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Yan Q, Su X, Chen Y, Wang Z, Han W, Xia Q, Mao Y, Si J, Li H, Duan S. LINC00941: a novel player involved in the progression of human cancers. Hum Cell 2024; 37:167-180. [PMID: 37995050 DOI: 10.1007/s13577-023-01002-5] [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: 07/18/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
LINC00941, also known as lncRNA-MUF, is an intergenic non-coding RNA located on chromosome 12p11.21. It actively participates in a complex competing endogenous RNA network, regulating the expression of microRNA and its downstream proteins. Through transcriptional and post-transcriptional regulation, LINC00941 plays a vital role in multiple signaling pathways, influencing cell behaviors such as tumor cell proliferation, epithelial-mesenchymal transition, migration, and invasion. Noteworthy is its consistently high expression in various tumor types, closely correlating with clinicopathological features and cancer prognoses. Elevated LINC00941 levels are associated with adverse clinical outcomes, including increased tumor size, extensive lymphatic metastasis, and distant metastasis, leading to poorer survival rates across different cancers. Additionally, LINC00941 and its associated genes are linked to various targeted drugs available in the market. In this comprehensive review, we systematically summarize existing studies, detailing LINC00941's differential expression, clinicopathological and prognostic implications, regulatory mechanisms, and associated therapeutic drugs. Our analysis includes relevant charts and incorporates bioinformatics analyses to verify LINC00941's differential expression in pan-cancer and explore potential transcriptional regulation patterns of downstream targets. This work not only establishes a robust data foundation but also guides future research directions. Given its potential as a significant cancer biomarker and therapeutic target, further investigation into LINC00941's differential expression and regulatory mechanisms is essential.
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Affiliation(s)
- Qibin Yan
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
| | - Xinming Su
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yunzhu Chen
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Zehua Wang
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Wenbo Han
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qing Xia
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Yunan Mao
- Department of Pharmacy, Hangzhou City University School of Medicine, Hangzhou, Zhejiang, China
| | - Jiahua Si
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Hanbing Li
- Institute of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China.
| | - Shiwei Duan
- Department of Clinical Medicine, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China.
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2
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Reggi E, Kaiser S, Sahnane N, Uccella S, La Rosa S, Diviani D. AKAP2-anchored protein phosphatase 1 controls prostatic neuroendocrine carcinoma cell migration and invasion. Biochim Biophys Acta Mol Basis Dis 2024; 1870:166916. [PMID: 37827203 DOI: 10.1016/j.bbadis.2023.166916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/20/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Prostate cancer (PC) is the second leading cause of cancer-related death in men. The growth of primary prostate cancer cells relies on circulating androgens and thus the standard therapy for the treatment of localized and advanced PC is the androgen deprivation therapy. Prostatic neuroendocrine carcinoma (PNEC) is an aggressive and highly metastatic subtype of prostate cancer, which displays poor prognosis and high lethality. Most of PNECs develop from prostate adenocarcinoma in response to androgen deprivation therapy, however the mechanisms involved in this transition and in the elevated biological aggressiveness of PNECs are poorly defined. Our current findings indicate that AKAP2 expression is dramatically upregulated in PNECs as compared to non-cancerous prostate tissues. Using a PNEC cell model, we could show that AKAP2 is localized both intracellularly and at the cell periphery where it colocalizes with F-actin. AKAP2 and F-actin interact directly through a newly identified actin-binding domain located on AKAP2. RNAi-mediated silencing of AKAP2 promotes the phosphorylation and deactivation of cofilin, a protein involved in actin turnover. This effect correlates with a significant reduction in cell migration and invasion. Co-immunoprecipitation experiments and proximity ligation assays revealed that AKAP2 forms a complex with the catalytic subunit of protein phosphatase 1 (PP1) in PNECs. Importantly, AKAP2-mediated anchoring of PP1 to the actin cytoskeleton regulates cofilin dephosphorylation and activation, which, in turn, enhances F-actin dynamics and favors migration and invasion. In conclusion, this study identified AKAP2 as an anchoring protein overexpressed in PNECs that controls cancer cell invasive properties by regulating cofilin phosphorylation.
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Affiliation(s)
- Erica Reggi
- Department of Biomedical Sciences, Faculty of Biology et Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Simon Kaiser
- Department of Biomedical Sciences, Faculty of Biology et Medicine, University of Lausanne, 1011 Lausanne, Switzerland
| | - Nora Sahnane
- Unit of Pathology, Department of Oncology, ASST Sette Laghi, Varese, Italy
| | - Silvia Uccella
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; Pathology Service, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS), Humanitas Research Hospital, Milan, Italy
| | - Stefano La Rosa
- Unit of Pathology, Department of Oncology, ASST Sette Laghi, Varese, Italy; Unit of Pathology, Department of Medicine and Technological Innovation, University of Insubria, Varese, Italy
| | - Dario Diviani
- Department of Biomedical Sciences, Faculty of Biology et Medicine, University of Lausanne, 1011 Lausanne, Switzerland.
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3
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Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. The EstroGene Database Reveals Diverse Temporal, Context-Dependent, and Bidirectional Estrogen Receptor Regulomes in Breast Cancer. Cancer Res 2023; 83:2656-2674. [PMID: 37272757 PMCID: PMC10527051 DOI: 10.1158/0008-5472.can-23-0539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/21/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
As one of the most successful cancer therapeutic targets, estrogen receptor-α (ER/ESR1) has been extensively studied over the past few decades. Sequencing technological advances have enabled genome-wide analysis of ER action. However, comparison of individual studies is limited by different experimental designs, and few meta-analyses are available. Here, we established the EstroGene database through unified processing of data from 246 experiments including 136 transcriptomic, cistromic, and epigenetic datasets focusing on estradiol (E2)-triggered ER activation across 19 breast cancer cell lines. A user-friendly browser (https://estrogene.org/) was generated for multiomic data visualization involving gene inquiry under user-defined experimental conditions and statistical thresholds. Notably, annotation of metadata associated with public datasets revealed a considerable lack of experimental details. Comparison of independent RNA-seq or ER ChIP-seq data with the same design showed large variability and only strong effects could be consistently detected. Temporal estrogen response metasignatures were defined, and the association of E2 response rate with temporal transcriptional factors, chromatin accessibility, and heterogeneity of ER expression was evaluated. Unexpectedly, harmonizing 146 E2-induced transcriptomic datasets uncovered a subset of genes harboring bidirectional E2 regulation, which was linked to unique transcriptional factors and highly associated with immune surveillance in the clinical setting. Furthermore, the context dependent E2 response programs were characterized in MCF7 and T47D cell lines, the two most frequently used models in the EstroGene database. Collectively, the EstroGene database provides an informative and practical resource to the cancer research community to uniformly evaluate key reproducible features of ER regulomes and unravels modes of ER signaling. SIGNIFICANCE A resource database integrating 246 publicly available ER profiling datasets facilitates meta-analyses and identifies estrogen response temporal signatures, a bidirectional program, and model-specific biases.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Tianqin Li
- School of Computer Science, Carnegie Mellon University, Pittsburgh PA, USA
| | - Megan E. Yates
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yang Wu
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Amanda Ferber
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Lyuqin Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Daniel D. Brown
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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4
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Shindo S, Kakizaki S, Sakaki T, Kawasaki Y, Sakuma T, Negishi M, Shizu R. Phosphorylation of nuclear receptors: Novelty and therapeutic implications. Pharmacol Ther 2023:108477. [PMID: 37330113 DOI: 10.1016/j.pharmthera.2023.108477] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/20/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023]
Abstract
Nuclear receptors (NR) collectively regulate several biological functions in various organs. While NRs can be characterized by activation of the transcription of their signature genes, they also have other diverse roles. Although most NRs are directly activated by ligand binding, which induces cascades of events leading to gene transcription, some NRs are also phosphorylated. Despite extensive investigations, primarily focusing on unique phosphorylation of amino acid residues in different NRs, the role of phosphorylation in the biological activity of NRs in vivo has not been firmly established. Recent studies on the phosphorylation of conserved phosphorylation motifs within the DNA- and ligand-binding domains confirmed has indicated the physiologically relevance of NR phosphorylation. This review focuses on estrogen and androgen receptors, and highlights the concept of phosphorylation as a drug target.
