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Baassiri A, Ghais A, Kurdi A, Rahal E, Nasr R, Shirinian M. The molecular signature of BCR::ABLP210 and BCR::ABLT315I in a Drosophila melanogaster chronic myeloid leukemia model. iScience 2024; 27:109538. [PMID: 38585663 PMCID: PMC10995885 DOI: 10.1016/j.isci.2024.109538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/01/2024] [Accepted: 03/18/2024] [Indexed: 04/09/2024] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal hematopoietic stem cell disorder resulting from a balanced translocation leading to BCR::ABL1 oncogene with increased tyrosine kinase activity. Despite the advancements in the development of tyrosine kinase inhibitors (TKIs), the T315I gatekeeper point mutation in the BCR::ABL1 gene remains a challenge. We have previously reported in a Drosophila CML model an increased hemocyte count and disruption in sessile hemocyte patterns upon expression of BCR::ABL1p210 and BCR::ABL1T315I in the hemolymph. In this study, we performed RNA sequencing to determine if there is a distinct gene expression that distinguishes BCR::ABL1p210 and BCR::ABL1T315I. We identified six genes that were consistently upregulated in the fly CML model and validated in adult and pediatric CML patients and in a mouse cell line expressing BCR::ABL1T315I. This study provides a comprehensive analysis of gene signatures in BCR::ABL1p210 and BCR::ABL1T315I, laying the groundwork for targeted investigations into the role of these genes in CML pathogenesis.
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Affiliation(s)
- Amro Baassiri
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ali Ghais
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Abdallah Kurdi
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Elias Rahal
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Margret Shirinian
- Department of Experimental Pathology and Immunology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
- Center for Infectious Diseases Research, American University of Beirut Medical Center, Beirut, Lebanon
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2
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Goggans KR, Belyaeva OV, Klyuyeva AV, Studdard J, Slay A, Newman RB, VanBuren CA, Everts HB, Kedishvili NY. Epidermal retinol dehydrogenases cyclically regulate stem cell markers and clock genes and influence hair composition. Commun Biol 2024; 7:453. [PMID: 38609439 PMCID: PMC11014975 DOI: 10.1038/s42003-024-06160-2] [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: 07/25/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
The hair follicle (HF) is a self-renewing adult miniorgan that undergoes drastic metabolic and morphological changes during precisely timed cyclic organogenesis. The HF cycle is known to be regulated by steroid hormones, growth factors and circadian clock genes. Recent data also suggest a role for a vitamin A derivative, all-trans-retinoic acid (ATRA), the activating ligand of transcription factors, retinoic acid receptors, in the regulation of the HF cycle. Here we demonstrate that ATRA signaling cycles during HF regeneration and this pattern is disrupted by genetic deletion of epidermal retinol dehydrogenases 2 (RDHE2, SDR16C5) and RDHE2-similar (RDHE2S, SDR16C6) that catalyze the rate-limiting step in ATRA biosynthesis. Deletion of RDHEs results in accelerated anagen to catagen and telogen to anagen transitions, altered HF composition, reduced levels of HF stem cell markers, and dysregulated circadian clock gene expression, suggesting a broad role of RDHEs in coordinating multiple signaling pathways.
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Affiliation(s)
- Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob Studdard
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Aja Slay
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Regina B Newman
- Department of Nutrition and Food Sciences, Texas Woman's University, Denton, TX, USA
| | - Christine A VanBuren
- Department of Nutrition and Food Sciences, Texas Woman's University, Denton, TX, USA
| | - Helen B Everts
- Department of Nutrition and Food Sciences, Texas Woman's University, Denton, TX, USA.
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
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3
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Guarrera L, Kurosaki M, Garattini SK, Gianni' M, Fasola G, Rossit L, Prisciandaro M, Di Bartolomeo M, Bolis M, Rizzo P, Nastasi C, Foglia M, Zanetti A, Paroni G, Terao M, Garattini E. Anti-tumor activity of all-trans retinoic acid in gastric-cancer: gene-networks and molecular mechanisms. J Exp Clin Cancer Res 2023; 42:298. [PMID: 37951921 PMCID: PMC10638833 DOI: 10.1186/s13046-023-02869-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Gastric-cancer is a heterogeneous type of neoplastic disease and it lacks appropriate therapeutic options. There is an urgent need for the development of innovative pharmacological strategies, particularly in consideration of the potential stratified/personalized treatment of this tumor. All-Trans Retinoic-acid (ATRA) is one of the active metabolites of vitamin-A. This natural compound is the first example of clinically approved cyto-differentiating agent, being used in the treatment of acute promyelocytic leukemia. ATRA may have significant therapeutic potential also in the context of solid tumors, including gastric-cancer. The present study provides pre-clinical evidence supporting the use of ATRA in the treatment of gastric-cancer using high-throughput approaches. METHODS We evaluated the anti-proliferative action of ATRA in 27 gastric-cancer cell-lines and tissue-slice cultures from 13 gastric-cancer patients. We performed RNA-sequencing studies in 13 cell-lines exposed to ATRA. We used these and the gastric-cancer RNA-sequencing data of the TCGA/CCLE datasets to conduct multiple computational analyses. RESULTS Profiling of our large panel of gastric-cancer cell-lines for their quantitative response to the anti-proliferative effects of ATRA indicate that approximately half of the cell-lines are characterized by sensitivity to the retinoid. The constitutive transcriptomic profiles of these cell-lines permitted the construction of a model consisting of 42 genes, whose expression correlates with ATRA-sensitivity. The model predicts that 45% of the TCGA gastric-cancers are sensitive to ATRA. RNA-sequencing studies performed in retinoid-treated gastric-cancer cell-lines provide insights into the gene-networks underlying ATRA anti-tumor activity. In addition, our data demonstrate that ATRA exerts significant immune-modulatory effects, which seem to be largely controlled by IRF1 up-regulation. Finally, we provide evidence of a feed-back loop between IRF1 and DHRS3, another gene which is up-regulated by ATRA. CONCLUSIONS ATRA is endowed with significant therapeutic potential in the stratified/personalized treatment gastric-cancer. Our data represent the fundaments for the design of clinical trials focusing on the use of ATRA in the personalized treatment of this heterogeneous tumor. Our gene-expression model will permit the development of a predictive tool for the selection of ATRA-sensitive gastric-cancer patients. The immune-regulatory responses activated by ATRA suggest that the retinoid and immune-checkpoint inhibitors constitute rational combinations for the management of gastric-cancer.
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Affiliation(s)
- Luca Guarrera
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Mami Kurosaki
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Silvio-Ken Garattini
- Department of Oncology, Academic Hospital of Udine ASUFC, Piazzale Santa Maria della Misericordia 15, Udine, 33100, UD, Italy
| | - Maurizio Gianni'
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Gianpiero Fasola
- Department of Oncology, Academic Hospital of Udine ASUFC, Piazzale Santa Maria della Misericordia 15, Udine, 33100, UD, Italy
| | - Luca Rossit
- Department of General Surgery, Academic Hospital of Udine ASUFC, Piazzale Santa Maria della Misericordia 15, Udine, 33100, UD, Italy
| | - Michele Prisciandaro
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, Milan, 20133, Italy
| | - Maria Di Bartolomeo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Via Venezian 1, Milan, 20133, Italy
| | - Marco Bolis
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
- Faculty of Biomedical Sciences, Institute of Oncology Research, USI, Bellinzona, 6500, TI, Switzerland
| | - Paola Rizzo
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Bergamo, 24100, Italy
| | - Claudia Nastasi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Marika Foglia
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Adriana Zanetti
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Gabriela Paroni
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Mineko Terao
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy
| | - Enrico Garattini
- Department of Biochemistry and Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, Milano, 20156, Italy.
