, France;
- INSERM UMR-S-MD 1197/Ministry of the Armed Forces, Biomedical Research Institute of the Armed Forces (IRBA), Paul-Brousse Hospital Villejuif and CTSA Clamart, 94807 Villejuif, France
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19
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Gaspar LS, Hesse J, Yalçin M, Santos B, Carvalhas-Almeida C, Ferreira M, Moita J, Relógio A, Cavadas C, Álvaro AR. Long-term continuous positive airway pressure treatment ameliorates biological clock disruptions in obstructive sleep apnea. EBioMedicine 2021; 65:103248. [PMID: 33647771 PMCID: PMC7920825 DOI: 10.1016/j.ebiom.2021.103248] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Obstructive Sleep Apnea (OSA) is a highly prevalent and underdiagnosed sleep disorder. Recent studies suggest that OSA might disrupt the biological clock, potentially causing or worsening OSA-associated comorbidities. However, the effect of OSA treatment on clock disruption is not fully understood. METHODS The impact of OSA and short- (four months) and long-term (two years) OSA treatment, with Continuous Positive Airway Pressure (CPAP), on the biological clock was investigated at four time points within 24 h, in OSA patients relative to controls subjects (no OSA) of the same sex and age group, in a case-control study. Plasma melatonin and cortisol, body temperature and the expression levels and rhythmicity of eleven clock genes in peripheral blood mononuclear cells (PBMCs) were assessed. Additional computational tools were used for a detailed data analysis. FINDINGS OSA impacts on clock outputs and on the expression of several clock genes in PBMCs. Neither short- nor long-term treatment fully reverted OSA-induced alterations in the expression of clock genes. However, long-term treatment was able to re-establish levels of plasma melatonin and cortisol and body temperature. Machine learning methods could discriminate controls from untreated OSA patients. Following long-term treatment, the distinction between controls and patients disappeared, suggesting a closer similarity of the phenotypes. INTERPRETATION OSA alters biological clock-related characteristics that differentially respond to short- and long-term CPAP treatment. Long-term CPAP was more efficient in counteracting OSA impact on the clock, but the obtained results suggest that it is not fully effective. A better understanding of the impact of OSA and OSA treatment on the clock may open new avenues to OSA diagnosis, monitoring and treatment.
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Affiliation(s)
- Laetitia S Gaspar
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Pólo I, Coimbra 3004-504, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; PhD Programme in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Janina Hesse
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany; Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany; Department of Human Medicine, Institute for Systems Medicine and Bioinformatics, MSH Medical School Hamburg-University of Applied Sciences and Medical University, Am Kaiserkai 1, Hamburg 20457, Germany
| | - Müge Yalçin
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany; Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Bárbara Santos
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Pólo I, Coimbra 3004-504, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal
| | - Catarina Carvalhas-Almeida
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Pólo I, Coimbra 3004-504, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal
| | - Mafalda Ferreira
- Sleep Medicine Centre, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Joaquim Moita
- Sleep Medicine Centre, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany; Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology, and Tumour Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany; Department of Human Medicine, Institute for Systems Medicine and Bioinformatics, MSH Medical School Hamburg-University of Applied Sciences and Medical University, Am Kaiserkai 1, Hamburg 20457, Germany.
| | - Cláudia Cavadas
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Pólo I, Coimbra 3004-504, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
| | - Ana Rita Álvaro
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Rua Larga, Pólo I, Coimbra 3004-504, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal.
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20
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Hesse J, Malhan D, Yalҫin M, Aboumanify O, Basti A, Relógio A. An Optimal Time for Treatment-Predicting Circadian Time by Machine Learning and Mathematical Modelling. Cancers (Basel) 2020; 12:cancers12113103. [PMID: 33114254 PMCID: PMC7690897 DOI: 10.3390/cancers12113103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Tailoring medical interventions to a particular patient and pathology has been termed personalized medicine. The outcome of cancer treatments is improved when the intervention is timed in accordance with the patient's internal time. Yet, one challenge of personalized medicine is how to consider the biological time of the patient. Prerequisite for this so-called chronotherapy is an accurate characterization of the internal circadian time of the patient. As an alternative to time-consuming measurements in a sleep-laboratory, recent studies in chronobiology predict circadian time by applying machine learning approaches and mathematical modelling to easier accessible observables such as gene expression. Embedding these results into the mathematical dynamics between clock and cancer in mammals, we review the precision of predictions and the potential usage with respect to cancer treatment and discuss whether the patient's internal time and circadian observables, may provide an additional indication for individualized treatment timing. Besides the health improvement, timing treatment may imply financial advantages, by ameliorating side effects of treatments, thus reducing costs. Summarizing the advances of recent years, this review brings together the current clinical standard for measuring biological time, the general assessment of circadian rhythmicity, the usage of rhythmic variables to predict biological time and models of circadian rhythmicity.
