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Cao W, Ji Z, Zhu S, Wang M, Sun R. Bioinformatic identification and experiment validation reveal 6 hub genes, promising diagnostic and therapeutic targets for Alzheimer's disease. BMC Med Genomics 2024; 17:6. [PMID: 38167011 PMCID: PMC10763315 DOI: 10.1186/s12920-023-01775-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a progressive neurodegenerative disease that can cause dementia. We aim to screen out the hub genes involved in AD based on microarray datasets. METHODS Gene expression profiles GSE5281 and GSE28146 were retrieved from Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). Gene Ontology and pathway enrichment were conducted using DAVID online tool. The STRING database and Cytoscape tools were employed to analyze protein-protein interactions and identify hub genes. The predictive value of hub genes was assessed by principal component analysis and receiver operating characteristic curves. AD mice model was constructed, and histology was then observed by hematoxylin-eosin staining. Gene expression levels were finally determined by real-time quantitative PCR. RESULTS We obtained 197 overlapping DEGs from GSE5281 and GSE28146 datasets. After constructing protein-protein interaction network, three highly interconnected clusters were identified and 6 hub genes (RBL1, BUB1, HDAC7, KAT5, SIRT2, and ITGB1) were selected. The hub genes could be used as basis to predict AD. Histological abnormalities of brain were observed, suggesting successful AD model was constructed. Compared with the control group, the mRNA expression levels of RBL1, BUB1, HDAC7, KAT5 and SIRT2 were significantly increased, while the mRNA expression level of ITGB1 was significantly decreased in AD groups. CONCLUSION RBL1, BUB1, HDAC7, KAT5, SIRT2 and ITGB1 are promising gene signatures for diagnosis and therapy of AD.
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Affiliation(s)
- Wenyuan Cao
- Department of Neurology Second Ward, Zibo Municipal Hospital, No. 139, Huangong Road, Linzi District, Zibo City, 255400, Shandong Province, China
| | - Zhangge Ji
- Department of Neurology Second Ward, Zibo Municipal Hospital, No. 139, Huangong Road, Linzi District, Zibo City, 255400, Shandong Province, China
| | - Shoulian Zhu
- Department of Neurology Second Ward, Zibo Municipal Hospital, No. 139, Huangong Road, Linzi District, Zibo City, 255400, Shandong Province, China
| | - Mei Wang
- Department of Rehabilitation, Zibo Municipal Hospital, No. 139, Huangong Road, Linzi District, Zibo City, 255400, Shandong Province, China
| | - Runming Sun
- Department of Neurology Second Ward, Zibo Municipal Hospital, No. 139, Huangong Road, Linzi District, Zibo City, 255400, Shandong Province, China.
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2
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Savić R, Yang J, Koplev S, An MC, Patel PL, O'Brien RN, Dubose BN, Dodatko T, Rogatsky E, Sukhavasi K, Ermel R, Ruusalepp A, Houten SM, Kovacic JC, Stewart AF, Yohn CB, Schadt EE, Laberge RM, Björkegren JLM, Tu Z, Argmann C. Integration of transcriptomes of senescent cell models with multi-tissue patient samples reveals reduced COL6A3 as an inducer of senescence. Cell Rep 2023; 42:113371. [PMID: 37938972 PMCID: PMC10955802 DOI: 10.1016/j.celrep.2023.113371] [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: 06/30/2021] [Revised: 05/23/2023] [Accepted: 10/17/2023] [Indexed: 11/10/2023] Open
Abstract
Senescent cells are a major contributor to age-dependent cardiovascular tissue dysfunction, but knowledge of their in vivo cell markers and tissue context is lacking. To reveal tissue-relevant senescence biology, we integrate the transcriptomes of 10 experimental senescence cell models with a 224 multi-tissue gene co-expression network based on RNA-seq data of seven tissues biopsies from ∼600 coronary artery disease (CAD) patients. We identify 56 senescence-associated modules, many enriched in CAD GWAS genes and correlated with cardiometabolic traits-which supports universality of senescence gene programs across tissues and in CAD. Cross-tissue network analyses reveal 86 candidate senescence-associated secretory phenotype (SASP) factors, including COL6A3. Experimental knockdown of COL6A3 induces transcriptional changes that overlap the majority of the experimental senescence models, with cell-cycle arrest linked to modulation of DREAM complex-targeted genes. We provide a transcriptomic resource for cellular senescence and identify candidate biomarkers, SASP factors, and potential drivers of senescence in human tissues.
