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Yu S, Zhou Z, Liang Z, Ruan C, Bai L, Pi Y. Silencing lncRNA GABPB1-AS1 alleviates cerebral ischemia reperfusion injury through the miR-641/NUCKS1 axis. Am J Transl Res 2024; 16:2963-2972. [PMID: 39114718 PMCID: PMC11301495 DOI: 10.62347/eagk7098] [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: 04/07/2024] [Accepted: 06/04/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVE To investigate the possible mechanism of lncRNA GA binding protein transcription factor beta subunit 1 antisense RNA 1 (GABPB1-AS1) in cerebral ischemia/reperfusion (CI/R) injury. METHODS RT-qPCR was applied to determine GABPB1-AS1 expression in oxygen-glucose deprivation/reoxygenation (OGD/R) cells. The targeting relationships between GABPB1-AS1 and miR-641, as well as between miR-641 and nuclear casein and cyclin-dependent kinase substrate 1 (NUCKS1) were examined by dual luciferase reporter assay. The protein expression of caspase-3, Bax, Bcl-2 and NUCKS1 was examined by western blot. Cell apoptosis was measured by flow cytometry (FCM) and western blot. Cell viability was evaluated by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RESULTS GABPB1-AS1 was significantly elevated in SH-SY5Y cells under OGD/R. Downregulation of GABPB1-AS1 accelerated cell viability and suppressed cell apoptosis. GABPB1-AS1 silencing reduced ROS and MDA levels in OGD/R-treated cells. Furthermore, miR-641 inhibitor aggravated damage from OGD/R, but GABPB1-AS1 silencing notably attenuated this effect. NUCKS1 was proven to be a target gene of miR-641. CONCLUSION GABPB1-AS1 silencing alleviated CI/R injury through the miR-641/NUCKS1 axis, indicating that GABPB1-AS1 might serve as a therapeutic target for CI/R injury.
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Affiliation(s)
- Shui Yu
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Zhangming Zhou
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Zhang Liang
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Chenbin Ruan
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Lei Bai
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
| | - Ying Pi
- Department of Neurosurgery, Dujiangyan People's Hospital Chengdu, Sichuan, China
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Reed TJ, Tyl MD, Tadych A, Troyanskaya OG, Cristea IM. Tapioca: a platform for predicting de novo protein-protein interactions in dynamic contexts. Nat Methods 2024; 21:488-500. [PMID: 38361019 PMCID: PMC11249048 DOI: 10.1038/s41592-024-02179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/12/2024] [Indexed: 02/17/2024]
Abstract
Protein-protein interactions (PPIs) drive cellular processes and responses to environmental cues, reflecting the cellular state. Here we develop Tapioca, an ensemble machine learning framework for studying global PPIs in dynamic contexts. Tapioca predicts de novo interactions by integrating mass spectrometry interactome data from thermal/ion denaturation or cofractionation workflows with protein properties and tissue-specific functional networks. Focusing on the thermal proximity coaggregation method, we improved the experimental workflow. Finely tuned thermal denaturation afforded increased throughput, while cell lysis optimization enhanced protein detection from different subcellular compartments. The Tapioca workflow was next leveraged to investigate viral infection dynamics. Temporal PPIs were characterized during the reactivation from latency of the oncogenic Kaposi's sarcoma-associated herpesvirus. Together with functional assays, NUCKS was identified as a proviral hub protein, and a broader role was uncovered by integrating PPI networks from alpha- and betaherpesvirus infections. Altogether, Tapioca provides a web-accessible platform for predicting PPIs in dynamic contexts.
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Affiliation(s)
- Tavis J Reed
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Matthew D Tyl
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Alicja Tadych
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Olga G Troyanskaya
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Princeton, NJ, USA.
- Department of Computer Science, Princeton University, Princeton, NJ, USA.
- Flatiron Institute, Simons Foundation, New York City, NY, USA.