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4
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Ebrahimi A, Bakhshaei Shahrebabaki P, Fouladi H, Mansoori Derakhshan S. The impact of microRNAs on the resistance of breast cancer subtypes to chemotherapy. Pathol Res Pract 2023; 249:154702. [PMID: 37562283 DOI: 10.1016/j.prp.2023.154702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023]
Abstract
Breast cancer (BC) formation is primarily influenced by genetics, epigenetics and environmental factors. Aberrant Genetics and epigenetics leads to a condition known as heterogeneity. The heterogeneity of BC can be divided into several subtypes. Among the epigenetic factors, microRNAs (miRNAs) have been shown to play a crucial role in the development and progression of malignancies. These small non-coding RNAs regulate gene expression through a variety of mechanisms, resulting in either mRNA degradation or translation repression. As miRNAs directly control many proteins, genetic anomalies affect tumor metastasis, apoptosis, proliferation, and cell transportation. Consequently, miRNA dysregulations contribute not only in cancer development but also in invasiveness, proliferation rate and more importantly, drug response. Findings mostly indicate subtype-specified identical miRNA profile in BC. Among the BC subtypes, TNBC, HER2 + and luminal are the most resistant to therapy, respectively. Therapy resistance is greatly associated with miRNA expression profile. Hence, concentration of miRNA is the first marker of its role in chemotherapy response. Overexpressed miRNAs may disrupt drug efflux transporters and decrease the drug accumulation in cell. While down-regulated miRNAs which mediate drug resistance processes are mostly correlated with poor treatment response. Moreover, other mechanisms in which miRNAs play crucial roles in chemoresistance such as cell receptor mediations, dysregulation by environmental factors, DNA defects, etc. Recently, several miRNA-based treatments have shown promising results in cancer treatment. Inhibition of up-regulated miRNAs is one of these therapeutic approaches whilst transfecting cell with down-regulated miRNAs also show promising results. Moreover, drug-resistance could also be determined while in the pre-treatment phase via expression levels of miRNAs. Therefore, miRNAs provide intriguing insights and challenges in overcoming chemoresistance. In this article, we have discussed how miRNAs regulate breast cancer subtypes-specific chemoresistance.
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Affiliation(s)
- Amir Ebrahimi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran
| | - Peyman Bakhshaei Shahrebabaki
- Department of Vascular and Endovascular Surgery, Ayatollah Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Fouladi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran
| | - Sima Mansoori Derakhshan
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Genetics, Tabriz, Iran.
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Shmarakov IO, Gusarova GA, Islam MN, Marhuenda-Muñoz M, Bhattacharya J, Blaner WS. Retinoids stored locally in the lung are required to attenuate the severity of acute lung injury in male mice. Nat Commun 2023; 14:851. [PMID: 36792627 PMCID: PMC9932169 DOI: 10.1038/s41467-023-36475-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Retinoids are potent transcriptional regulators that act in regulating cell proliferation, differentiation, and other cellular processes. We carried out studies in male mice to establish the importance of local cellular retinoid stores within the lung alveolus for maintaining its health in the face of an acute inflammatory challenge induced by intranasal instillation of lipopolysaccharide. We also undertook single cell RNA sequencing and bioinformatic analyses to identify roles for different alveolar cell populations involved in mediating these retinoid-dependent responses. Here we show that local retinoid stores and uncompromised metabolism and signaling within the lung are required to lessen the severity of an acute inflammatory challenge. Unexpectedly, our data also establish that alveolar cells other than lipofibroblasts, specifically microvascular endothelial and alveolar epithelial cells, are able to take up lipoprotein-transported retinoid and to accumulate cellular retinoid stores that are directly used to respond to an acute inflammatory challenge.
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Affiliation(s)
- Igor O Shmarakov
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
- Department of Animal Sciences, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA.
| | - Galina A Gusarova
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Mohammad N Islam
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - María Marhuenda-Muñoz
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Department of Nutrition, Food Science and Gastronomy, School of Pharmacy and Food Sciences and XIA, Institute of Nutrition and Food Safety (INSA-UB), University of Barcelona, 08921, Santa Coloma de Gramenet, Spain
| | - Jahar Bhattacharya
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - William S Blaner
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
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6
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Kaplan L, Drexler C, Pfaller AM, Brenna S, Wunderlich KA, Dimitracopoulos A, Merl-Pham J, Perez MT, Schlötzer-Schrehardt U, Enzmann V, Samardzija M, Puig B, Fuchs P, Franze K, Hauck SM, Grosche A. Retinal regions shape human and murine Müller cell proteome profile and functionality. Glia 2023; 71:391-414. [PMID: 36334068 DOI: 10.1002/glia.24283] [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: 07/17/2022] [Revised: 09/29/2022] [Accepted: 10/07/2022] [Indexed: 11/08/2022]
Abstract
The human macula is a highly specialized retinal region with pit-like morphology and rich in cones. How Müller cells, the principal glial cell type in the retina, are adapted to this environment is still poorly understood. We compared proteomic data from cone- and rod-rich retinae from human and mice and identified different expression profiles of cone- and rod-associated Müller cells that converged on pathways representing extracellular matrix and cell adhesion. In particular, epiplakin (EPPK1), which is thought to play a role in intermediate filament organization, was highly expressed in macular Müller cells. Furthermore, EPPK1 knockout in a human Müller cell-derived cell line led to a decrease in traction forces as well as to changes in cell size, shape, and filopodia characteristics. We here identified EPPK1 as a central molecular player in the region-specific architecture of the human retina, which likely enables specific functions under the immense mechanical loads in vivo.