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Affiliation(s)
- Radoslav Savić
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jialiang Yang
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Simon Koplev
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
| | - Mahru C An
- UNITY Biotechnology, South San Francisco, CA 94080, USA
| | | | | | | | - Tetyana Dodatko
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Eduard Rogatsky
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Katyayani Sukhavasi
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Raili Ermel
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia
| | - Arno Ruusalepp
- Department of Cardiac Surgery and The Heart Clinic, Tartu University Hospital, Tartu, Estonia; Clinical Gene Networks AB, Stockholm, Sweden
| | - Sander M Houten
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Jason C Kovacic
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Andrew F Stewart
- Diabetes Obesity Metabolism Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Eric E Schadt
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | | | - Johan L M Björkegren
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA; Clinical Gene Networks AB, Stockholm, Sweden; Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Zhidong Tu
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA
| | - Carmen Argmann
- Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6574, USA.
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Pan X. The Roles of Fatty Acids and Apolipoproteins in the Kidneys. Metabolites 2022; 12:metabo12050462. [PMID: 35629966 PMCID: PMC9145954 DOI: 10.3390/metabo12050462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 12/10/2022] Open
Abstract
The kidneys are organs that require energy from the metabolism of fatty acids and glucose; several studies have shown that the kidneys are metabolically active tissues with an estimated energy requirement similar to that of the heart. The kidneys may regulate the normal and pathological function of circulating lipids in the body, and their glomerular filtration barrier prevents large molecules or large lipoprotein particles from being filtered into pre-urine. Given the permeable nature of the kidneys, renal lipid metabolism plays an important role in affecting the rest of the body and the kidneys. Lipid metabolism in the kidneys is important because of the exchange of free fatty acids and apolipoproteins from the peripheral circulation. Apolipoproteins have important roles in the transport and metabolism of lipids within the glomeruli and renal tubules. Indeed, evidence indicates that apolipoproteins have multiple functions in regulating lipid import, transport, synthesis, storage, oxidation and export, and they are important for normal physiological function. Apolipoproteins are also risk factors for several renal diseases; for example, apolipoprotein L polymorphisms induce kidney diseases. Furthermore, renal apolipoprotein gene expression is substantially regulated under various physiological and disease conditions. This review is aimed at describing recent clinical and basic studies on the major roles and functions of apolipoproteins in the kidneys.
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Affiliation(s)
- Xiaoyue Pan
- Department of Foundations of Medicine, New York University Long Island School of Medicine, Mineola, New York, NY 11501, USA;
- Diabetes and Obesity Research Center, NYU Langone Hospital—Long Island, Mineola, New York, NY 11501, USA
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Shepherd TG, Dick FA. Principles of dormancy evident in high-grade serous ovarian cancer. Cell Div 2022; 17:2. [PMID: 35321751 PMCID: PMC8944075 DOI: 10.1186/s13008-022-00079-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/16/2022] [Indexed: 11/17/2022] Open
Abstract
In cancer, dormancy refers to a clinical state in which microscopic residual disease becomes non-proliferative and is largely refractory to chemotherapy. Dormancy was first described in breast cancer where disease can remain undetected for decades, ultimately leading to relapse and clinical presentation of the original malignancy. A long latency period can be explained by withdrawal from cell proliferation (cellular dormancy), or a balance between proliferation and cell death that retains low levels of residual disease (tumor mass dormancy). Research into cellular dormancy has revealed features that define this state. They include arrest of cell proliferation, altered cellular metabolism, and unique cell dependencies and interactions with the microenvironment. These characteristics can be shared by dormant cells derived from disparate primary disease sites, suggesting common features exist between them. High-grade serous ovarian cancer (HGSOC) disseminates to locations throughout the abdominal cavity by means of cellular aggregates called spheroids. These growth-arrested and therapy-resistant cells are a strong contributor to disease relapse. In this review, we discuss the similarities and differences between ovarian cancer cells in spheroids and dormant properties reported for other cancer disease sites. This reveals that elements of dormancy, such as cell cycle control mechanisms and changes to metabolism, may be similar across most forms of cellular dormancy. However, HGSOC-specific aspects of spheroid biology, including the extracellular matrix organization and microenvironment, are obligatorily disease site specific. Collectively, our critical review of current literature highlights places where HGSOC cell dormancy may offer a more tractable experimental approach to understand broad principles of cellular dormancy in cancer.