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Affiliation(s)
- Sawako Shindo
- Department of Environmental Toxicology, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Satoru Kakizaki
- Department of Clinical Research, National Hospital Organization Takasaki General Medical Center, 36 Takamatsu-cho, Takasaki, Gunma 370-0829, Japan
| | - Toshiyuki Sakaki
- Department of Pharmaceutical Engineering, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Yuki Kawasaki
- Laboratory of Public Health, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaourui-machi, Takasaki, Gunma 370-0033, Japan
| | - Tsutomu Sakuma
- School of Pharmaceutical Sciences, Ohu University, Koriyama, Fukushima 963-8611, Japan
| | - Masahiko Negishi
- Reproductive and Developmental Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
| | - Ryota Shizu
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan.
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5
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Steinert ND, Jorgenson KW, Lin KH, Hermanson JB, Lemens JL, Hornberger TA. A novel method for visualizing in-vivo rates of protein degradation provides insight into how TRIM28 regulates muscle size. iScience 2023; 26:106526. [PMID: 37070069 PMCID: PMC10105291 DOI: 10.1016/j.isci.2023.106526] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023] Open
Abstract
Skeletal muscle size is controlled by the balance between protein synthesis and protein degradation. Given the essential role of skeletal muscle in maintaining a high quality of life, understanding the mechanisms that modulate this balance are of critical importance. Previously, we demonstrated that muscle-specific knockout of TRIM28 reduces muscle size and function and in the current study, we discovered that this effect is associated with an increase in protein degradation and a dramatic reduction in the expression of Mettl21c. Importantly, we also determined that overexpression of Mettl21c is sufficient to induce hypertrophy in both control and TRIM28 knockout muscles. Moreover, we developed a simple pulse-chase biorthogonal non-canonical amino acid tagging technique that enabled us to visualize the in vivo rate of protein degradation, and with this technique were able to conclude that the hypertrophic effect of Mettl21c is due, at least in part, to an inhibition of protein degradation.
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Affiliation(s)
- Nathaniel D. Steinert
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Kent W. Jorgenson
- Department of Molecular and Cellular Pharmacology, University of Wisconsin - Madison, Madison, WI, USA
- School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, USA
| | - Kuan-Hung Lin
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake B. Hermanson
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Jake L. Lemens
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
| | - Troy A. Hornberger
- Department of Comparative Biosciences, University of Wisconsin - Madison, Madison, WI, USA
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, USA
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6
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Li Z, Li T, Yates ME, Wu Y, Ferber A, Chen L, Brown DD, Carroll JS, Sikora MJ, Tseng GC, Oesterreich S, Lee AV. EstroGene database reveals diverse temporal, context-dependent and directional estrogen receptor regulomes in breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526388. [PMID: 36778377 PMCID: PMC9915613 DOI: 10.1101/2023.01.30.526388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
As one of the most successful cancer therapeutic targets, estrogen receptor-α (ER/ESR1) has been extensively studied in decade-long. Sequencing technological advances have enabled genome-wide analysis of ER action. However, reproducibility is limited by different experimental design. Here, we established the EstroGene database through centralizing 246 experiments from 136 transcriptomic, cistromic and epigenetic datasets focusing on estradiol-treated ER activation across 19 breast cancer cell lines. We generated a user-friendly browser ( https://estrogene.org/ ) for data visualization and gene inquiry under user-defined experimental conditions and statistical thresholds. Notably, documentation-based meta-analysis revealed a considerable lack of experimental details. Comparison of independent RNA-seq or ER ChIP-seq data with the same design showed large variability and only strong effects could be consistently detected. We defined temporal estrogen response metasignatures and showed the association with specific transcriptional factors, chromatin accessibility and ER heterogeneity. Unexpectedly, harmonizing 146 transcriptomic analyses uncovered a subset of E2-bidirectionally regulated genes, which linked to immune surveillance in the clinical setting. Furthermore, we defined context dependent E2 response programs in MCF7 and T47D cell lines, the two most frequently used models in the field. Collectively, the EstroGene database provides an informative resource to the cancer research community and reveals a diverse mode of ER signaling.