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Affiliation(s)
- Lew Kaplan
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Corinne Drexler
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria.,Vienna Biocenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Anna M Pfaller
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Santra Brenna
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten A Wunderlich
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Dimitracopoulos
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Juliane Merl-Pham
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Maria-Theresa Perez
- Department of Clinical Sciences, Division of Ophthalmology, Lund University, Lund, Sweden.,NanoLund, Nanometer Structure Consortium, Lund University, Lund, Sweden
| | | | - Volker Enzmann
- Department of Ophthalmology, Bern University Hospital, Inselspital, University of Bern, Bern, Switzerland.,Department of BioMedical Research, University of Bern, Bern, Switzerland
| | - Marijana Samardzija
- Department of Ophthalmology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Berta Puig
- Neurology Department, Experimental Research in Stroke and Inflammation (ERSI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Fuchs
- Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna Biocenter Campus (VBC), Vienna, Austria
| | - Kristian Franze
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.,Institute of Medical Physics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.,Max-Planck-Zentrum für Physik und Medizin, Erlangen, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science and Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Antje Grosche
- Department of Physiological Genomics, Ludwig-Maximilians-Universität München, Munich, Germany
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7
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Xu J, Si H, Zeng Y, Wu Y, Zhang S, Liu Y, Li M, Shen B. Transcriptome-wide association study identifies new susceptibility genes for degenerative cervical spondylosis. Bone Joint Res 2023; 12:80-90. [PMID: 36660900 PMCID: PMC9872045 DOI: 10.1302/2046-3758.121.bjr-2022-0225.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIMS Degenerative cervical spondylosis (DCS) is a common musculoskeletal disease that encompasses a wide range of progressive degenerative changes and affects all components of the cervical spine. DCS imposes very large social and economic burdens. However, its genetic basis remains elusive. METHODS Predicted whole-blood and skeletal muscle gene expression and genome-wide association study (GWAS) data from a DCS database were integrated, and functional summary-based imputation (FUSION) software was used on the integrated data. A transcriptome-wide association study (TWAS) was conducted using FUSION software to assess the association between predicted gene expression and DCS risk. The TWAS-identified genes were verified via comparison with differentially expressed genes (DEGs) in DCS RNA expression profiles in the Gene Expression Omnibus (GEO) (Accession Number: GSE153761). The Functional Mapping and Annotation (FUMA) tool for genome-wide association studies and Meta tools were used for gene functional enrichment and annotation analysis. RESULTS The TWAS detected 420 DCS genes with p < 0.05 in skeletal muscle, such as ribosomal protein S15A (RPS15A) (PTWAS = 0.001), and 110 genes in whole blood, such as selectin L (SELL) (PTWAS = 0.001). Comparison with the DCS RNA expression profile identified 12 common genes, including Apelin Receptor (APLNR) (PTWAS = 0.001, PDEG = 0.025). In total, 148 DCS-enriched Gene Ontology (GO) terms were identified, such as mast cell degranulation (GO:0043303); 15 DCS-enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, such as the sphingolipid signalling pathway (ko04071). Nine terms, such as degradation of the extracellular matrix (R-HSA-1474228), were common to the TWAS enrichment results and the RNA expression profile. CONCLUSION Our results identify putative susceptibility genes; these findings provide new ideas for exploration of the genetic mechanism of DCS development and new targets for preclinical intervention and clinical treatment.Cite this article: Bone Joint Res 2023;12(1):80-90.
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Affiliation(s)
- Jiawen Xu
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Haibo Si
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Yi Zeng
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Yuangang Wu
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Shaoyun Zhang
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Yuan Liu
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Mingyang Li
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China
| | - Bin Shen
- Department of Orthopedics, Sichuan University West China Hospital, Chengdu, China, Bin Shen. E-mail:
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Abstract
Vitamin A (retinol) is a critical micronutrient required for the control of stem cell functions, cell differentiation, and cell metabolism in many different cell types, both during embryogenesis and in the adult organism. However, we must obtain vitamin A from food sources. Thus, the uptake and metabolism of vitamin A by intestinal epithelial cells, the storage of vitamin A in the liver, and the metabolism of vitamin A in target cells to more biologically active metabolites, such as retinoic acid (RA) and 4-oxo-RA, must be precisely regulated. Here, I will discuss the enzymes that metabolize vitamin A to RA and the cytochrome P450 Cyp26 family of enzymes that further oxidize RA. Because much progress has been made in understanding the regulation of ALDH1a2 (RALDH2) actions in the intestine, one focus of this review is on the metabolism of vitamin A in intestinal epithelial cells and dendritic cells. Another focus is on recent data that 4-oxo-RA is a ligand required for the maintenance of hematopoietic stem cell dormancy and the important role of RARβ (RARB) in these stem cells. Despite this progress, many questions remain in this research area, which links vitamin A metabolism to nutrition, immune functions, developmental biology, and nuclear receptor pharmacology.
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Affiliation(s)
- Lorraine J Gudas
- Department of Pharmacology, and Revlon Pharmaceutical Professor of Pharmacology and Toxicology, Pharmacology Department, and the Meyer Cancer Center of Weill Cornell Medicine of Cornell University, 1300 York Ave, New York, NY 10065
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9
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Pierro JD, Ahir BK, Baker NC, Kleinstreuer NC, Xia M, Knudsen TB. Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling. Front Pharmacol 2022; 13:971296. [PMID: 36172177 PMCID: PMC9511990 DOI: 10.3389/fphar.2022.971296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
All-trans retinoic acid (ATRA) gradients determine skeletal patterning morphogenesis and can be disrupted by diverse genetic or environmental factors during pregnancy, leading to fetal skeleton defects. Adverse Outcome Pathway (AOP) frameworks for ATRA metabolism, signaling, and homeostasis allow for the development of new approach methods (NAMs) for predictive toxicology with less reliance on animal testing. Here, a data-driven model was constructed to identify chemicals associated with both ATRA pathway bioactivity and prenatal skeletal defects. The phenotype data was culled from ToxRefDB prenatal developmental toxicity studies and produced a list of 363 ToxRefDB chemicals with altered skeletal observations. Defects were classified regionally as cranial, post-cranial axial, appendicular, and other (unspecified) features based on ToxRefDB descriptors. To build a multivariate statistical model, high-throughput screening bioactivity data from >8,070 chemicals in ToxCast/Tox21 across 10 in vitro assays relevant to the retinoid signaling system were evaluated and compared to literature-based candidate reference chemicals in the dataset. There were 48 chemicals identified for effects on both in vivo skeletal defects and in vitro ATRA pathway targets for computational modeling. The list included 28 chemicals with prior evidence of skeletal defects linked to retinoid toxicity and 20 chemicals without prior evidence. The combination of thoracic cage defects and DR5 (direct repeats of 5 nucleotides for RAR/RXR transactivation) disruption was the most frequently occurring phenotypic and target disturbance, respectively. This data model provides valuable AOP elucidation and validates current mechanistic understanding. These findings also shed light on potential avenues for new mechanistic discoveries related to ATRA pathway disruption and associated skeletal dysmorphogenesis due to environmental exposures.