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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3
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Booms A, Pierce SE, van der Schans EJ, Coetzee GA. Parkinson's disease risk enhancers in microglia. iScience 2024; 27:108921. [PMID: 38323005 PMCID: PMC10845915 DOI: 10.1016/j.isci.2024.108921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/05/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Genome-wide association studies have identified thousands of single nucleotide polymorphisms that associate with increased risk for Parkinson's disease (PD), but the functions of most of them are unknown. Using assay for transposase-accessible chromatin (ATAC) and H3K27ac chromatin immunoprecipitation (ChIP) sequencing data, we identified 73 regulatory elements in microglia that overlap PD risk SNPs. To determine the target genes of a "risk enhancer" within intron two of SNCA, we used CRISPR-Cas9 to delete the open chromatin region where two PD risk SNPs reside. The loss of the enhancer led to reduced expression of multiple genes including SNCA and the adjacent gene MMRN1. It also led to expression changes of genes involved in glucose metabolism, a process that is known to be altered in PD patients. Our work expands the role of SNCA in PD and provides a connection between PD-associated genetic variants and underlying biology that points to a risk mechanism in microglia.
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Affiliation(s)
- Alix Booms
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
- Van Andel Institute graduate student, Grand Rapids, MI 49503, USA
| | - Steven E. Pierce
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Gerhard A. Coetzee
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
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Flanagan T, Foster TP, Galbato TE, Lum PY, Louie B, Song G, Halberstadt AL, Billac GB, Nichols CD. Serotonin-2 Receptor Agonists Produce Anti-inflammatory Effects through Functionally Selective Mechanisms That Involve the Suppression of Disease-Induced Arginase 1 Expression. ACS Pharmacol Transl Sci 2024; 7:478-492. [PMID: 38357283 PMCID: PMC10863441 DOI: 10.1021/acsptsci.3c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/16/2024]
Abstract
Functional selectivity in the context of serotonin 2A (5-HT2A) receptor agonists is often described as differences psychedelic compounds have in the activation of Gq vs β-arrestin signaling in the brain and how that may relate to inducing psychoactive and hallucinatory properties with respect to each other. However, the presence of 5-HT2A receptors throughout the body in several cell types, including endothelial, endocrine, and immune-related tissues, suggests that functional selectivity may exist in the periphery as well. Here, we examine functional selectivity between two 5-HT2A receptor agonists of the phenylalkylamine class: (R)-2,5-dimethoxy-4-iodoamphetamine [(R)-DOI] and (R)-2,5-dimethoxy-4-trifluoromethylamphetamine [(R)-DOTFM]. Despite comparable in vitro activity at the 5-HT2A receptor as well as similar behavioral potency, (R)-DOTFM does not exhibit an ability to prevent inflammation or elevated airway hyperresponsiveness (AHR) in an acute murine ovalbumin-induced asthma model as does (R)-DOI. Furthermore, there are distinct differences between protein expression and inflammatory-related gene expression in pulmonary tissues between the two compounds. Using (R)-DOI and (R)-DOTFM as tools, we further elucidated the anti-inflammatory mechanisms underlying the powerful anti-inflammatory effects of certain psychedelics and identified key mechanistic components of the anti-inflammatory effects of psychedelics, including suppression of arginase 1 expression.
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Affiliation(s)
- Thomas
W. Flanagan
- Department
of Pharmacology and Experimental TherapeuticsLouisiana State University Health Sciences CenterNew Orleans, Louisiana70112, United States
| | - Timothy P. Foster
- Department
of Microbiology, Immunology, and ParasitologyLouisiana State University Health Sciences CenterNew Orleans, Louisiana70112, United States
| | - Thomas E. Galbato
- Department
of Microbiology, Immunology, and ParasitologyLouisiana State University Health Sciences CenterNew Orleans, Louisiana70112, United States
| | - Pek Yee Lum
- Auransa
Inc.Palo Alto, California94301, United States
| | - Brent Louie
- Auransa
Inc.Palo Alto, California94301, United States
| | - Gavin Song
- Auransa
Inc.Palo Alto, California94301, United States
| | - Adam L. Halberstadt
- Department
of PsychiatryUniversity of San Diego, California, San Diego, California92093, United States
| | - Gerald B. Billac
- Department
of Pharmacology and Experimental TherapeuticsLouisiana State University Health Sciences CenterNew Orleans, Louisiana70112, United States