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Affiliation(s)
- Zheqi Li
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Tianqin Li
- School of Computer Science, Carnegie Mellon University, Pittsburgh PA, USA
| | - Megan E. Yates
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Medical Scientist Training Program, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Yang Wu
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Amanda Ferber
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Lyuqin Chen
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
| | - Daniel D. Brown
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jason S. Carroll
- Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Matthew J. Sikora
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - George C. Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh PA, USA
| | - Steffi Oesterreich
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V. Lee
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh PA, USA
- Women’s Cancer Research Center, Magee Women’s Research Institute, UPMC Hillman Cancer Center, Pittsburgh PA, USA
- Integrative Systems Biology Program, University of Pittsburgh, Pittsburgh, PA, USA
- Institute for Precision Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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7
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Cohen AO, Woo SH, Zhang J, Cho J, Ruiz ME, Gong J, Du R, Yarygina O, Jafri DZ, Bachelor MA, Finlayson MO, Soni RK, Hayden MS, Owens DM. Tbc1d10c is a selective, constitutive suppressor of the CD8 T-cell anti-tumor response. Oncoimmunology 2022; 11:2141011. [PMID: 36338148 PMCID: PMC9635554 DOI: 10.1080/2162402x.2022.2141011] [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] [Indexed: 11/06/2022] Open
Abstract
Cancer immunotherapy approaches target signaling pathways that are highly synonymous between CD4 and CD8 T-cell subsets and, therefore, often stimulate nonspecific lymphocyte activation, resulting in cytotoxicity to otherwise healthy tissue. The goal of our study was to identify intrinsic modulators of basic T lymphocyte activation pathways that could discriminately bolster CD8 anti-tumor effector responses. Using a Tbc1d10c null mouse, we observed marked resistance to a range of tumor types conferred by Tbc1d10c deficiency. Moreover, tumor-bearing Tbc1d10c null mice receiving PD-1 or CTLA-4 monotherapy exhibited a 33% or 90% cure rate, respectively. While Tbc1d10c was not expressed in solid tumor cells, Tbc1d10c disruption selectively augmented CD8 T-cell activation and cytotoxic effector responses and adoptive transfer of CD8 T cells alone was sufficient to recapitulate Tbc1d10c null tumor resistance. Mechanistically, Tbc1d10c suppressed CD8 T-cell activation and anti-tumor function by intersecting canonical NF-κB pathway activation via regulation of Map3k3-mediated IKKβ phosphorylation. Strikingly, none of these cellular or molecular perturbations in the NF-κB pathway were featured in Tbc1d10c null CD4 T cells. Our findings identify a Tbc1d10c-Map3k3-NF-κB signaling axis as a viable therapeutic target to promote CD8 T-cell anti-tumor immunity while circumventing CD4 T cell-associated cytotoxicity and NF-κB activation in tumor cells.
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Affiliation(s)
- Adrienne O. Cohen
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA
| | - Seung-Hyun Woo
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Discovery Biology Division, Velia Therapeutics, San Diego, CA, USA
| | - Junya Zhang
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA
| | - Jiyoon Cho
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Global Safety Assurance, Reckitt Benckiser Inc., Montvale, NJ, USA
| | - Marlon E. Ruiz
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Olink Proteomics, Los Angeles, CA90045, USA
| | - Jianli Gong
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Processing Cell Sciences, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Rong Du
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA
| | - Olga Yarygina
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA
| | - Danya Z. Jafri
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA
| | - Michael A. Bachelor
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Boston Scientific, Center for Biological Innovation, Global Preclinical Sciences, Marlborough, MA, USA
| | - Michael O. Finlayson
- Department of Systems Biology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY, USA,Simons Foundation, New York, NY10010, USA
| | - Rajesh K. Soni
- Proteomics & Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY10032, USA
| | - Matthew S. Hayden
- Department of Surgery, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - David M. Owens
- Department of Dermatology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY10032, USA,Department of Pathology & Cell Biology, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, New York, NY, USA,CONTACT David M. Owens Russ Berrie Medical Science Pavilion, 1150 St. Nicholas Ave., Room 312A, New York, NY10032
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8
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Ng ASN, Zhang S, Mak VCY, Zhou Y, Yuen Y, Sharma R, Lu Y, Zhuang G, Zhao W, Pang HH, Cheung LWT. AKTIP loss is enriched in ERα-positive breast cancer for tumorigenesis and confers endocrine resistance. Cell Rep 2022; 41:111821. [PMID: 36516775 PMCID: PMC9837615 DOI: 10.1016/j.celrep.2022.111821] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/30/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Recurrent deletion of 16q12.2 is observed in luminal breast cancer, yet the causal genomic alterations in this region are largely unknown. In this study, we identify that loss of AKTIP, which is located on 16q12.2, drives tumorigenesis of estrogen receptor alpha (ERα)-positive, but not ERα-negative, breast cancer cells and is associated with poor prognosis of patients with ERα-positive breast cancer. Intriguingly, AKTIP-depleted tumors have increased ERα protein level and activity. Cullin-associated and neddylation-dissociated protein 1 (CAND1), which regulates the cullin-RING E3 ubiquitin ligases, protects ERα from cullin 2-dependent proteasomal degradation. Apart from ERα signaling, AKTIP loss triggers JAK2-STAT3 activation, which provides an alternative survival signal when ERα is inhibited. AKTIP-depleted MCF7 cells and ERα-positive patient-derived organoids are more resistant to ERα antagonists. Importantly, the resistance can be overcome by co-inhibition of JAK2/STAT3. Together, our results highlight the subtype-specific functional consequences of AKTIP loss and provide a mechanistic explanation for the enriched AKTIP copy-number loss in ERα-positive breast cancer.
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Affiliation(s)
- Angel S N Ng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shibo Zhang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Victor C Y Mak
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yuan Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yin Yuen
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Rakesh Sharma
- Proteomics and Metabolomics Core, Center for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yiling Lu
- Department of Genomic Medicine, Division of Cancer Medicine, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200240, China
| | - Wei Zhao
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Herbert H Pang
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lydia W T Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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9
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Leach DA, Brooke GN, Bevan CL. Roles of steroid receptors in the lung and COVID-19. Essays Biochem 2021; 65:1025-1038. [PMID: 34328182 PMCID: PMC8628186 DOI: 10.1042/ebc20210005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 12/15/2022]
Abstract
COVID-19 symptoms and mortality are largely due to its devastating effects in the lungs. The disease is caused by the SARS (Severe Acute Respiratory Syndrome)-CoV-2 coronavirus, which requires host cell proteins such as ACE2 (angiotensin-converting enzyme 2) and TMPRSS2 (transmembrane serine protease 2) for infection of lung epithelia. The expression and function of the steroid hormone receptor family is important in many aspects that impact on COVID-19 effects in the lung - notably lung development and function, the immune system, and expression of TMPRSS2 and ACE2. This review provides a brief summary of current knowledge on the roles of the steroid hormone receptors [androgen receptor (AR), glucocorticoid receptor (GR), progesterone receptor (PR), mineralocorticoid receptor (MR) and oestrogen receptor (ER)] in the lung, their effects on host cell proteins that facilitate SARS-CoV-2 uptake, and provides a snapshot of current clinical trials investigating the use of steroid receptor (SR) ligands to treat COVID-19.