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Affiliation(s)
- Jocylin D. Pierro
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
| | - Bhavesh K. Ahir
- Eurofins Medical Device Testing, Lancaster, PA, United States
| | - Nancy C. Baker
- Scientific Computing and Data Curation Division (SCDCD), Leidos Contractor, Center for Computational Toxicology and Exposure (CCTE), USEPA/ORD, Research Triangle Park, NC, United States
| | - Nicole C. Kleinstreuer
- Interagency Center for the Evaluation of Alternative Toxicological Methods (NICEATM), National Toxicology Program, National Institutes of Health, Research Triangle Park, NC, United States
| | - Menghang Xia
- Division for Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Thomas B. Knudsen
- Center for Computational Toxicology and Exposure (CCTE), Computational Toxicology and Bioinformatics Branch (CTBB), Office of Research and Development (ORD), U.S. Environmental Protection Agency (USEPA), Research Triangle Park, NC, United States
- *Correspondence: Thomas B. Knudsen, , orcid.org/0000-0002-5036-596x
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10
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Schoenfeld DA, Zhou R, Zairis S, Su W, Steinbach N, Mathur D, Bansal A, Zachem AL, Tavarez B, Hasson D, Bernstein E, Rabadan R, Parsons R. Loss of PBRM1 Alters Promoter Histone Modifications and Activates ALDH1A1 to Drive Renal Cell Carcinoma. Mol Cancer Res 2022; 20:1193-1207. [PMID: 35412614 PMCID: PMC9357026 DOI: 10.1158/1541-7786.mcr-21-1039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/22/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023]
Abstract
Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the tumor-suppressor protein PBRM1 (BAF180), as well as ARID2 (BAF200), that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). Here, we integrate RNA-seq, histone modification ChIP-seq, and ATAC-seq data to show that loss of PBRM1 results in de novo gains in H3K4me3 peaks throughout the epigenome, including activation of a retinoic acid biosynthesis and signaling gene signature. We show that one such target gene, ALDH1A1, which regulates a key step in retinoic acid biosynthesis, is consistently upregulated with PBRM1 loss in ccRCC cell lines and primary tumors, as well as non-malignant cells. We further find that ALDH1A1 increases the tumorigenic potential of ccRCC cells. Using biochemical methods, we show that ARID2 remains bound to other PBAF subunits after loss of PBRM1 and is essential for increased ALDH1A1 after loss of PBRM1, whereas other core SWI/SNF components are dispensable, including the ATPase subunit BRG1. In total, this study uses global epigenomic approaches to uncover novel mechanisms of PBRM1 tumor suppression in ccRCC. IMPLICATIONS This study implicates the SWI/SNF subunit and tumor-suppressor PBRM1 in the regulation of promoter histone modifications and retinoic acid biosynthesis and signaling pathways in ccRCC and functionally validates one such target gene, the aldehyde dehydrogenase ALDH1A1.
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Affiliation(s)
| | - Royce Zhou
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sakellarios Zairis
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - William Su
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nicole Steinbach
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Deepti Mathur
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ankita Bansal
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexis L. Zachem
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bertilia Tavarez
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dan Hasson
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Emily Bernstein
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Raul Rabadan
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Ramon Parsons
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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11
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O’Connor C, Varshosaz P, Moise AR. Mechanisms of Feedback Regulation of Vitamin A Metabolism. Nutrients 2022; 14:nu14061312. [PMID: 35334970 PMCID: PMC8950952 DOI: 10.3390/nu14061312] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023] Open
Abstract
Vitamin A is an essential nutrient required throughout life. Through its various metabolites, vitamin A sustains fetal development, immunity, vision, and the maintenance, regulation, and repair of adult tissues. Abnormal tissue levels of the vitamin A metabolite, retinoic acid, can result in detrimental effects which can include congenital defects, immune deficiencies, proliferative defects, and toxicity. For this reason, intricate feedback mechanisms have evolved to allow tissues to generate appropriate levels of active retinoid metabolites despite variations in the level and format, or in the absorption and conversion efficiency of dietary vitamin A precursors. Here, we review basic mechanisms that govern vitamin A signaling and metabolism, and we focus on retinoic acid-controlled feedback mechanisms that contribute to vitamin A homeostasis. Several approaches to investigate mechanistic details of the vitamin A homeostatic regulation using genomic, gene editing, and chromatin capture technologies are also discussed.
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Affiliation(s)
- Catherine O’Connor
- MD Program, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada;
| | - Parisa Varshosaz
- Biology and Biomolecular Sciences Ph.D. Program, Northern Ontario School of Medicine, Laurentian University, Sudbury, ON P3E 2C6, Canada;
| | - Alexander R. Moise
- Medical Sciences Division, Northern Ontario School of Medicine, 317-MSE Bldg., 935 Ramsey Lake Rd., Sudbury, ON P3E 2C6, Canada
- Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada
- Correspondence: ; Tel.: +1-705-662-7253
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12
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Zhao X, Wang W, Yao Y, Li X, Huang X, Wang Y, Ding M, Huang X. An RDH‐Plin2 axis modulates lipid droplet size by antagonizing Bmm lipase. EMBO Rep 2022; 23:e52669. [PMID: 35132760 PMCID: PMC8892243 DOI: 10.15252/embr.202152669] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 12/04/2021] [Accepted: 12/21/2021] [Indexed: 12/18/2022] Open
Abstract
The size of lipid droplets varies greatly in vivo and is determined by both intrinsic and extrinsic factors. From an RNAi screen in Drosophila, we found that knocking down subunits of COP9 signalosome (CSN) results in enlarged lipid droplets under high‐fat, but not normal, conditions. We identified CG2064, a retinol dehydrogenase (RDH) homolog, as the proteasomal degradation target of CSN in regulating lipid droplet size. RDH/CG2064 interacts with the lipid droplet‐resident protein Plin2 and the RDH/CG2064‐Plin2 axis acts to reduce the overall level and lipid droplet localization of Bmm/ATGL lipase. This axis is important for larval survival under prolonged starvation. Thus, we discovered an RDH‐Plin2 axis modulates lipid droplet size.
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Affiliation(s)
- Xuefan Zhao
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Wei Wang
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Yan Yao
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Xia Li
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Mei Ding
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
| | - Xun Huang
- State Key Laboratory of Molecular Developmental Biology Institute of Genetics and Developmental Biology Innovation Academy for Seed Design Chinese Academy of Sciences Beijing China
- University of Chinese Academy of Sciences Beijing China
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13
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Zhou J, Sun C, Yang L, Wang J, Jn-Simon N, Zhou C, Bryant A, Cao Q, Li C, Petersen B, Pi L. Liver regeneration and ethanol detoxification: A new link in YAP regulation of ALDH1A1 during alcohol-related hepatocyte damage. FASEB J 2022; 36:e22224. [PMID: 35218575 PMCID: PMC9126254 DOI: 10.1096/fj.202101686r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Yes-associated protein (YAP), a central effector in the Hippo pathway, is involved in the regulation of organ size, stem cell self-renewal, and tissue regeneration. In this study, we observed YAP activation in patients with alcoholic steatosis, hepatitis, and cirrhosis. Accumulation of this protein in the nucleus was also observed in murine livers that were damaged after chronic-plus-single binge or moderate ethanol ingestion combined with carbon tetrachloride intoxication (ethanol/CCl4 ). To understand the role of this transcriptional coactivator in alcohol-related liver injury, we knocked out the Yap1 gene in hepatocytes of floxed homozygotes through adeno-associated virus (AAV8)-mediated deletion utilizing Cre recombinase. Yap1 hepatocyte-specific knockouts (KO) exhibited hemorrhage, massive hepatic necrosis, enhanced oxidative stress, elevated hypoxia, and extensive infiltration of CD11b+ inflammatory cells into hepatic microenvironments rich for connective tissue growth factor (Ctgf) during ethanol/CCl4 -induced liver damage. Analysis of whole-genome transcriptomics indicated upregulation of genes involved in hypoxia and extracellular matrix (ECM) remodeling, whereas genes related to hepatocyte proliferation, progenitor cell activation, and ethanol detoxification were downregulated in the damaged livers of Yap1 KO. Acetaldehyde dehydrogenase (Aldh)1a1, a gene that encodes a detoxification enzyme for aldehyde substrates, was identified as a potential YAP target because this gene could be transcriptionally activated by a hyperactive YAP mutant. The ectopic expression of the human ALDH1A1 gene caused increase in hepatocyte proliferation and decrease in hepatic necrosis, oxidative stress, ECM remodeling, and inflammation during ethanol/CCl4 -induced liver damage. Taken together, these observations indicated that YAP was crucial for liver repair during alcohol-associated injury. Its regulation of ALDH1A1 represents a new link in liver regeneration and detoxification.