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Affiliation(s)
- Janina Hesse
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Müge Yalҫin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Ouda Aboumanify
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Human Medicine, Institute for Systems Medicine and Bioinformatics, MSH Medical School Hamburg—University of Applied Sciences and Medical University, 20457 Hamburg, Germany
- Correspondence: or
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21
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Hu F, Wang Q, Yang Z, Zhang Z, Liu X. Network-based identification of biomarkers for colon adenocarcinoma. BMC Cancer 2020; 20:668. [PMID: 32680494 PMCID: PMC7367377 DOI: 10.1186/s12885-020-07157-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background As one of the most common cancers with high mortality in the world, we are still facing a huge challenge in the prevention and treatment of colon cancer. With the rapid development of high throughput technologies, new biomarkers identification for colon cancer has been confronted with the new opportunities and challenges. Methods We firstly constructed functional networks for each sample of colon adenocarcinoma (COAD) by using a sample-specific network (SSN) method which can construct individual-specific networks based on gene expression profiles of a single sample. The functional genes and interactions were identified from the functional networks, respectively. Results Classification and subtyping were used to test the function of the functional genes and interactions. The results of classification showed that the functional genes could be used as diagnostic biomarkers. The subtypes displayed different mechanisms, which were shown by the functional and pathway enrichment analysis for the representative genes of each subtype. Besides, subtype-specific molecular patterns were also detected, such as subtype-specific clinical and mutation features. Finally, 12 functional genes and 13 functional edges could serve as prognosis biomarkers since they were associated with the survival rate of COAD. Conclusions In conclusion, the functional genes and interactions in the constructed functional network could be used as new biomarkers for COAD.
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Affiliation(s)
- Fuyan Hu
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, China
| | - Qing Wang
- Department of Traditional Chinese Medicine of Wuhan Puren Hospital, Affiliated Hospital of Wuhan University of Science and Technology, Benxi Street 1#, Qingshan District, Wuhan, Hubei, P.R. China
| | - Zhiyuan Yang
- College of Life Information Science & Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Zeng Zhang
- Department of Statistics, School of Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan, China
| | - Xiaoping Liu
- School of Mathematics and Statistics, Shandong University, Weihai, 264209, China.
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22
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Režen T, Zmrzljak UP, Bensa T, Tomaš TC, Cirnski K, Stojan J, Rozman D. Novel insights into biological roles of inducible cAMP early repressor ICER. Biochem Biophys Res Commun 2020; 530:396-401. [PMID: 32534736 DOI: 10.1016/j.bbrc.2020.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/03/2020] [Indexed: 11/16/2022]
Abstract
ICER corresponds to a group of alternatively spliced Inducible cAMP Early Repressors with high similarity, but multiple roles, including in circadian rhythm, and are involved in attenuation of cAMP-dependent gene expression. We present experimental and in silico data revealing biological differences between the isoforms with exon gamma (ICER) or without it (ICERγ). Both isoforms are expressed in the liver and the adrenal glands and can derive from differential splicing. In adrenals the expression is circadian, with maximum at ZT12 and higher amplitude of Icerγ. In the liver, the expression of Icerγ is lower than Icer in the 24 h time frame. Icer mRNA has a delayed early response to forskolin. The longer ICER protein binds to three DNA grooves of the Per1 promoter, while ICERγ only to two, as deduced by molecular modelling. This is in line with gel shift competition assays showing stronger binding of ICER to Per1 promotor. Only Icerγ siRNA provoked an increase of Per1 expression. In conclusion, we show that ICER and ICERγ have distinct biochemical properties in tissue expression, DNA binding, and response to forskolin. Data are in favour of ICERγ as the physiologically important form in hepatic cells where weaker binding of repressor might be preferred in guiding the cAMP-dependent response.