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Affiliation(s)
- Damien A. Leach
- Division of Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, U.K
| | - Greg N. Brooke
- Division of Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, U.K
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, U.K
| | - Charlotte L. Bevan
- Division of Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, U.K
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10
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Wang XL, Li L. Cell type-specific potential pathogenic genes and functional pathways in Alzheimer's Disease. BMC Neurol 2021; 21:381. [PMID: 34600516 PMCID: PMC8487122 DOI: 10.1186/s12883-021-02407-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/28/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is a pervasive age-related and highly heritable neurodegenerative disorder but has no effective therapy. The complex cellular microenvironment in the AD brain impedes our understanding of pathogenesis. Thus, a comprehensive investigation of cell type-specific responses in AD is crucial to provide precise molecular and cellular targets for therapeutic development. METHODS Here, we integrated analyzed 4,441 differentially expressed genes (DEGs) that were identified from 263,370 single-cells in cortex samples by single-nucleus RNA sequencing (snRNA-seq) between 42 AD-pathology subjects and 39 normal controls within 3 studies. DEGs were analyzed in microglia, astrocytes, oligodendrocytes, excitatory neurons, inhibitory neurons, and endothelial cells, respectively. In each cell type, we identified both common DEGs which were observed in all 3 studies, and overlapping DEGs which have been seen in at least 2 studies. Firstly, we showed the common DEGs expression and explained the biological functions by comparing with existing literature or multil-omics signaling pathways knowledgebase. We then determined the significant modules and hub genes, and explored the biological processes using the overlapping DEGs. Finally, we identified the common and distinct dysregulated pathways using overall DEGs and overlapping DEGs in a cell type-specific manner. RESULTS Up-regulated LINGO1 has been seen in both oligodendrocytes and excitatory neurons across 3 studies. Interestingly, genes enriched in the mitochondrial module were up-regulated across all cell types, which indicates mitochondrial dysfunction in the AD brain. The estrogen signaling pathway seems to be the most common pathway that is disrupted in AD. CONCLUSION Together, these analyses provide detailed information of cell type-specific and overall transcriptional changes and pathways underlying the human AD-pathology. These findings may provide important insights for drug development to tackle this disease.
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Affiliation(s)
- Xiao-Lan Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Université de Strasbourg, Strasbourg, France
| | - Lianjian Li
- Department of Surgery, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061 China
- Hubei Province Academy of Traditional Chinese Medicine, Wuhan, 430076 China
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11
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Jungwirth E, Panzitt K, Marschall HU, Thallinger GG, Wagner M. Meta-analysis and Consolidation of Farnesoid X Receptor Chromatin Immunoprecipitation Sequencing Data Across Different Species and Conditions. Hepatol Commun 2021; 5:1721-1736. [PMID: 34558825 PMCID: PMC8485886 DOI: 10.1002/hep4.1749] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/25/2021] [Indexed: 12/24/2022] Open
Abstract
Farnesoid X receptor (FXR) is a nuclear receptor that controls gene regulation of different metabolic pathways and represents an upcoming drug target for various liver diseases. Several data sets on genome-wide FXR binding in different species and conditions exist. We have previously reported that these data sets are heterogeneous and do not cover the full spectrum of potential FXR binding sites. Here, we report the first meta-analysis of all publicly available FXR chromatin immunoprecipitation sequencing (ChIP-seq) data sets from mouse, rat, and human across different conditions using a newly generated analysis pipeline. All publicly available single data sets were biocurated in a standardized manner and compared on every relevant level from raw reads to affected functional pathways. Individual murine data sets were then virtually merged into a single unique "FXR binding atlas" spanning all potential binding sites across various conditions. Comparison of the single biocurated data sets showed that the overlap of FXR binding sites between different species is modest and ranges from 48% (mouse-human) to 55% (mouse-rat). Moreover, in vivo data among different species are more similar than human in vivo data compared to human in vitro data. The consolidated murine global FXR binding atlas virtually increases sequencing depth and allows recovering more and novel potential binding sites and signaling pathways that were missed in the individual data sets. The FXR binding atlas is publicly searchable (https://fxratlas.tugraz.at). Conclusion: Published single FXR ChIP-seq data sets and large-scale integrated omics data sets do not cover the full spectrum of FXR binding. Combining different individual data sets and creating an "FXR super-binding atlas" enhances understanding of FXR signaling capacities across different conditions. This is important when considering the potential wide spectrum for drugs targeting FXR in liver diseases.
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Affiliation(s)
- Emilian Jungwirth
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria.,Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
| | - Katrin Panzitt
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine/Wallenberg LaboratorySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Gerhard G Thallinger
- Institute of Biomedical InformaticsGraz University of TechnologyGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
| | - Martin Wagner
- Research Unit for Translational Nuclear Receptor ResearchDivision of Gastroenterology and HepatologyMedical University GrazGrazAustria.,OMICS Center GrazGrazAustria.,BioTechMed-GrazGrazAustria
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12
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Evidence of a dysregulated vitamin D endocrine system in SARS-CoV-2 infected patient's lung cells. Sci Rep 2021; 11:8570. [PMID: 33883570 PMCID: PMC8060306 DOI: 10.1038/s41598-021-87703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Although a defective vitamin D endocrine system has been widely suspected to be associated in SARS-CoV-2 pathobiology, the status of the vitamin D endocrine system and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown. To understand the significance of the vitamin D endocrine system in SARS-CoV-2 pathobiology, computational approaches were applied to transcriptomic datasets from bronchoalveolar lavage fluid (BALF) cells of such patients or healthy individuals. Levels of vitamin D receptor, retinoid X receptor, and CYP27A1 in BALF cells of patients infected with SARS-CoV-2 were found to be reduced. Additionally, 107 differentially expressed, predominantly downregulated genes, as potentially modulated by vitamin D endocrine system, were identified in transcriptomic datasets from patient’s cells. Further analysis of differentially expressed genes provided eight novel genes with a conserved motif with vitamin D-responsive elements, implying the role of both direct and indirect mechanisms of gene expression by the dysregulated vitamin D endocrine system in SARS-CoV-2-infected cells. Protein–protein interaction network of differentially expressed vitamin D-modulated genes were enriched in the immune system, NF-κB/cytokine signaling, and cell cycle regulation as top predicted pathways that might be affected in the cells of such patients. In brief, the results presented here povide computational evidence to implicate a dysregulated vitamin D endocrine system in the pathobiology of SARS-CoV-2 infection.