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Affiliation(s)
- Junmei Zhou
- Guangxi Key Laboratory of Molecular Medicine in Liver Injury and Repair, The Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Chunbao Sun
- Department of Pathology, Tulane University, New Orleans, Louisiana, USA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Jinhui Wang
- Integrative Genomics Core, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Natacha Jn-Simon
- Department of Pathology, Tulane University, New Orleans, Louisiana, USA
| | - Chen Zhou
- Department of Medical Chemistry, University of Florida, Gainesville, Florida, USA
| | - Andrew Bryant
- Department of Medicine, University of Florida, Gainesville, Florida, USA
| | - Qi Cao
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Chenglong Li
- Department of Medical Chemistry, University of Florida, Gainesville, Florida, USA
| | - Bryon Petersen
- Department of Pediatrics, University of Florida, Gainesville, Florida, USA
| | - Liya Pi
- Department of Pathology, Tulane University, New Orleans, Louisiana, USA
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14
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Enhanced Loss of Retinoic Acid Network Genes in Xenopus laevis Achieves a Tighter Signal Regulation. Cells 2022; 11:cells11030327. [PMID: 35159137 PMCID: PMC8834563 DOI: 10.3390/cells11030327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Retinoic acid (RA) is a major regulatory signal during embryogenesis produced from vitamin A (retinol) by an extensive, autoregulating metabolic and signaling network to prevent fluctuations that result in developmental malformations. Xenopus laevis is an allotetraploid hybrid frog species whose genome includes L (long) and S (short) chromosomes from the originating species. Evolutionarily, the X. laevis subgenomes have been losing either L or S homoeologs in about 43% of genes to generate singletons. In the RA network, out of the 47 genes, about 47% have lost one of the homoeologs, like the genome average. Interestingly, RA metabolism genes from storage (retinyl esters) to retinaldehyde production exhibit enhanced gene loss with 75% singletons out of 28 genes. The effect of this gene loss on RA signaling autoregulation was studied. Employing transient RA manipulations, homoeolog gene pairs were identified in which one homoeolog exhibits enhanced responses or looser regulation than the other, while in other pairs both homoeologs exhibit similar RA responses. CRISPR/Cas9 targeting of individual homoeologs to reduce their activity supports the hypothesis where the RA metabolic network gene loss results in tighter network regulation and more efficient RA robustness responses to overcome complex regulation conditions.
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15
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Li J, Garavaglia S, Ye Z, Moretti A, Belyaeva OV, Beiser A, Ibrahim M, Wilk A, McClellan S, Klyuyeva AV, Goggans KR, Kedishvili NY, Salter EA, Wierzbicki A, Migaud ME, Mullett SJ, Yates NA, Camacho CJ, Rizzi M, Sobol RW. A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells. Commun Biol 2021; 4:1420. [PMID: 34934174 PMCID: PMC8692581 DOI: 10.1038/s42003-021-02949-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/07/2021] [Indexed: 01/31/2023] Open
Abstract
Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH+ cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Zhaofeng Ye
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Andrea Moretti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Md Ibrahim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steve McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - E Alan Salter
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steven J Mullett
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nathan A Yates
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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16
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Parihar M, Bendelac-Kapon L, Gur M, Abbou T, Belorkar A, Achanta S, Kinberg K, Vadigepalli R, Fainsod A. Retinoic Acid Fluctuation Activates an Uneven, Direction-Dependent Network-Wide Robustness Response in Early Embryogenesis. Front Cell Dev Biol 2021; 9:747969. [PMID: 34746144 PMCID: PMC8564372 DOI: 10.3389/fcell.2021.747969] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/23/2021] [Indexed: 01/15/2023] Open
Abstract
Robustness is a feature of regulatory pathways to ensure signal consistency in light of environmental changes or genetic polymorphisms. The retinoic acid (RA) pathway, is a central developmental and tissue homeostasis regulatory signal, strongly dependent on nutritional sources of retinoids and affected by environmental chemicals. This pathway is characterized by multiple proteins or enzymes capable of performing each step and their integration into a self-regulating network. We studied RA network robustness by transient physiological RA signaling disturbances followed by kinetic transcriptomic analysis of the recovery during embryogenesis. The RA metabolic network was identified as the main regulated module to achieve signaling robustness using an unbiased pattern analysis. We describe the network-wide responses to RA signal manipulation and found the feedback autoregulation to be sensitive to the direction of the RA perturbation: RA knockdown exhibited an upper response limit, whereas RA addition had a minimal feedback-activation threshold. Surprisingly, our robustness response analysis suggests that the RA metabolic network regulation exhibits a multi-objective optimization, known as Pareto optimization, characterized by trade-offs between competing functionalities. We observe that efficient robustness to increasing RA is accompanied by worsening robustness to reduced RA levels and vice versa. This direction-dependent trade-off in the network-wide feedback response, results in an uneven robustness capacity of the RA network during early embryogenesis, likely a significant contributor to the manifestation of developmental defects.
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Affiliation(s)
- Madhur Parihar
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Liat Bendelac-Kapon
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Michal Gur
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Tali Abbou
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Abha Belorkar
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Sirisha Achanta
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Keren Kinberg
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
| | - Rajanikanth Vadigepalli
- Daniel Baugh Institute for Functional Genomics and Computational Biology, Department of Pathology, Anatomy, and Cell Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Abraham Fainsod
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Jerusalem, Israel
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17
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Characterization of subunit interactions in the hetero-oligomeric retinoid oxidoreductase complex. Biochem J 2021; 478:3597-3611. [PMID: 34542554 DOI: 10.1042/bcj20210589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022]
Abstract
The hetero-oligomeric retinoid oxidoreductase complex (ROC) catalyzes the interconversion of all-trans-retinol and all-trans-retinaldehyde to maintain the steady-state output of retinaldehyde, the precursor of all-trans-retinoic acid that regulates the transcription of numerous genes. The interconversion is catalyzed by two distinct components of the ROC: the NAD(H)-dependent retinol dehydrogenase 10 (RDH10) and the NADP(H)-dependent dehydrogenase reductase 3 (DHRS3). The binding between RDH10 and DHRS3 subunits in the ROC results in mutual activation of the subunits. The molecular basis for their activation is currently unknown. Here, we applied site-directed mutagenesis to investigate the roles of amino acid residues previously implied in subunit interactions in other SDRs to obtain the first insight into the subunit interactions in the ROC. The results of these studies suggest that the cofactor binding to RDH10 subunit is critical for the activation of DHRS3 subunit and vice versa. The C-terminal residues 317-331 of RDH10 are critical for the activity of RDH10 homo-oligomers but not for the binding to DHRS3. The C-terminal residues 291-295 are required for DHRS3 subunit activity of the ROC. The highly conserved C-terminal cysteines appear to be involved in inter-subunit communications, affecting the affinity of the cofactor binding site in RDH10 homo-oligomers as well as in the ROC. Modeling of the ROC quaternary structure based on other known structures of SDRs suggests that its integral membrane-associated subunits may be inserted in adjacent membranes of the endoplasmic reticulum (ER), making the formation and function of the ROC dependent on the dynamic nature of the tubular ER network.