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Affiliation(s)
- Tadeja Režen
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Uršula Prosenc Zmrzljak
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Tjaša Bensa
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Tanja Cvitanović Tomaš
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Katarina Cirnski
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Jure Stojan
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia
| | - Damjana Rozman
- Centre for Functional Genomics and Bio-Chip, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia; Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Slovenia.
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23
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Zhang Y, Devocelle A, Souza L, Foudi A, Tenreira Bento S, Desterke C, Sherrard R, Ballesta A, Adam R, Giron-Michel J, Chang Y. BMAL1 knockdown triggers different colon carcinoma cell fates by altering the delicate equilibrium between AKT/mTOR and P53/P21 pathways. Aging (Albany NY) 2020; 12:8067-8083. [PMID: 32388500 PMCID: PMC7244025 DOI: 10.18632/aging.103124] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 03/24/2020] [Indexed: 12/15/2022]
Abstract
Dysregulation of the circadian timing system (CTS) frequently appears during colorectal cancer (CRC) progression. In order to better understand the role of the circadian clock in CRC progression, this study evaluated in vitro how knockdown of a core circadian protein BMAL1 (BMAL1-KD) influenced the behavior of two primary human CRC cell lines (HCT116 and SW480) and a metastatic CRC cell line (SW620).Unexpectedly, BMAL1-KD induced CRC cell-type specific responses rather than the same phenomenon throughout. First, BMAL1-KD increased AKT/mTOR activation in each CRC cell line, but to different extents. Second, BMAL1-KD-induced P53 activation varied with cell context. In a wild type P53 background, HCT116 BMAL1-KD cells quickly underwent apoptosis after shBMAL1 lentivirus transduction, while surviving cells showed less P53 but increased AKT/mTOR activation, which ultimately caused higher proliferation. In the presence of a partially functional mutant P53, SW480 BMAL1-KD cells showed moderate P53 and mTOR activation simultaneously with cell senescence. With a moderate increased AKT but unchanged mutant P53 activation, SW620 BMAL1-KD cells grew faster.Thus, under different CRC cellular pathological contexts, BMAL1 knockdown induced relatively equal effects on AKT/mTOR activation but different effects on P53 activation, which finally triggered different CRC cell fates.
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Affiliation(s)
- Yuan Zhang
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Aurore Devocelle
- Paris-Saclay University, Saint-Aubin, France
- INSERM, UMR1197 Interactions between Stem Cells and Their Niches in Physiology, Tumors and Tissue Repair, Villejuif, France
| | - Lucas Souza
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Adlen Foudi
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Sabrina Tenreira Bento
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Christophe Desterke
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Rachel Sherrard
- Sorbonne Université and CNRS, Institut de Biologie Paris Seine, UMR8256 Biological Adaptation and Aging (B2A), Paris, France
| | - Annabelle Ballesta
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
| | - Rene Adam
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
- Hôpital Paul Brousse AP-HP, Villejuif, France
| | - Julien Giron-Michel
- Paris-Saclay University, Saint-Aubin, France
- INSERM, UMR1197 Interactions between Stem Cells and Their Niches in Physiology, Tumors and Tissue Repair, Villejuif, France
| | - Yunhua Chang
- INSERM, UMR935, Malignant and Therapeutic Stem Cells Models, Villejuif, France
- Paris-Saclay University, Saint-Aubin, France
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Yang Y, Li Y, Sancar A, Oztas O. The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation. J Biol Chem 2020; 295:7608-7619. [PMID: 32303634 DOI: 10.1074/jbc.ra120.013513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Indexed: 01/24/2023] Open
Abstract
The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.
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Affiliation(s)
- Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina.,Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina.,Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Onur Oztas
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
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25
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Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington's Disease. Cancers (Basel) 2020; 12:cancers12040963. [PMID: 32295075 PMCID: PMC7226183 DOI: 10.3390/cancers12040963] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 02/06/2023] Open
Abstract
Accumulating evidence points to a link between circadian clock dysfunction and the molecular events that drive tumorigenesis. Here, we investigated the connection between the circadian clock and the hallmarks of cancer in an in vitro model of colorectal cancer (CRC). We used a cross-platform data normalization method to concatenate and compare available microarray and RNA-sequencing time series data of CRC cell lines derived from the same patient at different disease stages. Our data analysis suggests differential regulation of molecular pathways between the CRC cells and identifies several of the circadian and likely clock-controlled genes (CCGs) as cancer hallmarks and circadian drug targets. Notably, we found links of the CCGs to Huntington’s disease (HD) in the metastasis-derived cells. We then investigated the impact of perturbations of our candidate genes in a cohort of 439 patients with colon adenocarcinoma retrieved from the Cancer Genome Atlas (TCGA). The analysis revealed a correlation of the differential expression levels of the candidate genes with the survival of patients. Thus, our study provides a bioinformatics workflow that allows for a comprehensive analysis of circadian properties at different stages of colorectal cancer, and identifies a new association between cancer and HD.