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13
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Smith CM, Kadin JA, Baldarelli RM, Beal JS, Blodgett O, Giannatto SC, Richardson JE, Ringwald M. GXD's RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5756137. [PMID: 32140729 PMCID: PMC7058436 DOI: 10.1093/database/baaa002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/28/2022]
Abstract
The Gene Expression Database (GXD), an extensive community resource of curated expression information for the mouse, has developed an RNA-Seq and Microarray Experiment Search (http://www.informatics.jax.org/gxd/htexp_index). This tool allows users to quickly and reliably find specific experiments in ArrayExpress and the Gene Expression Omnibus (GEO) that study endogenous gene expression in wild-type and mutant mice. Standardized metadata annotations, curated by GXD, allow users to specify the anatomical structure, developmental stage, mutated gene, strain and sex of samples of interest, as well as the study type and key parameters of the experiment. These searches, powered by controlled vocabularies and ontologies, can be combined with free text searching of experiment titles and descriptions. Search result summaries include link-outs to ArrayExpress and GEO, providing easy access to the expression data itself. Links to the PubMed entries for accompanying publications are also included. More information about this tool and GXD can be found at the GXD home page (http://www.informatics.jax.org/expression.shtml). Database URL:http://www.informatics.jax.org/expression.shtml
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Affiliation(s)
| | - James A Kadin
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | | | - Jonathan S Beal
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | - Olin Blodgett
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
| | | | | | - Martin Ringwald
- The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609, USA
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14
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Santoso CS, Li Z, Lal S, Yuan S, Gan KA, Agosto LM, Liu X, Pro SC, Sewell JA, Henderson A, Atianand MK, Fuxman Bass JI. Comprehensive mapping of the human cytokine gene regulatory network. Nucleic Acids Res 2020; 48:12055-12073. [PMID: 33179750 PMCID: PMC7708076 DOI: 10.1093/nar/gkaa1055] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
Proper cytokine gene expression is essential in development, homeostasis and immune responses. Studies on the transcriptional control of cytokine genes have mostly focused on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait of cytokine gene regulation. Here, we used enhanced yeast one-hybrid (eY1H) assays to derive a comprehensive network comprising 1380 interactions between 265 TFs and 108 cytokine gene promoters. Our eY1H-derived network greatly expands the known repertoire of TF–cytokine gene interactions and the set of TFs known to regulate cytokine genes. We found an enrichment of nuclear receptors and confirmed their role in cytokine regulation in primary macrophages. Additionally, we used the eY1H-derived network as a framework to identify pairs of TFs that can be targeted with commercially-available drugs to synergistically modulate cytokine production. Finally, we integrated the eY1H data with single cell RNA-seq and phenotypic datasets to identify novel TF–cytokine regulatory axes in immune diseases and immune cell lineage development. Overall, the eY1H data provides a rich resource to study cytokine regulation in a variety of physiological and disease contexts.
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Affiliation(s)
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Sneha Lal
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Samson Yuan
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Kok Ann Gan
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Luis M Agosto
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xing Liu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Andrew Henderson
- Department of Medicine, Section of Infectious Diseases, Boston University School of Medicine, Boston, MA 02118, USA
| | - Maninjay K Atianand
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA 02215, USA.,Bioinformatics Program, Boston University, Boston, MA 02215, USA
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15
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Posttranscriptional regulation of human endogenous retroviruses by RNA-binding motif protein 4, RBM4. Proc Natl Acad Sci U S A 2020; 117:26520-26530. [PMID: 33020268 DOI: 10.1073/pnas.2005237117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts. Most studies of RBPs have concentrated on their action on host protein-encoding mRNAs, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements, termed endogenous retroviruses (ERVs), that comprise ∼8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions, suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown how broadly RBPs and ERV transcripts directly interact to provide a posttranscriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA-sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-binding motif protein 4 (RBM4). We used photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in an elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the LTRs of HERV-K-10, -K-11, and -K-20, and validated the functionality of this site using reporter assays. In summary, we systematically identified RBPs that may regulate ERV function and demonstrate a role for RBM4 in controlling ERV expression.
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16
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Negishi M, Kobayashi K, Sakuma T, Sueyoshi T. Nuclear receptor phosphorylation in xenobiotic signal transduction. J Biol Chem 2020; 295:15210-15225. [PMID: 32788213 DOI: 10.1074/jbc.rev120.007933] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/05/2020] [Indexed: 12/11/2022] Open
Abstract
Nuclear pregnane X receptor (PXR, NR1I2) and constitutive active/androstane receptor (CAR, NR1I3) are nuclear receptors characterized in 1998 by their capability to respond to xenobiotics and activate cytochrome P450 (CYP) genes. An anti-epileptic drug, phenobarbital (PB), activates CAR and its target CYP2B genes, whereas PXR is activated by drugs such as rifampicin and statins for the CYP3A genes. Inevitably, both nuclear receptors have been investigated as ligand-activated nuclear receptors by identifying and characterizing xenobiotics and therapeutics that directly bind CAR and/or PXR to activate them. However, PB, which does not bind CAR directly, presented an alternative research avenue for an indirect ligand-mediated nuclear receptor activation mechanism: phosphorylation-mediated signal regulation. This review summarizes phosphorylation-based mechanisms utilized by xenobiotics to elicit cell signaling. First, the review presents how PB activates CAR (and other nuclear receptors) through a conserved phosphorylation motif located between two zinc fingers within its DNA-binding domain. PB-regulated phosphorylation at this motif enables nuclear receptors to form communication networks, integrating their functions. Next, the review discusses xenobiotic-induced PXR activation in the absence of the conserved DNA-binding domain phosphorylation motif. In this case, phosphorylation occurs at a motif located within the ligand-binding domain to transduce cell signaling that regulates hepatic energy metabolism. Finally, the review delves into the implications of xenobiotic-induced signaling through phosphorylation in disease development and progression.
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Affiliation(s)
- Masahiko Negishi
- Pharmacogenetics Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.
| | - Kaoru Kobayashi
- Department of Biopharmaceutics, Meiji Pharmaceutical University, Kiyose, Tokyo, Japan
| | - Tsutomu Sakuma
- School of Pharmaceutical Sciences, Ohu University, Koriyama, Fukushima, Japan
| | - Tatsuya Sueyoshi
- Pharmacogenetics Section, Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
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17
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D’Ignazio L, Shakir D, Batie M, Muller HA, Rocha S. HIF-1β Positively Regulates NF-κB Activity via Direct Control of TRAF6. Int J Mol Sci 2020; 21:ijms21083000. [PMID: 32344511 PMCID: PMC7216149 DOI: 10.3390/ijms21083000] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/13/2022] Open
Abstract
NF-κB signalling is crucial for cellular responses to inflammation but is also associated with the hypoxia response. NF-κB and hypoxia inducible factor (HIF) transcription factors possess an intense molecular crosstalk. Although it is known that HIF-1α modulates NF-κB transcriptional response, very little is understood regarding how HIF-1β contributes to NF-κB signalling. Here, we demonstrate that HIF-1β is required for full NF-κB activation in cells following canonical and non-canonical stimuli. We found that HIF-1β specifically controls TRAF6 expression in human cells but also in Drosophila melanogaster. HIF-1β binds to the TRAF6 gene and controls its expression independently of HIF-1α. Furthermore, exogenous TRAF6 expression is able to rescue all of the cellular phenotypes observed in the absence of HIF-1β. These results indicate that HIF-1β is an important regulator of NF-κB with consequences for homeostasis and human disease.
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Affiliation(s)
- Laura D’Ignazio
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK;
- The Lieber Institute for Brain Development, Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Dilem Shakir
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (D.S.); (M.B.)
| | - Michael Batie
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (D.S.); (M.B.)
| | - H. Arno Muller
- Developmental Genetics Unit, Institute of Biology, University of Kassel, 34132 Kassel, Germany;
| | - Sonia Rocha
- Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (D.S.); (M.B.)