| | - Charles D. Nichols
- Department
of Pharmacology and Experimental TherapeuticsLouisiana State University Health Sciences CenterNew Orleans, Louisiana70112, United States
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5
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Tang R, Lin W, Shen C, Hu X, Yu L, Meng T, Zhang L, Eggenhuizen PJ, Ooi JD, Jin P, Ding X, Xiao X, Zhong Y. Single-cell transcriptomics uncover hub genes and cell-cell crosstalk in patients with hypertensive nephropathy. Int Immunopharmacol 2023; 125:111104. [PMID: 37897949 DOI: 10.1016/j.intimp.2023.111104] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/15/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
Hypertensive nephropathy (HTN) is one of the leading causes of end-stage renal disease, yet the molecular mechanisms are still unknown. To explore novel mechanisms and gene targets for HTN, the gene expression profiles of renal biopsy samples obtained from 2 healthy living donor controls and 5 HTN patients were determined by single-cell RNA sequencing. Key hub genes expression were validated by the Nephroseq v5 platform. The HTN endothelium upregulated cellular adhesion genes (ICAM2 and CEACAM1), inflammatory genes (ETS2 and IFI6) and apoptosis related genes (CNN3). Proximal tubules in HTN highly expressed hub genes including BBOX1, TPM1, TMSB10, SDC4, and NUP58, which might be potential novel targets for proximal tubular injury. The upregulated genes in tubules of HTN were mainly participating in inflammatory signatures including IFN-γ signature, NF-κB signaling, IL-12 signaling and Wnt signaling pathway. Receptor-ligand interaction analysis indicated potential cell-cell crosstalk between endothelial cells or mesangial cells with other renal resident cells in HTN. Together, our data identify a distinct cell-specific gene expression profile, pathogenic inflammatory signaling and potential cell-cell communications between endothelial cells or mesangial cells with other renal resident cells in HTN. These findings may provide a promising novel landscape for mechanisms and treatment of human HTN.
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Affiliation(s)
- Rong Tang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Lin
- Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chanjuan Shen
- Department of Hematology, The Affiliated Zhuzhou Hospital Xiangya Medical College, Central South University, Zhuzhou, Hunan, China
| | - Xueling Hu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Leilin Yu
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Department of Nephrology, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, China
| | - Ting Meng
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Zhang
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Peter J Eggenhuizen
- Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton, VIC, Australia
| | - Joshua D Ooi
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Centre for Inflammatory Diseases, Monash University Department of Medicine, Monash Medical Centre, Clayton, VIC, Australia
| | - Peng Jin
- Department of Organ Transplantation, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiang Ding
- Department of Organ Transplantation, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangcheng Xiao
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yong Zhong
- Department of Nephrology, Xiangya Hospital, Central South University, Changsha, Hunan, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD. A rat liver cell atlas reveals intrahepatic myeloid heterogeneity. iScience 2023; 26:108213. [PMID: 38026201 PMCID: PMC10651689 DOI: 10.1016/j.isci.2023.108213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 08/20/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
The large size and vascular accessibility of the laboratory rat (Rattus norvegicus) make it an ideal hepatic animal model for diseases that require surgical manipulation. Often, the disease susceptibility and outcomes of inflammatory pathologies vary significantly between strains. This study uses single-cell transcriptomics to better understand the complex cellular network of the rat liver, as well as to unravel the cellular and molecular sources of inter-strain hepatic variation. We generated single-cell and single-nucleus transcriptomic maps of the livers of healthy Dark Agouti and Lewis rat strains and developed a factor analysis-based bioinformatics analysis pipeline to study data covariates, such as strain and batch. Using this approach, we discovered transcriptomic variation within the hepatocyte and myeloid populations that underlie distinct cell states between rat strains. This finding will help provide a reference for future investigations on strain-dependent outcomes of surgical experiment models.