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The Cancer Clock Is (Not) Ticking: Links between Circadian Rhythms and Cancer. Clocks Sleep 2019; 1:435-458. [PMID: 33089179 PMCID: PMC7445810 DOI: 10.3390/clockssleep1040034] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/10/2019] [Indexed: 12/23/2022] Open
Abstract
Circadian rhythms regulate many physiological and behavioral processes, including sleep, metabolism and cell division, which have a 24-h oscillation pattern. Rhythmicity is generated by a transcriptional–translational feedback loop in individual cells, which are synchronized by the central pacemaker in the brain and external cues. Epidemiological and clinical studies indicate that disruption of these rhythms can increase both tumorigenesis and cancer progression. Environmental changes (shift work, jet lag, exposure to light at night), mutations in circadian regulating genes, and changes to clock gene expression are recognized forms of disruption and are associated with cancer risk and/or cancer progression. Experimental data in animals and cell cultures further supports the role of the cellular circadian clock in coordinating cell division and DNA repair, and disrupted cellular clocks accelerate cancer cell growth. This review will summarize studies linking circadian disruption to cancer biology and explore how such disruptions may be further altered by common characteristics of tumors including hypoxia and acidosis. We will highlight how circadian rhythms might be exploited for cancer drug development, including how delivery of current chemotherapies may be enhanced using chronotherapy. Understanding the role of circadian rhythms in carcinogenesis and tumor progression will enable us to better understand causes of cancer and how to treat them.
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27
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Genov N, Castellana S, Scholkmann F, Capocefalo D, Truglio M, Rosati J, Turco EM, Biagini T, Carbone A, Mazza T, Relógio A, Mazzoccoli G. A Multi-Layered Study on Harmonic Oscillations in Mammalian Genomics and Proteomics. Int J Mol Sci 2019; 20:ijms20184585. [PMID: 31533246 PMCID: PMC6770795 DOI: 10.3390/ijms20184585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/08/2019] [Accepted: 09/10/2019] [Indexed: 12/27/2022] Open
Abstract
Cellular, organ, and whole animal physiology show temporal variation predominantly featuring 24-h (circadian) periodicity. Time-course mRNA gene expression profiling in mouse liver showed two subsets of genes oscillating at the second (12-h) and third (8-h) harmonic of the prime (24-h) frequency. The aim of our study was to identify specific genomic, proteomic, and functional properties of ultradian and circadian subsets. We found hallmarks of the three oscillating gene subsets, including different (i) functional annotation, (ii) proteomic and electrochemical features, and (iii) transcription factor binding motifs in upstream regions of 8-h and 12-h oscillating genes that seemingly allow the link of the ultradian gene sets to a known circadian network. Our multifaceted bioinformatics analysis of circadian and ultradian genes suggests that the different rhythmicity of gene expression impacts physiological outcomes and may be related to transcriptional, translational and post-translational dynamics, as well as to phylogenetic and evolutionary components.
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Affiliation(s)
- Nikolai Genov
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, Germany.
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
| | - Stefano Castellana
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Felix Scholkmann
- Research Office for Complex Physical and Biological Systems (ROCoS), 8006 Zurich, Switzerland.
- Department of Neonatology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland.
| | - Daniele Capocefalo
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Mauro Truglio
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Jessica Rosati
- Cell Reprogramming Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Elisa Maria Turco
- Cell Reprogramming Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Tommaso Biagini
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Annalucia Carbone
- Division of Internal Medicine and Chronobiology Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 1011 Berlin, Germany.
- Medical Department of Hematology, Oncology, and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 13353 Berlin, Germany.
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine and Chronobiology Unit, Fondazione IRCCS "Casa Sollievo della Sofferenza", 71013 San Giovanni Rotondo (FG), Italy.