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Affiliation(s)
- Trevor G Shepherd
- London Regional Cancer Program, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Obstetrics & Gynaecology, Western University, London, ON, N6A 5C1, Canada
| | - Frederick A Dick
- London Regional Cancer Program, London Health Sciences Centre, London, ON, N6A 5W9, Canada. .,Department of Pathology and Laboratory Medicine, Western University, London, ON, N6A 5C1, Canada. .,Children's Health Research Institute, London, ON, N6A 4V2, Canada.
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Ventura E, Iannuzzi CA, Pentimalli F, Giordano A, Morrione A. RBL1/p107 Expression Levels Are Modulated by Multiple Signaling Pathways. Cancers (Basel) 2021; 13:cancers13195025. [PMID: 34638509 PMCID: PMC8507926 DOI: 10.3390/cancers13195025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022] Open
Abstract
The members of the retinoblastoma (RB) protein family, RB1/p105, retinoblastoma-like (RBL)1/p107 and RBL2/p130 are critical modulators of the cell cycle and their dysregulation has been associated with tumor initiation and progression. The activity of RB proteins is regulated by numerous pathways including oncogenic signaling, but the molecular mechanisms of these functional interactions are not fully defined. We previously demonstrated that RBL2/p130 is a direct target of AKT and it is a key mediator of the apoptotic process induced by AKT inhibition. Here we demonstrated that RBL1/p107 levels are only minorly modulated by the AKT signaling pathway. In contrast, we discovered that RBL1/p107 levels are regulated by multiple pathways linked directly or indirectly to Ca2+-dependent signaling. Inhibition of the multifunctional calcium/calmodulin-dependent kinases (CaMKs) significantly reduced RBL1/p107 expression levels and phosphorylation, increased RBL1/p107 nuclear localization and led to cell cycle arrest in G0/G1. Targeting the Ca2+-dependent endopeptidase calpain stabilized RBL1/p107 levels and counteracted the reduction of RBL1/p107 levels associated with CaMKs inhibition. Thus, these novel observations suggest a complex regulation of RBL1/p107 expression involving different components of signaling pathways controlled by Ca2+ levels, including CaMKs and calpain, pointing out a significant difference with the mechanisms modulating the close family member RBL2/p130.
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Affiliation(s)
- Elisa Ventura
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (E.V.); (A.G.)
| | - Carmelina Antonella Iannuzzi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, I-80131 Napoli, Italy; (C.A.I.); (F.P.)
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCCS, Fondazione G. Pascale, I-80131 Napoli, Italy; (C.A.I.); (F.P.)
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (E.V.); (A.G.)
- Department of Medical Biotechnologies, University of Siena, I-53100 Siena, Italy
| | - Andrea Morrione
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA; (E.V.); (A.G.)
- Correspondence: ; Tel.: +215-204-2450
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Abstract
Perfectly orchestrated periodic gene expression during cell cycle progression is essential for maintaining genome integrity and ensuring that cell proliferation can be stopped by environmental signals. Genetic and proteomic studies during the past two decades revealed remarkable evolutionary conservation of the key mechanisms that control cell cycle-regulated gene expression, including multisubunit DNA-binding DREAM complexes. DREAM complexes containing a retinoblastoma family member, an E2F transcription factor and its dimerization partner, and five proteins related to products of Caenorhabditis elegans multivulva (Muv) class B genes lin-9, lin-37, lin-52, lin-53, and lin-54 (comprising the MuvB core) have been described in diverse organisms, from worms to humans. This review summarizes the current knowledge of the structure, function, and regulation of DREAM complexes in different organisms, as well as the role of DREAM in human disease. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Hayley Walston
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA;
| | - Audra N Iness
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA
| | - Larisa Litovchick
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia 23298, USA; .,Division of Hematology, Oncology and Palliative Care, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, USA.,Massey Cancer Center, Richmond, Virginia 23298, USA
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