- Correspondence: ; Tel.: +44-(0)151-794-9084
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18
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Ochsner SA, McKenna NJ. No Dataset Left Behind: Mechanistic Insights into Thyroid Receptor Signaling Through Transcriptomic Consensome Meta-Analysis. Thyroid 2020; 30:621-639. [PMID: 31910096 PMCID: PMC7187985 DOI: 10.1089/thy.2019.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Background: Discovery-scale omics datasets relevant to thyroid receptors (TRs) and their physiological and synthetic bioactive small-molecule ligands allow for genome-wide interrogation of TR-regulated genes. These datasets have considerable collective value as a reference resource to allow researchers to routinely generate hypotheses addressing the mechanisms underlying the cell biology and physiology of TR signaling in normal and disease states. Methods: Here, we searched the Gene Expression Omnibus database to identify a population of publicly archived transcriptomic datasets involving genetic or pharmacological manipulation of either TR isoform in a mouse tissue or cell line. After initial quality control, samples were organized into contrasts (experiments), and transcript differential expression values and associated measures of significance were generated and committed to a consensome (for consensus omics) meta-analysis pipeline. To gain insight into tissue-selective functions of TRs, we generated liver- and central nervous system (CNS)-specific consensomes and identified evidence for genes that were selectively responsive to TR signaling in each organ. Results: The TR transcriptomic consensome ranks genes based on the frequency of their significant differential expression over the entire group of experiments. The TR consensome assigns elevated rankings both to known TR-regulated genes and to genes previously uncharacterized as TR-regulated, which shed mechanistic light on known cellular and physiological roles of TR signaling in different organs. We identify evidence for unreported genomic targets of TR signaling for which it exhibits strikingly distinct regulatory preferences in the liver and CNS. Moreover, the intersection of the TR consensome with consensomes for other cellular receptors sheds light on transcripts potentially mediating crosstalk between TRs and these other signaling paradigms. Conclusions: The mouse TR datasets and consensomes are freely available in the Signaling Pathways Project website for hypothesis generation, data validation, and modeling of novel mechanisms of TR regulation of gene expression. Our results demonstrate the insights into the mechanistic basis of thyroid hormone action that can arise from an ongoing commitment on the part of the research community to the deposition of discovery-scale datasets.
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Affiliation(s)
- Scott A. Ochsner
- The Signaling Pathways Project, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Neil J. McKenna
- The Signaling Pathways Project, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
- Address correspondence to: Neil J. McKenna, PhD, The Signaling Pathways Project, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030
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19
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Ochsner SA, Abraham D, Martin K, Ding W, McOwiti A, Kankanamge W, Wang Z, Andreano K, Hamilton RA, Chen Y, Hamilton A, Gantner ML, Dehart M, Qu S, Hilsenbeck SG, Becnel LB, Bridges D, Ma'ayan A, Huss JM, Stossi F, Foulds CE, Kralli A, McDonnell DP, McKenna NJ. The Signaling Pathways Project, an integrated 'omics knowledgebase for mammalian cellular signaling pathways. Sci Data 2019; 6:252. [PMID: 31672983 PMCID: PMC6823428 DOI: 10.1038/s41597-019-0193-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Mining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifications of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus 'omics signatures, or consensomes, which ranked genes based on measures of their significant differential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specific node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confirming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible at https://www.signalingpathways.org .
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Affiliation(s)
- Scott A Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - David Abraham
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Kirt Martin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wei Ding
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Apollo McOwiti
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Wasula Kankanamge
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zichen Wang
- Icahn School of Medicine, Mount Sinai University, New York, NY, 10029, USA
| | - Kaitlyn Andreano
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Yue Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angelica Hamilton
- Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Marin L Gantner
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Michael Dehart
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shijing Qu
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Susan G Hilsenbeck
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Lauren B Becnel
- Duncan NCI Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dave Bridges
- University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA
| | - Avi Ma'ayan
- Icahn School of Medicine, Mount Sinai University, New York, NY, 10029, USA
| | - Janice M Huss
- Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, 91010, USA
| | - Fabio Stossi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Anastasia Kralli
- Department of Chemical Physiology, Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Donald P McDonnell
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Neil J McKenna
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
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20
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Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021211] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form of perturbations. Such resources enable the characterization of signatures from novel perturbations based on similarity; provide a global view of the space of many themed perturbations; and allow the ability to predict cellular, tissue, and organismal phenotypes for perturbagens. A signature search engine enables hypothesis generation by finding connections between query signatures and the database of signatures. This framework has been used to identify connections between small molecules and their targets, to discover cell-specific responses to perturbations and ways to reverse disease expression states with small molecules, and to predict small-molecule mimickers for existing drugs. This review provides a historical perspective and the current state of connectivity mapping resources with a focus on both methodology and community implementations.
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Affiliation(s)
- Alexandra B. Keenan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan L. Wojciechowicz
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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21
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Wang C, Nanni L, Novakovic B, Megchelenbrink W, Kuznetsova T, Stunnenberg HG, Ceri S, Logie C. Extensive epigenomic integration of the glucocorticoid response in primary human monocytes and in vitro derived macrophages. Sci Rep 2019; 9:2772. [PMID: 30809020 PMCID: PMC6391480 DOI: 10.1038/s41598-019-39395-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/22/2019] [Indexed: 12/12/2022] Open
Abstract
Glucocorticoid receptor is a transcription factor that is ubiquitously expressed. Glucocorticoids are circadian steroids that regulate a wide range of bodily functions, including immunity. Here we report that synthetic glucocorticoids affect 1035 mRNAs in isolated healthy human blood monocytes but only 165 in the respective six day-old monocyte-derived macrophages. The majority of the glucocorticoid response in monocytes concerns genes that are dynamic upon monocyte to macrophage differentiation, whereby macrophage-like mRNA levels are often reached in monocytes within four hours of treatment. Concomitantly, over 5000 chromosomal H3K27ac regions undergo remodelling, of which 60% involve increased H3K27ac signal. We find that chromosomal glucocorticoid receptor binding sites correlate with positive but not with negative local epigenomic effects. To investigate further we assigned our data to topologically associating domains (TADs). This shows that about 10% of macrophage TADs harbour at least one GR binding site and that half of all the glucocorticoid-induced H3K27ac regions are confined to these TADs. Our analyses are therefore consistent with the notion that TADs naturally accommodate information from sets of distal glucocorticoid response elements.
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Affiliation(s)
- Cheng Wang
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Luca Nanni
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Boris Novakovic
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Wout Megchelenbrink
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Tatyana Kuznetsova
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
- Department of Medical Biochemistry, Academic Medical Centre of the University of Amsterdam, Amsterdam, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands
| | - Stefano Ceri
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133, Milano, Italy
| | - Colin Logie
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Faculty of Science Radboud University, PO box 9101, 6500 HG, Nijmegen, The Netherlands.