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El-Athman R, Knezevic D, Fuhr L, Relógio A. A Computational Analysis of Alternative Splicing across Mammalian Tissues Reveals Circadian and Ultradian Rhythms in Splicing Events. Int J Mol Sci 2019; 20:E3977. [PMID: 31443305 PMCID: PMC6721216 DOI: 10.3390/ijms20163977] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023] Open
Abstract
Mounting evidence points to a role of the circadian clock in the temporal regulation of post-transcriptional processes in mammals, including alternative splicing (AS). In this study, we carried out a computational analysis of circadian and ultradian rhythms on the transcriptome level to characterise the landscape of rhythmic AS events in published datasets covering 76 tissues from mouse and olive baboon. Splicing-related genes with 24-h rhythmic expression patterns showed a bimodal distribution of peak phases across tissues and species, indicating that they might be controlled by the circadian clock. On the output level, we identified putative oscillating AS events in murine microarray data and pairs of differentially rhythmic splice isoforms of the same gene in baboon RNA-seq data that peaked at opposing times of the day and included oncogenes and tumour suppressors. We further explored these findings using a new circadian RNA-seq dataset of human colorectal cancer cell lines. Rhythmic isoform expression patterns differed between the primary tumour and the metastatic cell line and were associated with cancer-related biological processes, indicating a functional role of rhythmic AS that might be implicated in tumour progression. Our data shows that rhythmic AS events are widespread across mammalian tissues and might contribute to a temporal diversification of the proteome.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Dora Knezevic
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany.
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
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Gaspar LS, Álvaro AR, Carmo‐Silva S, Mendes AF, Relógio A, Cavadas C. The importance of determining circadian parameters in pharmacological studies. Br J Pharmacol 2019; 176:2827-2847. [PMID: 31099023 PMCID: PMC6637036 DOI: 10.1111/bph.14712] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 04/01/2019] [Indexed: 12/25/2022] Open
Abstract
In mammals, most molecular and cellular processes show circadian changes, leading to daily variations in physiology and ultimately in behaviour. Such daily variations induce a temporal coordination of processes that is essential to ensure homeostasis and health. Thus, it is of no surprise that pharmacokinetics (PK) and pharmacodynamics (PD) of many drugs are also subject to circadian variations, profoundly affecting their efficacy and tolerability. Understanding how circadian rhythms influence drug PK, PD, and toxicity might significantly improve treatment efficacy and decrease related side effects. Therefore, it is essential to take circadian variations into account and to determine circadian parameters in pharmacological studies, especially when drugs have a short half-life or target rhythmic processes. This review provides an overview of the current knowledge on circadian rhythms and their relevance to the field of pharmacology. Methodologies to evaluate circadian rhythms in vitro, in rodent models and in humans, from experimental to computational approaches, are described and discussed. Lastly, we aim at alerting the scientific, medical, and regulatory communities to the relevance of the physiological time, as a key parameter to be considered when designing pharmacological studies. This will eventually lead to more successful preclinical and clinical trials and pave the way to a more personalized treatment to the benefit of the patients.
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Affiliation(s)
- Laetitia S. Gaspar
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Institute for Interdisciplinary Research (IIIUC)University of CoimbraCoimbraPortugal
| | - Ana Rita Álvaro
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Sara Carmo‐Silva
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
| | - Alexandrina Ferreira Mendes
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
| | - Angela Relógio
- Institute for Theoretical BiologyCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
- Medical Department of Hematology, Oncology, and Tumor Immunology, Molecular Cancer Research CenterCharité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt—Universität zu Berlin, and Berlin Institute of HealthBerlinGermany
| | - Cláudia Cavadas
- CNC—Center for Neuroscience and Cell BiologyUniversity of CoimbraCoimbraPortugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB)University of CoimbraCoimbraPortugal
- Faculty of PharmacyUniversity of CoimbraCoimbraPortugal
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A bioinformatic analysis identifies circadian expression of splicing factors and time-dependent alternative splicing events in the HD-MY-Z cell line. Sci Rep 2019; 9:11062. [PMID: 31363108 PMCID: PMC6667479 DOI: 10.1038/s41598-019-47343-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
The circadian clock regulates key cellular processes and its dysregulation is associated to several pathologies including cancer. Although the transcriptional regulation of gene expression by the clock machinery is well described, the role of the clock in the regulation of post-transcriptional processes, including splicing, remains poorly understood. In the present work, we investigated the putative interplay between the circadian clock and splicing in a cancer context. For this, we applied a computational pipeline to identify oscillating genes and alternatively spliced transcripts in time-course high-throughput data sets from normal cells and tissues, and cancer cell lines. We investigated the temporal phenotype of clock-controlled genes and splicing factors, and evaluated their impact in alternative splice patterns in the Hodgkin Lymphoma cell line HD-MY-Z. Our data points to a connection between clock-controlled genes and splicing factors, which correlates with temporal alternative splicing in several genes in the HD-MY-Z cell line. These include the genes DPYD, SS18, VIPR1 and IRF4, involved in metabolism, cell cycle, apoptosis and proliferation. Our results highlight a role for the clock as a temporal regulator of alternative splicing, which may impact malignancy in this cellular model.