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Affiliation(s)
- Delaram Pouyabahar
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Sai W. Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Olivia I. Pezzutti
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Catia T. Perciani
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xinle Wang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xue-Zhong Ma
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Chao Jiang
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Damra Camat
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Trevor Chung
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Manmeet Sekhon
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Justin Manuel
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Xu-Chun Chen
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Ian D. McGilvray
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
| | - Sonya A. MacParland
- Ajmera Transplant Centre, Toronto General Hospital Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Gary D. Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON, Canada
- The Multiscale Human Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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7
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Zheng S, Ji R, He H, Li N, Han C, Han J, Li X, Zhang L, Wang Y, Zhao W. NUCKS1, a LINC00629-upregulated gene, facilitated osteosarcoma progression and metastasis by elevating asparagine synthesis. Cell Death Dis 2023; 14:489. [PMID: 37528150 PMCID: PMC10393983 DOI: 10.1038/s41419-023-06010-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 08/03/2023]
Abstract
Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) has been reported to play an oncogenic role in several cancers. However, the biological functions and regulatory mechanism of NUCKS1 in osteosarcoma have not been fully understood. In this study, we reported that NUCKS1 was significantly increased in osteosarcoma. Depletion of NUCKS1 decreased osteosarcoma cell proliferation and metastasis in vivo and in vitro. Overexpression of NUCKS1 accelerated osteosarcoma cell aggressiveness. Mechanistically, NUCKS1 facilitated asparagine (Asn) synthesis by transcriptionally upregulating asparagine synthetase (ASNS) expression and elevating the levels of Asn in osteosarcoma cells, leading to increased cell growth and metastasis. Inhibition of ASNS or reduction of Asn decreased osteosarcoma cell aggressiveness and impaired the promoting effects of NUCKS1 on tumorigenesis and metastasis. Furthermore, we also found that by acting as a sponge for miR-4768-3p, LINC00629 promoted NUCKS1 expression. Collectively, our findings highlight the role of NUCKS1 in regulating asparagine metabolism and reveal that LINC00629 is an important regulator of NUCKS1 that contributes to NUCKS1 upregulation in osteosarcoma.
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Affiliation(s)
- Shuo Zheng
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China
| | - Renchen Ji
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China
| | - Hongtao He
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China
| | - Na Li
- National-Local Joint Engineering Research Center for Drug-Research and Development (R&D) of Neurodegenerative Diseases, Dalian Medical University, Dalian, 116044, People's Republic of China
| | - Chuanchun Han
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China
| | - Jian Han
- Department of Orthopedics, The Third People's Hospital of Dalian, Dalian Medical University, Dalian, Liaoning, 116033, P.R. China
| | - Xiaodong Li
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China.
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China.
| | - Lu Zhang
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China.
| | - Yuan Wang
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China.
| | - Wenzhi Zhao
- The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, 116044, P.R. China.
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miR-641 Inhibited Cell Proliferation and Induced Apoptosis by Targeting NUCKS1/PI3K/AKT Signaling Pathway in Breast Cancer. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5203839. [PMID: 35069784 PMCID: PMC8769837 DOI: 10.1155/2022/5203839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 01/30/2023]
Abstract
Objective Studies revealed an important role of microRNAs (miRNAs) in multiple cancers, including breast cancer. In the present study, we evaluated the role and function of miR-641 in breast cancer. Methods The expression level of miR-641 in breast cancer cell lines (Hs-578T, MCF7, HCC1937, and MAD-MB-231) was determined by real-time PCR. Functional analyses, including CCK-8 assay, transwell assay, wound-healing assay, and apoptosis detection, were carried out to explore the roles of miRNA-641 in malignant behaviors of breast cancer. Luciferase report assay was used to investigate the regulatory association of miRNA-641 with its potential targets. Results The expression levels of miR-641 were downregulated, while the expression levels of nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) were increased in breast cancer cell lines. The in vitro results showed that miR-641 repressed proliferation and migration/invasion and promoted apoptosis of breast cancer cells. NUCKS1, a positive regulator of phosphatidylinositol-3-kinases (PI3K)/protein-serine-threonine kinase (AKT) pathway, was confirmed as a direct target of miR-641. The of treatment of the PI3K agonist, 740Y-P, could abrogate the antioncogenic potentials of miR-641 in breast cancer cells. Conclusion miR-641 functioned as a tumor suppressor through the PI3K/AKT signaling pathway via targeting NUCKS1 in breast cancer.