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22
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Gong Y, Cao R, Ding G, Hong S, Zhou W, Lu W, Damle M, Fang B, Wang CC, Qian J, Lie N, Lanzillotta C, Rabinowitz JD, Sun Z. Integrated omics approaches to characterize a nuclear receptor corepressor-associated histone deacetylase in mouse skeletal muscle. Mol Cell Endocrinol 2018; 471:22-32. [PMID: 28554803 PMCID: PMC5702591 DOI: 10.1016/j.mce.2017.05.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 12/22/2022]
Abstract
Nuclear receptors regulate gene expression by differentially binding to coactivators or corepressors in a ligand-dependent manner, which further recruits a set of epigenome-modifying enzymes that remodel chromatin conformation. Histone acetylation is a major epigenomic change controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs). HDAC3 is the only HDAC that confers the enzymatic activity to the complexes nucleated by nuclear receptor corepressors NCoR and SMRT. To address the metabolic function of HDAC3, we have deleted it specifically in mouse skeletal muscles. We have performed the following omics profiling in skeletal muscles of these mice: (1) RNA-seq profiling of total RNA; (2) Global nuclear run-on (GRO-seq) analysis of nascent RNAs; (3) Chromatin immuno-precipitation (ChIP-seq) of HDAC3 at both early evening and early morning; (4) proteomics profiling with mass spectrometry; (5) snap-shot metabolomics profiling of water-soluble metabolites at the basal condition; (6) snap-shot metabolomics profiling of lipid species at the basal condition; (7) kinetic fluxomics analysis of glucose utilization using 13C6-glucose In vivo during treadmill running exercise. These approaches have provided several novel insights into how nuclear receptors regulate circadian rhythm of skeletal muscle fuel metabolism, which has been published elsewhere. Here we present the original datasets and technical details during the execution, analysis, and interpretation of these omics studies.
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Affiliation(s)
- Yingyun Gong
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Rui Cao
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Guolian Ding
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Sungguan Hong
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wenjun Zhou
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Wenyun Lu
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Manashree Damle
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Bin Fang
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Chuhan C Wang
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Justin Qian
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Natasha Lie
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Cristina Lanzillotta
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, The Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, United States
| | - Zheng Sun
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, United States.
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23
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Simandi Z, Horvath A, Cuaranta-Monroy I, Sauer S, Deleuze JF, Nagy L. RXR heterodimers orchestrate transcriptional control of neurogenesis and cell fate specification. Mol Cell Endocrinol 2018; 471:51-62. [PMID: 28778663 DOI: 10.1016/j.mce.2017.07.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/20/2017] [Accepted: 07/28/2017] [Indexed: 12/27/2022]
Abstract
Retinoid X Receptors (RXRs) are unique and enigmatic members of the nuclear receptor (NR) family with extensive and complex biological functions in cellular differentiation. On the one hand, RXRs through permissive heterodimerization with other NRs are able to integrate multiple lipid signaling pathways and are believed to play a central role to coordinate the development of the central nervous system. On the other hand, RXRs may have heterodimer-independent functions as well. Therefore, a more RXR-centric analysis is warranted to identify its genomic binding sites and regulated gene networks, which are orchestrating the earliest events in neuronal differentiation. Recently developed genome-wide approaches allow systematic analyses of the RXR-driven neural differentiation. Here we applied next generation sequencing-based methodology to track the dynamic redistribution of the RXR cistrome along the path of embryonic stem cell to glutamatergic neuron differentiation. We identified Retinoic Acid Receptor (RAR) and Liver X Receptor (LXR) as dominant heterodimeric partners of RXR in these cellular stages. Our data presented here characterize the RAR:RXR and LXR:RXR-mediated transcriptional program in embryonic stem cells, neural progenitors and terminally differentiated neurons. Considering the growing evidence for dysregulated RXR-mediated signaling in neurodegenerative disorders, such as Alzheimer's Disease or Amyotrophic Lateral Sclerosis, the data presented here will be also a valuable resource for the field of neuro(patho)biology.
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Affiliation(s)
- Zoltan Simandi
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Ixchelt Cuaranta-Monroy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sascha Sauer
- Max Delbruck Center for Molecular Medicine (BISMB and BIH), Germany
| | - Jean-Francois Deleuze
- Centre National de Recherche en Genomique Humaine, Institute de Biologie Francois Jacob, CEA, Evry, France
| | - Laszlo Nagy
- Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL, USA; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; MTA-DE "Lendulet" Immunogenomics Research Group, University of Debrecen, Debrecen, Hungary.
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24
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Frahm KA, Waldman JK, Luthra S, Rudine AC, Monaghan-Nichols AP, Chandran UR, DeFranco DB. A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells. Mol Cell Endocrinol 2018; 471:42-50. [PMID: 28554804 PMCID: PMC5702594 DOI: 10.1016/j.mce.2017.05.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/09/2017] [Accepted: 05/23/2017] [Indexed: 12/11/2022]
Abstract
Fetal exposure to synthetic glucocorticoids reprograms distinct neural circuits in the developing brain, often in a sex-specific manner, via mechanisms that remain poorly understood. To reveal whether such reprogramming is associated with select molecular signatures, we characterized the transcriptome of primary, embryonic mouse cerebral cortical and hypothalamic neural progenitor/stem cells derived from individual male and female embryos exposed to the synthetic glucocorticoid, dexamethasone. Gene expression profiling by RNA-Seq identified differential expression of common and unique genes based upon brain region, sex, and/or dexamethasone exposure. These gene expression datasets provide a unique resource that will inform future studies examining the molecular mechanisms responsible for region- and sex-specific reprogramming of the fetal brain brought about by in utero exposure to excess glucocorticoids.
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Affiliation(s)
- Krystle A Frahm
- Department of Medicine Division of Endocrinology and Metabolism, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jacob K Waldman
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Soumya Luthra
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anthony C Rudine
- Department of Pediatrics Division of Newborn Medicine, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | | | - Uma R Chandran
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donald B DeFranco
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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25
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Webb MS, Miller AL, Howard TL, Johnson BH, Chumakov S, Fofanov Y, Nguyen-Vu T, Lin CY, Thompson EB. Sequential gene regulatory events leading to glucocorticoid-evoked apoptosis of CEM human leukemic cells:interactions of MAPK, MYC and glucocorticoid pathways. Mol Cell Endocrinol 2018; 471:118-130. [PMID: 29596968 PMCID: PMC6075652 DOI: 10.1016/j.mce.2018.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 02/13/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022]
Abstract
Gene expression responses to glucocorticoid (GC) in the hours preceding onset of apoptosis were compared in three clones of human acute lymphoblastic leukemia CEM cells. Between 2 and 20h, all three clones showed increasing numbers of responding genes. Each clone had many unique responses, but the two responsive clones showed a group of responding genes in common, different from the resistant clone. MYC levels and the balance of activities between the three major groups of MAPKs are known important regulators of glucocorticoid-driven apoptosis in several lymphoid cell systems. Common to the two sensitive clones were changed transcript levels from genes that decrease amounts or activity of anti-apoptotic ERK/MAPK1 and JNK2/MAPK9, or of genes that increase activity of pro-apoptotic p38/MAPK14. Down-regulation of MYC and several MYC-regulated genes relevant to MAPKs also occurred in both sensitive clones. Transcriptomine comparisons revealed probable NOTCH-GC crosstalk in these cells.