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18
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Endo S, Matsunaga T, Nishinaka T. The Role of AKR1B10 in Physiology and Pathophysiology. Metabolites 2021; 11:332. [PMID: 34063865 PMCID: PMC8224097 DOI: 10.3390/metabo11060332] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/16/2022] Open
Abstract
AKR1B10 is a human nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductase belonging to the aldo-keto reductase (AKR) 1B subfamily. It catalyzes the reduction of aldehydes, some ketones and quinones, and interacts with acetyl-CoA carboxylase and heat shock protein 90α. The enzyme is highly expressed in epithelial cells of the stomach and intestine, but down-regulated in gastrointestinal cancers and inflammatory bowel diseases. In contrast, AKR1B10 expression is low in other tissues, where the enzyme is upregulated in cancers, as well as in non-alcoholic fatty liver disease and several skin diseases. In addition, the enzyme's expression is elevated in cancer cells resistant to clinical anti-cancer drugs. Thus, growing evidence supports AKR1B10 as a potential target for diagnosing and treating these diseases. Herein, we reviewed the literature on the roles of AKR1B10 in a healthy gastrointestinal tract, the development and progression of cancers and acquired chemoresistance, in addition to its gene regulation, functions, and inhibitors.
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Affiliation(s)
- Satoshi Endo
- Laboratory of Biochemistry, Gifu Pharmaceutical University, Gifu 501-1196, Japan
| | - Toshiyuki Matsunaga
- Education Center of Green Pharmaceutical Sciences, Gifu Pharmaceutical University, Gifu 502-8585, Japan;
| | - Toru Nishinaka
- Laboratory of Biochemistry, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi 584-8540, Osaka, Japan;
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19
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Czuba LC, Wu X, Huang W, Hollingshead N, Roberto JB, Kenerson HL, Yeung RS, Crispe IN, Isoherranen N. Altered vitamin A metabolism in human liver slices corresponds to fibrogenesis. Clin Transl Sci 2021; 14:976-989. [PMID: 33382909 PMCID: PMC8212748 DOI: 10.1111/cts.12962] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 12/13/2022] Open
Abstract
All-trans-retinoic acid (atRA), the active metabolite of vitamin A, has antifibrogenic properties in vitro and in animal models. Liver vitamin A homeostasis is maintained by cell-specific enzymatic activities including storage in hepatic stellate cells (HSCs), secretion into circulation from hepatocytes, and formation and clearance of atRA. During chronic liver injury, HSC activation is associated with a decrease in liver retinyl esters and retinol concentrations. atRA is synthesized through two enzymatic steps from retinol, but it is unknown if the loss of retinoid stores is associated with changes in atRA formation and which cell types contribute to the metabolic changes. The aim of this study was to determine if the vitamin A metabolic flux is perturbed in acute liver injury, and if changes in atRA concentrations are associated with HSC activation and collagen expression. At basal levels, HSC and Kupffer cells expressed key genes involved in vitamin A metabolism, whereas after acute liver injury, complex changes to the metabolic flux were observed in liver slices. These changes include a reproducible spike in atRA tissue concentrations, decreased retinyl ester and atRA formation rate, and time-dependent changes to the expression of metabolizing enzymes. Kinetic simulations suggested that oxidoreductases are important in determining retinoid metabolic flux after liver injury. These early changes precede HSC activation and upregulation of profibrogenic gene expression, which were inversely correlated with atRA tissue concentrations, suggesting that HSC and Kupffer cells are key cells involved in changes to vitamin A metabolic flux and signaling after liver injury. Study Highlights WHAT IS THE CURRENT KNOWLEDGE ON THE TOPIC? Vitamin A is metabolized in the liver for storage as retinyl esters in hepatic stellate cell (HSCs) or to all-trans-retinoic acid (atRA), an active metabolite with antifibrogenic properties. Following chronic liver injury, vitamin A metabolic flux is perturbed, and HSC activation leads to diminished retinoid stores. WHAT QUESTION DID THIS STUDY ADDRESS? Do changes in the expression of vitamin A metabolizing enzymes explain changes in atRA concentrations and the regulation of fibrosis following acute liver injury? WHAT DOES THIS STUDY ADD TO OUR KNOWLEDGE? In healthy liver, both HSC and Kupffer cells may mediate vitamin A homeostasis. Following acute liver injury, complex changes in metabolizing enzyme expression/activity alter the metabolic flux of retinoids, resulting in a transient peak in atRA concentrations. The atRA concentrations are inversely correlated with profibrogenic gene expression, HSC activation, and collagen deposition. HOW MIGHT THIS CHANGE CLINICAL PHARMACOLOGY OR TRANSLATIONAL SCIENCE? Improved understanding of altered vitamin A metabolic flux in acute liver injury may provide insight into cell-specific contributions to vitamin A loss and lead to novel interventions in liver fibrosis.
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Affiliation(s)
- Lindsay C. Czuba
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
| | - Xia Wu
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Weize Huang
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
| | - Nicole Hollingshead
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Jessica B. Roberto
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | | | - Raymond S. Yeung
- Department of SurgeryUniversity of WashingtonSeattleWashingtonUSA
| | - Ian N. Crispe
- Department of Laboratory Medicine and PathologyUniversity of WashingtonSeattleWashingtonUSA
| | - Nina Isoherranen
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
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20
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Gallina AL, Rykaczewska U, Wirka RC, Caravaca AS, Shavva VS, Youness M, Karadimou G, Lengquist M, Razuvaev A, Paulsson-Berne G, Quertermous T, Gisterå A, Malin SG, Tarnawski L, Matic L, Olofsson PS. AMPA-Type Glutamate Receptors Associated With Vascular Smooth Muscle Cell Subpopulations in Atherosclerosis and Vascular Injury. Front Cardiovasc Med 2021; 8:655869. [PMID: 33959644 PMCID: PMC8093397 DOI: 10.3389/fcvm.2021.655869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022] Open
Abstract
Objectives and Aims: Vascular smooth muscle cells (VSMCs) are key constituents of both normal arteries and atherosclerotic plaques. They have an ability to adapt to changes in the local environment by undergoing phenotypic modulation. An improved understanding of the mechanisms that regulate VSMC phenotypic changes may provide insights that suggest new therapeutic targets in treatment of cardiovascular disease (CVD). The amino-acid glutamate has been associated with CVD risk and VSMCs metabolism in experimental models, and glutamate receptors regulate VSMC biology and promote pulmonary vascular remodeling. However, glutamate-signaling in human atherosclerosis has not been explored. Methods and Results: We identified glutamate receptors and glutamate metabolism-related enzymes in VSMCs from human atherosclerotic lesions, as determined by single cell RNA sequencing and microarray analysis. Expression of the receptor subunits glutamate receptor, ionotropic, α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic (AMPA)-type subunit 1 (GRIA1) and 2 (GRIA2) was restricted to cells of mesenchymal origin, primarily VSMCs, as confirmed by immunostaining. In a rat model of arterial injury and repair, changes of GRIA1 and GRIA2 mRNA level were most pronounced at time points associated with VSMC proliferation, migration, and phenotypic modulation. In vitro, human carotid artery SMCs expressed GRIA1, and selective AMPA-type receptor blocking inhibited expression of typical contractile markers and promoted pathways associated with VSMC phenotypic modulation. In our biobank of human carotid endarterectomies, low expression of AMPA-type receptor subunits was associated with higher content of inflammatory cells and a higher frequency of adverse clinical events such as stroke. Conclusion: AMPA-type glutamate receptors are expressed in VSMCs and are associated with phenotypic modulation. Patients suffering from adverse clinical events showed significantly lower mRNA level of GRIA1 and GRIA2 in their atherosclerotic lesions compared to asymptomatic patients. These results warrant further mapping of neurotransmitter signaling in the pathogenesis of human atherosclerosis.