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Pandini C, Garofalo M, Rey F, Garau J, Zucca S, Sproviero D, Bordoni M, Berzero G, Davin A, Poloni TE, Pansarasa O, Carelli S, Gagliardi S, Cereda C. MINCR: A long non-coding RNA shared between cancer and neurodegeneration. Genomics 2021; 113:4039-4051. [PMID: 34662711 DOI: 10.1016/j.ygeno.2021.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 01/21/2023]
Abstract
The multitasking nature of lncRNAs allows them to play a central role in both physiological and pathological conditions. Often the same lncRNA can participate in different diseases. Specifically, the MYC-induced Long non-Coding RNA MINCR is upregulated in various cancer types, while downregulated in Amyotrophic Lateral Sclerosis patients. Therefore, this work aims to investigate MINCR potential mechanisms of action and its implications in cancer and neurodegeneration in relation to its expression levels in SH-SY5Y cells through RNA-sequencing approach. Our results show that MINCR overexpression causes massive alterations in cancer-related genes, leading to disruption in many fundamental processes, such as cell cycle and growth factor signaling. On the contrary, MINCR downregulation influences a small number of genes involved in different neurodegenerative disorders, mostly concerning RNA metabolism and inflammation. Thus, understanding the cause and functional consequences of MINCR deregulation gives important insights on potential pathogenetic mechanisms both in cancer and in neurodegeneration.
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Affiliation(s)
- Cecilia Pandini
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Maria Garofalo
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy; Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia 27100, Italy
| | - Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan 20157, Italy; Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano 20157, Italy
| | - Jessica Garau
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | | | - Daisy Sproviero
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Matteo Bordoni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di Milano, Milano 20157, Italy
| | - Giulia Berzero
- Neuroncology Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Annalisa Davin
- Laboratory of Neurobiology and Neurogenetic, Golgi Cenci Foundation, Abbiategrasso, Milan 20081, Italy
| | - Tino Emanuele Poloni
- Neurology and Neuropathololgy Department Golgi-Cenci Foundation & ASP Golgi-Redaelli, Abbiategrasso, Milan 20081, Italy
| | - Orietta Pansarasa
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan 20157, Italy; Pediatric Clinical Research Center Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano 20157, Italy
| | - Stella Gagliardi
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy.
| | - Cristina Cereda
- Genomic and post-Genomic Unit, IRCCS Mondino Foundation, Pavia 27100, Italy.
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10
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Wen X, Xu X, Luo X, Yin J, Liang C, Zhu J, Nong X, Zhu X, Ning F, Gu S, Xiong S, Fu J, Zhu D, Dai Z, Lv D, Lin Z, Lin J, Li Y, Ma G, Wang Y. Nucks1 gene polymorphism rs823114 is associated with the positive symptoms and neurocognitive function of patients with schizophrenia in parts of southern China. Psychiatr Genet 2021; 31:119-125. [PMID: 34030174 PMCID: PMC8265546 DOI: 10.1097/ypg.0000000000000285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/23/2021] [Indexed: 01/14/2023]
Abstract
Nuclear casein kinase and cyclin-dependent kinase substrate 1 (nucks1) are considered a potential susceptibility gene for certain neurological diseases, such as Parkinson's disease (PD). In our study, we genotyped three single nucleotide polymorphisms (SNPs) (rs4951261, rs823114 and rs951366) of the nucks1 gene in 774 schizophrenic patients and 819 healthy controls using the improved multiplex ligation detection reaction (imLDR) technique. Furthermore, we also studied the relationship between the above SNPs and the clinical psychiatric symptoms and neurocognitive function of the patients. Genotype distributions and allele frequencies of these SNPs showed no significant differences and were found between patients and healthy controls. However, in an analysis of the positive symptom score of rs823114 among male patients, we found that the score of the A/A genotype was lower than that of the G/A+G/G genotypes (P = 0.001, P(corr) = 0.003]. Additionally, we also found that among the female patients, G allele carriers with rs823114 had lower semantic fluency scores than subjects with the A/A genotype (P = 0.010, P(corr) = 0.030]. Our data show for the first time that rs823114 polymorphism of nucks1 may affect positive symptoms and neurocognitive function in patients with schizophrenia in parts of southern China.