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Affiliation(s)
- M S Webb
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - A L Miller
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - T L Howard
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - B H Johnson
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - S Chumakov
- Dept. of Computer Science, Dept. of Physics, University of Guadalahara, Gaudalahara, Jalisco, Mexico
| | - Y Fofanov
- Dept. of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston TX 77555, USA
| | - T Nguyen-Vu
- Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA
| | - C Y Lin
- Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA
| | - E B Thompson
- Dept. of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston TX 77555, USA; Center for Nuclear Receptors & Cell Signaling, Dept. of Biology & Biochemistry, University of Houston, Houston TX 77204, USA.
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26
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Su Y, Shen X, Chen J, Isales CM, Zhao J, Shi XM. Differentially expressed genes in PPARγ-deficient MSCs. Mol Cell Endocrinol 2018; 471:97-104. [PMID: 28774780 PMCID: PMC5792374 DOI: 10.1016/j.mce.2017.07.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 07/26/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a key regulator of adipogenesis. It is also a central player in energy metabolism, inflammation and immunity. As an important nuclear transcription factor, PPARγ can regulate the expression and function of genes or biological processes directly or indirectly via association with other factors and thus modulate their activities. To better understand the impact of PPARγ on the global gene expression profile, we evaluated the bioinformatic data, which revealed the changes that occurred in genes and their pathways in the absence of PPARγ. In brief, we performed RNA deep sequencing (RNA-Seq) analysis using RNA samples isolated from multipotent mesenchymal stromal cells (MSCs) of PPARγ knockout and wild type control mice. The RNA-Seq data sets were then subjected to bioinformatic analyses from various angles to better reveal the breadth of PPARγ function in different biological processes. Our results reveal novel genes and networks modulated by PPARγ and provides new insights into our understanding of the physiologic and pathophysiologic role this nuclear receptor plays in health and disease.
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Affiliation(s)
- Yun Su
- Department of Neuroscience & Regenerative Medicine, USA
| | - Xiaona Shen
- Department of Mathematics, Logistical Engineering University, Chongqing, China
| | - Jie Chen
- Department of Biostatistics and Epidemiology, Augusta University, Augusta, GA, USA
| | - Carlos M Isales
- Department of Neuroscience & Regenerative Medicine, USA; Orthopaedic Surgery, Augusta University, Augusta, GA, USA
| | - Jing Zhao
- Department of Mathematics, Logistical Engineering University, Chongqing, China.
| | - Xing-Ming Shi
- Department of Neuroscience & Regenerative Medicine, USA; Orthopaedic Surgery, Augusta University, Augusta, GA, USA.
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27
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Régnier M, Polizzi A, Lippi Y, Fouché E, Michel G, Lukowicz C, Smati S, Marrot A, Lasserre F, Naylies C, Batut A, Viars F, Bertrand-Michel J, Postic C, Loiseau N, Wahli W, Guillou H, Montagner A. Insights into the role of hepatocyte PPARα activity in response to fasting. Mol Cell Endocrinol 2018; 471:75-88. [PMID: 28774777 DOI: 10.1016/j.mce.2017.07.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/04/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022]
Abstract
The liver plays a central role in the regulation of fatty acid metabolism. Hepatocytes are highly sensitive to nutrients and hormones that drive extensive transcriptional responses. Nuclear hormone receptors are key transcription factors involved in this process. Among these factors, PPARα is a critical regulator of hepatic lipid catabolism during fasting. This study aimed to analyse the wide array of hepatic PPARα-dependent transcriptional responses during fasting. We compared gene expression in male mice with a hepatocyte specific deletion of PPARα and their wild-type littermates in the fed (ad libitum) and 24-h fasted states. Liver samples were acquired, and transcriptome and lipidome analyses were performed. Our data extended and confirmed the critical role of hepatocyte PPARα as a central for regulator of gene expression during starvation. Interestingly, we identified novel PPARα-sensitive genes, including Cxcl-10, Rab30, and Krt23. We also found that liver phospholipid remodelling was a novel fasting-sensitive pathway regulated by PPARα. These results may contribute to investigations on transcriptional control in hepatic physiology and underscore the clinical relevance of drugs that target PPARα in liver pathologies, such as non-alcoholic fatty liver disease.
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Affiliation(s)
- Marion Régnier
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Arnaud Polizzi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Yannick Lippi
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Edwin Fouché
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Géraldine Michel
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Céline Lukowicz
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Sarra Smati
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Alain Marrot
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Frédéric Lasserre
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Claire Naylies
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Aurélie Batut
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Fanny Viars
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Justine Bertrand-Michel
- Metatoul-Lipidomic Facility, MetaboHUB, Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France
| | - Catherine Postic
- Institut National de La Santé et de La Recherche Médicale (INSERM), U1016, Institut Cochin, Paris, France
| | - Nicolas Loiseau
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France
| | - Walter Wahli
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, 11 Mandalay Road, 308232, Singapore; Center for Integrative Genomics, Université de Lausanne, Le Génopode, CH-1015 Lausanne, Switzerland
| | - Hervé Guillou
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France.
| | - Alexandra Montagner
- Institut National de La Recherche Agronomique (INRA), UMR1331 ToxAlim, Toulouse, France; Institut National de La Santé et de La Recherche Médicale (INSERM), UMR1048, Institute of Metabolic and Cardiovascular Diseases, Toulouse, France.
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28
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Xu S. Transcriptome Profiling in Systems Vascular Medicine. Front Pharmacol 2017; 8:563. [PMID: 28970795 PMCID: PMC5609594 DOI: 10.3389/fphar.2017.00563] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 08/08/2017] [Indexed: 02/06/2023] Open
Abstract
In the post-genomic, big data era, our understanding of vascular diseases has been deepened by multiple state-of-the-art “–omics” approaches, including genomics, epigenomics, transcriptomics, proteomics, lipidomics and metabolomics. Genome-wide transcriptomic profiling, such as gene microarray and RNA-sequencing, emerges as powerful research tools in systems medicine and revolutionizes transcriptomic analysis of the pathological mechanisms and therapeutics of vascular diseases. In this article, I will highlight the workflow of transcriptomic profiling, outline basic bioinformatics analysis, and summarize recent gene profiling studies performed in vascular cells as well as in human and mice diseased samples. Further mining of these public repository datasets will shed new light on our understanding of the cellular basis of vascular diseases and offer novel potential targets for therapeutic intervention.
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Affiliation(s)
- Suowen Xu
- Department of Medicine, Aab Cardiovascular Research Institute, University of Rochester School of Medicine and Dentistry, RochesterNY, United States
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