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Affiliation(s)
- Alessandro L Gallina
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Urszula Rykaczewska
- Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Robert C Wirka
- Division of Cardiology, University of North Carolina School of Medicine, Chapel Hill, NC, United States
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC, United States
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC, United States
| | - April S Caravaca
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Vladimir S Shavva
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mohamad Youness
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Cardiovascular Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Glykeria Karadimou
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mariette Lengquist
- Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Anton Razuvaev
- Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Gabrielle Paulsson-Berne
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Thomas Quertermous
- Division of Cardiovascular Medicine and Cardiovascular Institute, School of Medicine, Stanford University, California, CA, United States
| | - Anton Gisterå
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stephen G Malin
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Laura Tarnawski
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Ljubica Matic
- Vascular Surgery, Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Peder S Olofsson
- Laboratory of Immunobiology, Center for Bioelectronic Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, United States
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21
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Integrating transcriptome-wide association study and mRNA expression profile identified candidate genes related to hand osteoarthritis. Arthritis Res Ther 2021; 23:81. [PMID: 33691763 PMCID: PMC7948369 DOI: 10.1186/s13075-021-02458-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 02/18/2021] [Indexed: 02/08/2023] Open
Abstract
Background Osteoarthritis (OA) is a common skeletal system disease that has been partially attributed to genetic factors. The hand is frequently affected, which seriously affects the patient’s quality of life. However, the pathogenetic mechanism of hand osteoarthritis (hand OA) is still elusive. Methods A genome-wide association study (GWAS) summary of hand OA was obtained from the UK Biobank dataset, which contains data from a total of 452,264 White British individuals, including 37,782 OA patients. The transcriptome-wide association study (TWAS) of hand OA was performed using FUnctional Summary-based ImputatiON (FUSION) with the skeletal muscle and blood as gene expression references. The significant genes identified by TWAS were further subjected to gene set enrichment analysis (GSEA) with the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool. Furthermore, we compared the genes and gene sets identified by our TWAS with that of a knee OA mRNA expression profile to detect the genes and gene sets shared by TWAS and mRNA expression profiles in OA. The mRNA expression profiles of 18 normal knee cartilages and 20 OA knee cartilages were acquired from the Gene Expression Omnibus database (accession number: GSE114007). Results TWAS identified 177 genes with P < 0.05 for the skeletal muscle, including ANKRD44 (P = 0.0001), RIC3 (P = 0.0003), and AC005154.6 (P = 0.0004). TWAS identified 423 genes with P < 0.05 for the blood, including CRIM1 (P = 0.0002), ZNF880 (P = 0.0002), and NCKIPSD (P = 0.0003). After comparing the results of the TWAS to those of the mRNA expression profiling of OA, we identified 5 common genes, including DHRS3 (log2fold = − 1.85, P = 3.31 × 10− 9) and SKP2 (log2fold = 1.36, P = 1.62 × 10− 8). GSEA of TWAS identified 51 gene ontology (GO) terms for hand OA, for example, protein binding (P = 0.0003) and cytosol (P = 0.0020). We also detected 6 common GO terms shared by TWAS and mRNA expression profiling, including protein binding (PTWAS = 2.54 × 10− 4, PmRNA = 3.42 × 10− 8), extracellular exosome (PTWAS = 0.02, PmRNA = 1.18 × 10− 4), and cytoplasm (PTWAS = 0.0183, PmRNA = 0.0048). Conclusion In this study, we identified 5 candidate genes and 6 GO terms related to hand OA, which may help to uncover the pathogenesis of hand OA. It should be noted that the possible difference in the gene expression profiles between hand OA and knee OA may affect our study results, which should be interpreted with caution. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02458-2.
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22
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Klyuyeva AV, Belyaeva OV, Goggans KR, Krezel W, Popov KM, Kedishvili NY. Changes in retinoid metabolism and signaling associated with metabolic remodeling during fasting and in type I diabetes. J Biol Chem 2021; 296:100323. [PMID: 33485967 PMCID: PMC7949101 DOI: 10.1016/j.jbc.2021.100323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 01/11/2021] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
Liver is the central metabolic hub that coordinates carbohydrate and lipid metabolism. The bioactive derivative of vitamin A, retinoic acid (RA), was shown to regulate major metabolic genes including phosphoenolpyruvate carboxykinase, fatty acid synthase, carnitine palmitoyltransferase 1, and glucokinase among others. Expression levels of these genes undergo profound changes during adaptation to fasting or in metabolic diseases such as type 1 diabetes (T1D). However, it is unknown whether the levels of hepatic RA change during metabolic remodeling. This study investigated the dynamics of hepatic retinoid metabolism and signaling in the fed state, in fasting, and in T1D. Our results show that fed-to-fasted transition is associated with significant decrease in hepatic retinol dehydrogenase (RDH) activity, the rate-limiting step in RA biosynthesis, and downregulation of RA signaling. The decrease in RDH activity correlates with the decreased abundance and altered subcellular distribution of RDH10 while Rdh10 transcript levels remain unchanged. In contrast to fasting, untreated T1D is associated with upregulation of RA signaling and an increase in hepatic RDH activity, which correlates with the increased abundance of RDH10 in microsomal membranes. The dynamic changes in RDH10 protein levels in the absence of changes in its transcript levels imply the existence of posttranscriptional regulation of RDH10 protein. Together, these data suggest that the downregulation of hepatic RA biosynthesis, in part via the decrease in RDH10, is an integral component of adaptation to fasting. In contrast, the upregulation of hepatic RA biosynthesis and signaling in T1D might contribute to metabolic inflexibility associated with this disease.
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Affiliation(s)
- Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Wojciech Krezel
- Institute of Genetics and Molecular and Cellular Biology (IGBMC) - INSERM, University of Strasbourg, Strasbourg, France
| | - Kirill M Popov
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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23
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An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae. Sci Rep 2020; 10:20654. [PMID: 33244091 PMCID: PMC7691524 DOI: 10.1038/s41598-020-77201-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/06/2020] [Indexed: 12/17/2022] Open
Abstract
Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two "raw" transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture.
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24
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Evolution from adherent to suspension: systems biology of HEK293 cell line development. Sci Rep 2020; 10:18996. [PMID: 33149219 PMCID: PMC7642379 DOI: 10.1038/s41598-020-76137-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.