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Affiliation(s)
- Xia Wen
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan
| | - Xusan Xu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan
| | - Xudong Luo
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Jinwen Yin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Chunmei Liang
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | | | | | - Xiudeng Zhu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | - Fan Ning
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | - Shanshan Gu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | - Susu Xiong
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Jiawu Fu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | - Dongjian Zhu
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Zhun Dai
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Dong Lv
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Zhixiong Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - Juda Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang
| | - You Li
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
| | - Guoda Ma
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjian
- Maternal and Children’s Health Research Institute, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan
| | - Yajun Wang
- Medical Genetics Laboratory, Shunde Women and Children’s Hospital, Guangdong Medical University, Foshan, China
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11
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Ma H, Xu J, Zhao R, Qi Y, Ji Y, Ma K. Upregulation of NUCKS1 in Lung Adenocarcinoma is Associated with a Poor Prognosis. Cancer Invest 2021; 39:435-444. [PMID: 33683970 DOI: 10.1080/07357907.2021.1899199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
To evaluate the clinicopathologic features and survival analysis of NUCKS1 expression in human lung adenocarcinoma (LA), we used bioinformatic methods to obtain NUCKS1 gene status and correlated it with prognosis in LA. We compared NUCKS1 expression in 70 samples of LA with intrinsically normal lung alveoli (NLA) by immunohistochemistry, and analyzed their clinicopathologic features. NUCKS1 was overexpressed in LA components(LACs) relative to NLA, and was significantly correlated to patient with 5-year disease-free survival (DFS) and overall survival(OS). Elevated NUCKS1 expression in LACs was shown to be an independent prognostic indicator for OS and a biomarker in LA.
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Affiliation(s)
- Hongfei Ma
- Department of Thoracic Surgery, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, China.,Department of Thoracic Surgery, The Affiliated Hospital, Qingdao University, Qingdao, China
| | - Jing Xu
- Department of Pathology, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Ruixia Zhao
- Department of Pathology, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Yongyun Qi
- Department of Pathology, Affiliated Qingdao Central Hospital, Qingdao University, Qingdao, China
| | - Yong Ji
- Medical Department, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Shenzhen, China
| | - Kai Ma
- Department of Thoracic Surgery, The Affiliated Hospital, Qingdao University, Qingdao, China.,Department of Thoracic Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
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12
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Zhao S, Wang B, Ma Y, Kuang J, Liang J, Yuan Y. NUCKS1 Promotes Proliferation, Invasion and Migration of Non-Small Cell Lung Cancer by Upregulating CDK1 Expression. Cancer Manag Res 2021; 12:13311-13323. [PMID: 33380837 PMCID: PMC7769091 DOI: 10.2147/cmar.s282181] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/18/2020] [Indexed: 12/14/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) is a predominant type of lung cancer with a high mortality rate. Objective The aim of this study is to investigate the roles of nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) in NSCLC and to identify the potential mechanisms. Materials and Methods The expression of NUCKS1 in several NSCLC cells was detected firstly. Then, NUCKS1 was overexpressed or silenced in both A549 and NCI-H460 cells, where cell proliferation, invasion and migration were, respectively, determined, using CCK-8, colony formation assay, transwell and wound healing assays. Cell cycle analysis was performed, and the expression-associated proteins were detected by Western blotting. Subsequently, NCI-H460 cells with NUCKS1 overexpression for the subsequent tumor-bearing experiment. And the NUCKS1 expression in tumor tissues was measured by means of immunohistochemistry and Western blotting. Additionally, the STRING database predicted that Cyclin-Dependent Kinase 1 (CDK1) would bind to NUSK1, which was verified by the co-immunoprecipitation assay. Then, CDK1 was silenced by transfection with short hairpin RNA (shRNA)-CDK-1 or by exposure to CDK1 inhibitor p2767-00. And the biological characteristics of proliferation, invasion and migration were examined. Results Results indicated that NUCKS1 was overly expressed in NSCLC cells, and its overexpression promoted proliferation, invasion and migration of both A549 and NCI-H460 cells while NUCKS1 knockdown displayed the opposite effects. Moreover, the results of the xenograft experiments revealed that NUCKS1-upregulation promoted the tumor growth. Furthermore, the immunoprecipitation assay verified CDK1’s interaction with NUCKS1, and CDK1 knockdown alleviates the impact of NUCKS1 overexpression on NSCLC cell proliferation, invasion and migration. Conclusion Taken together, these findings demonstrated that NUCKS1 promotes proliferation, invasion and migration of NSCLC by upregulating CDK1, providing a novel putative target for the clinical treatment of NSCLC.