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Temporal Splicing Switches in Elements of the TNF-Pathway Identified by Computational Analysis of Transcriptome Data for Human Cell Lines. Int J Mol Sci 2019; 20:ijms20051182. [PMID: 30857150 PMCID: PMC6429354 DOI: 10.3390/ijms20051182] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing plays an important role in numerous cellular processes and aberrant splice decisions are associated with cancer. Although some studies point to a regulation of alternative splicing and its effector mechanisms in a time-dependent manner, the extent and consequences of such a regulation remains poorly understood. In the present work, we investigated the time-dependent production of isoforms in two Hodgkin lymphoma cell lines of different progression stages (HD-MY-Z, stage IIIb and L-1236, stage IV) compared to a B lymphoblastoid cell line (LCL-HO) with a focus on tumour necrosis factor (TNF) pathway-related elements. For this, we used newly generated time-course RNA-sequencing data from the mentioned cell lines and applied a computational pipeline to identify genes with isoform-switching behaviour in time. We analysed the temporal profiles of the identified events and evaluated in detail the potential functional implications of alterations in isoform expression for the selected top-switching genes. Our data indicate that elements within the TNF pathway undergo a time-dependent variation in isoform production with a putative impact on cell migration, proliferation and apoptosis. These include the genes TRAF1, TNFRSF12A and NFKB2. Our results point to a role of temporal alternative splicing in isoform production, which may alter the outcome of the TNF pathway and impact on tumorigenesis.
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Liu Z, Yu K, Zheng J, Lin H, Zhao Q, Zhang X, Feng W, Wang L, Xu J, Xie D, Zuo ZX, Liu ZX, Zheng Q. Dysregulation, functional implications, and prognostic ability of the circadian clock across cancers. Cancer Med 2019; 8:1710-1720. [PMID: 30791227 PMCID: PMC6488113 DOI: 10.1002/cam4.2035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/15/2019] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
It has been proposed that the circadian rhythm generally plays important roles in tumor suppression, but there is also evidence that disruption of the canonical circadian pathway has anticancer effects. In this study, we systematically analyzed the aberrances of circadian clock genes across cancers based on data from The Cancer Genome Atlas (TCGA). These data showed that the frequencies of mutations and copy number alterations in core clock genes (PER1/2/3, CLOCK, CRY1/2, and ARNTL) were low, but that the expression levels of core clock genes were downregulated by the higher levels of DNA methylation in most tumors. The circadian clock index (CCI) was established through a principal component analysis, and this measure well represents the overall expression of the core clock genes. In fact, the CCI was significantly lower in hepatocellular carcinoma with HBV infection than in other cancers. Furthermore, pathways such as the MAPK, JAK‐STAT, and immune‐related signaling pathways were enriched in tumors with high CCI values. Interestingly, the CCI was generally positively related to the immunophenoscores and immunophenotypes of tumors. Additionally, the expression levels of core clock genes and the CCI were also generally positively related to survival across cancers. Taken together, the results of this study provide a comprehensive analysis of circadian clock aberrances in cancer, and the results should aid further investigations of the molecular mechanisms of cancer and the development of therapeutic strategies.
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Affiliation(s)
- Zekun Liu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Kai Yu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jian Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Huan Lin
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qi Zhao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xiaolong Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Weiyi Feng
- Big Data Research Center, School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Liyu Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianjun Xu
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dawei Xie
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Xiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ze-Xian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qichang Zheng
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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