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Affiliation(s)
- Shufen Zhao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou City, Guangdong Province 510515, People's Republic of China
| | - Baiyao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou City, Guangdong Province 510095, People's Republic of China
| | - Yanning Ma
- Shunde Hospital, Southern Medical University, Foshan City, Guangdong Province 528308, People's Republic of China
| | - Junjie Kuang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou City, Guangdong Province 510515, People's Republic of China
| | - Jiyun Liang
- Shunde Hospital, Southern Medical University, Foshan City, Guangdong Province 528308, People's Republic of China
| | - Yawei Yuan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou City, Guangdong Province 510515, People's Republic of China.,Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou City, Guangdong Province 510095, People's Republic of China
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13
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Mukherjee S, Biswas D, Gadre R, Jain P, Syed N, Stylianou J, Zeng Q, Mahadevan A, Epari S, Shetty P, Moiyadi A, Roy Ball G, Srivastava S. Comprehending Meningioma Signaling Cascades Using Multipronged Proteomics Approaches & Targeted Validation of Potential Markers. Front Oncol 2020; 10:1600. [PMID: 32974197 PMCID: PMC7482667 DOI: 10.3389/fonc.2020.01600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 12/29/2022] Open
Abstract
Meningiomas are one of the most prevalent primary brain tumors. Our study aims to obtain mechanistic insights of meningioma pathobiology using mass spectrometry-based label-free quantitative proteome analysis to identifying druggable targets and perturbed pathways for therapeutic intervention. Label-free based proteomics study was done from peptide samples of 21 patients and 8 non-tumor controls which were followed up with Phosphoproteomics to identify the kinases and phosphorylated components of the perturbed pathways. In silico approaches revealed perturbations in extracellular matrix remodeling and associated cascades. To assess the extent of influence of Integrin and PI3K-Akt pathways, we used an Integrin Linked Kinase inhibitor on patient-derived meningioma cell line and performed a transcriptomic analysis of the components. Furthermore, we designed a Targeted proteomics assay which to the best of our knowledge for very first-time enables identification of peptides from 54 meningioma patients via SRM assay to validate the key proteins emerging from our study. This resulted in the identification of peptides from CLIC1, ES8L2, and AHNK many of which are receptors and kinases and are difficult to be characterized using conventional approaches. Furthermore, we were also able to monitor transitions for proteins like NEK9 and CKAP4 which have been reported to be associated with meningioma pathobiology. We believe, this study can aid in designing peptide-based validation assays for meningioma patients as well as IHC studies for clinical applications.
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Affiliation(s)
- Shuvolina Mukherjee
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Deeptarup Biswas
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Rucha Gadre
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
| | - Pooja Jain
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Nelofer Syed
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, United Kingdom
| | - Julianna Stylianou
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, United Kingdom
| | - Qingyu Zeng
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, United Kingdom
| | - Anita Mahadevan
- Department of Neuropathology, Human Brain Tissue Repository (Brain Bank), NIMHANS, Bengaluru, India
| | - Sridhar Epari
- Department of Pathology, Tata Memorial Centre, Mumbai, India
| | - Prakash Shetty
- Department of Neurosurgery, Tata Memorial Centre, Mumbai, India
| | | | - Graham Roy Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Sanjeeva Srivastava
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India
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14
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Singh S, Seth PK. Functional association between NUCKS1 gene and Parkinson disease: A potential susceptibility biomarker. Bioinformation 2019; 15:548-556. [PMID: 31719764 PMCID: PMC6822519 DOI: 10.6026/97320630015548] [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: 07/30/2019] [Accepted: 08/14/2019] [Indexed: 12/26/2022] Open
Abstract
Several Genome Wide Association Studies (GWASs) have reported that PARK16 gene locus possibly regulate the risk of Parkinson's disease (PD). It contains functionally interesting candidate genes for PD, regulated by number of SNPs. In present study rs823093 polymorphism in NUCKS1 gene has been evaluated as significant performer in PD though its mechanism is not yet known. Here various regulatory and functional analyses were performed using computational tools and information from databases. The rs823093 variant was predicted to locate in enhancer histone marks in blood and have strong transcription in various parts of brain, heart, kidney and liver. PhenoScanner (a database of human genotype-phenotype associations) identified significant associations of this variant with many other diseases and phenotypic conditions as well. Gene expression analysis shows significant association with multiple human tissues and multiple genes together with NUCKS1. Further, the post mortem brain samples showed diverse expressions of NUCKS1 gene in PD patients compared to healthy samples. Besides, the metabolite analysis shows significant association with serotonin a known neurotransmitter, and other 15 metabolites. In addition, NUCKS1 also showed co-expression with ZNF43 and PLIN1 genes involved in cell cycle regulation presume their association in PD. Thus, these data links NUCKS1 gene as a potential disease susceptibility biomarker for PD.
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Affiliation(s)
- Sarita Singh
- Biotech Park, Sector-G Jankipram, Kursi Road, Lucknow, India
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15
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Yuan X, Zhang M, Ao J, Zhen Z, Gao X, Li M. NUCKS1 is a novel regulator of milk synthesis in and proliferation of mammary epithelial cells via the mTOR signaling pathway. J Cell Physiol 2019; 234:15825-15835. [PMID: 30710349 DOI: 10.1002/jcp.28240] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/06/2019] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) is a highly phosphorylated nuclear protein ubiquitously expressed in vertebrates. NUCKS1 has been reported to be a key chromatin modifier and transcriptional regulator of a number of signaling pathways, but the physiological role and detailed mechanism are still limited. In this study, we assessed the role of NUCKS1 on milk synthesis in and proliferation of mammary epithelial cells from a dairy cow. NUCKS1 was located in the nucleus of mammary epithelial cells, and the expression of NUCKS1 was stimulated by amino acids (Met and Leu) and hormones (estrogen and prolactin). Gene function study approaches detected that NUCKS1 positively regulated milk protein, milk fat, and lactose synthesis, and also increased the cell number, cell viability, and cell cycle progression. NUCKS1 mediated the stimulation of amino acids and hormones on the messenger RNA expression of the mechanistic target of rapamycin (mTOR), SREBP-1c, and Cyclin D1. The expression of NUCKS1 is dramatically higher in mouse mammary tissue of lactating period, compared with that in puberty and dry period. Taken together, these results reveal that NUCKS1 is a new mediator of milk synthesis in and proliferation of mammary epithelial cells via regulating the mTOR signaling pathway.
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Affiliation(s)
- Xiaohan Yuan
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Minghui Zhang
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jinxia Ao
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Zhen Zhen
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Xuejun Gao
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
| | - Meng Li
- The Key Laboratory of Dairy Science of Education Ministry, College of Life Science, Northeast Agricultural University, Harbin, China
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16
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Cruz-Rivera YE, Perez-Morales J, Santiago YM, Gonzalez VM, Morales L, Cabrera-Rios M, Isaza CE. A Selection of Important Genes and Their Correlated Behavior in Alzheimer's Disease. J Alzheimers Dis 2019; 65:193-205. [PMID: 30040709 PMCID: PMC6087431 DOI: 10.3233/jad-170799] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In 2017, approximately 5 million Americans were living with Alzheimer’s disease (AD), and it is estimated that by 2050 this number could increase to 16 million. In this study, we apply mathematical optimization to approach microarray analysis to detect differentially expressed genes and determine the most correlated structure among their expression changes. The analysis of GSE4757 microarray dataset, which compares expression between AD neurons without neurofibrillary tangles (controls) and with neurofibrillary tangles (cases), was casted as a multiple criteria optimization (MCO) problem. Through the analysis it was possible to determine a series of Pareto efficient frontiers to find the most differentially expressed genes, which are here proposed as potential AD biomarkers. The Traveling Sales Problem (TSP) model was used to find the cyclical path of maximal correlation between the expression changes among the genes deemed important from the previous stage. This leads to a structure capable of guiding biological exploration with enhanced precision and repeatability. Ten genes were selected (FTL, GFAP, HNRNPA3, COX1, ND2, ND3, ND4, NUCKS1, RPL41, and RPS10) and their most correlated cyclic structure was found in our analyses. The biological functions of their products were found to be linked to inflammation and neurodegenerative diseases and some of them had not been reported for AD before. The TSP path connects genes coding for mitochondrial electron transfer proteins. Some of these proteins are closely related to other electron transport proteins already reported as important for AD.
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Affiliation(s)
- Yazeli E Cruz-Rivera
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Jaileene Perez-Morales
- Department of Basic Science-Biochemistry Division, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Yaritza M Santiago
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Valerie M Gonzalez
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Luisa Morales
- Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico
| | - Mauricio Cabrera-Rios
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico
| | - Clara E Isaza
- The Applied Optimization Group/Department of Industrial Engineering, University of Puerto Rico, Mayagüez Campus, Mayagüez, Puerto Rico.,Public Health Program, Ponce Health Sciences University, Ponce, Puerto Rico
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