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25
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Retinoids and developmental neurotoxicity: Utilizing toxicogenomics to enhance adverse outcome pathways and testing strategies. Reprod Toxicol 2020; 96:102-113. [PMID: 32544423 DOI: 10.1016/j.reprotox.2020.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/17/2022]
Abstract
The use of genomic approaches in toxicological studies has greatly increased our ability to define the molecular profiles of environmental chemicals associated with developmental neurotoxicity (DNT). Integration of these approaches with adverse outcome pathways (AOPs), a framework that translates environmental exposures to adverse developmental phenotypes, can potentially inform DNT testing strategies. Here, using retinoic acid (RA) as a case example, we demonstrate that the integration of toxicogenomic profiles into the AOP framework can be used to establish a paradigm for chemical testing. RA is a critical regulatory signaling molecule involved in multiple aspects of mammalian central nervous system (CNS) development, including hindbrain formation/patterning and neuronal differentiation, and imbalances in RA signaling pathways are linked with DNT. While the mechanisms remain unresolved, environmental chemicals can cause DNT by disrupting the RA signaling pathway. First, we reviewed literature evidence of RA and other retinoid exposures and DNT to define a provisional AOP related to imbalances in RA embryonic bioavailability and hindbrain development. Next, by integrating toxicogenomic datasets, we defined a relevant transcriptomic signature associated with RA-induced developmental neurotoxicity (RA-DNT) in human and rodent models that was tested against zebrafish model data, demonstrating potential for integration into an AOP framework. Finally, we demonstrated how these approaches may be systematically utilized to identify chemical hazards by testing the RA-DNT signature against azoles, a proposed class of compounds that alters RA-signaling. The provisional AOP from this study can be expanded in the future to better define DNT biomarkers relevant to RA signaling and toxicity.
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26
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von Lintig J, Moon J, Babino D. Molecular components affecting ocular carotenoid and retinoid homeostasis. Prog Retin Eye Res 2020; 80:100864. [PMID: 32339666 DOI: 10.1016/j.preteyeres.2020.100864] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 12/15/2022]
Abstract
The photochemistry of vision employs opsins and geometric isomerization of their covalently bound retinylidine chromophores. In different animal classes, these light receptors associate with distinct G proteins that either hyperpolarize or depolarize photoreceptor membranes. Vertebrates also use the acidic form of chromophore, retinoic acid, as the ligand of nuclear hormone receptors that orchestrate eye development. To establish and sustain these processes, animals must acquire carotenoids from the diet, transport them, and metabolize them to chromophore and retinoic acid. The understanding of carotenoid metabolism, however, lagged behind our knowledge about the biology of their receptor molecules. In the past decades, much progress has been made in identifying the genes encoding proteins that mediate the transport and enzymatic transformations of carotenoids and their retinoid metabolites. Comparative analysis in different animal classes revealed how evolutionary tinkering with a limited number of genes evolved different biochemical strategies to supply photoreceptors with chromophore. Mutations in these genes impair carotenoid metabolism and induce various ocular pathologies. This review summarizes this advancement and introduces the involved proteins, including the homeostatic regulation of their activities.
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Affiliation(s)
- Johannes von Lintig
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
| | - Jean Moon
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Darwin Babino
- Department of Ophthalmology, School of Medicine, University of Washington, Seattle, WA, USA
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27
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Shannon SR, Yu J, Defnet AE, Bongfeldt D, Moise AR, Kane MA, Trainor PA. Identifying vitamin A signaling by visualizing gene and protein activity, and by quantification of vitamin A metabolites. Methods Enzymol 2020; 637:367-418. [PMID: 32359653 DOI: 10.1016/bs.mie.2020.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Vitamin A (retinol) is an essential nutrient for embryonic development and adult homeostasis. Signaling by vitamin A is carried out by its active metabolite, retinoic acid (RA), following a two-step conversion. RA is a small, lipophilic molecule that can diffuse from its site of synthesis to neighboring RA-responsive cells where it binds retinoic acid receptors within RA response elements of target genes. It is critical that both vitamin A and RA are maintained within a tight physiological range to protect against developmental disorders and disease. Therefore, a series of compensatory mechanisms exist to ensure appropriate levels of each. This strict regulation is provided by a number synthesizing and metabolizing enzymes that facilitate the precise spatiotemporal control of vitamin A metabolism, and RA synthesis and signaling. In this chapter we describe protocols that (1) biochemically isolate and quantify vitamin A and its metabolites and (2) visualize the spatiotemporal activity of genes and proteins involved in the signaling pathway.
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Affiliation(s)
- Stephen R Shannon
- Stowers Institute for Medical Research, Kansas City, MO, United States; University of Kansas Medical Center, Department of Anatomy and Cell Biology, Kansas City, KS, United States
| | - Jianshi Yu
- University of Maryland Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, United States
| | - Amy E Defnet
- University of Maryland Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, United States
| | - Danika Bongfeldt
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON, Canada; Departments of Chemistry and Biochemistry, and Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada
| | - Alexander R Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON, Canada; Departments of Chemistry and Biochemistry, and Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, Canada
| | - Maureen A Kane
- University of Maryland Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, Baltimore, MD, United States
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, United States; University of Kansas Medical Center, Department of Anatomy and Cell Biology, Kansas City, KS, United States.
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Abstract
As the first organ to form and function in all vertebrates, the heart is crucial to development. Tightly-regulated levels of retinoic acid (RA) are critical for the establishment of the regulatory networks that drive normal cardiac development. Thus, the heart is an ideal organ to investigate RA signaling, with much work remaining to be done in this area. Herein, we highlight the role of RA signaling in vertebrate heart development and provide an overview of the field's inception, its current state, and in what directions it might progress so that it may yield fruitful insight for therapeutic applications within the domain of regenerative medicine.
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29
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Adams MK, Belyaeva OV, Kedishvili NY. Generation and isolation of recombinant retinoid oxidoreductase complex. Methods Enzymol 2020; 637:77-93. [PMID: 32359661 DOI: 10.1016/bs.mie.2020.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
All-trans-retinoic acid (RA) is a bioactive lipid that influences many processes in embryonic and adult tissues. Given its bioactive nature, cellular concentrations of this molecule are highly regulated. The oxidation of all-trans-retinol to all-trans-retinaldehyde represents the first and rate-limiting step of the RA synthesis pathway. As such, it is the target of mechanisms that fine-tune RA levels within the cell. RDH10 is one enzyme responsible for the oxidation of all-trans-retinol to all-trans-retinaldehyde, and together with the all-trans-retinaldehyde reductase DHRS3 forms an oligomeric protein complex. The resulting retinoid oxidoreductase complex (ROC) is bifunctional and has the capacity to regulate steady-state levels of the direct precursor of RA, all-trans-retinaldehyde. As ROC represents a major regulatory element within the RA synthesis pathway, it is essential that methods are in place that allow for the study of this complex. Here we describe the production and isolation of recombinant ROC using a baculovirus expression system. Recombinant proteins retain enzymatic activities in intact microsomes and can be affinity purified for analysis. These methods can be used to assist in the assessment of ROC properties and the regulation of this protein complex's functional attributes.
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Affiliation(s)
- Mark K Adams
- Stowers Institute for Medical Research, Kansas City, MO, United States.
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, United States
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Abstract
Generation of the autacoid all-trans-retinoic acid (ATRA) from retinol (vitamin A) relies on a complex metabolon that includes retinol binding-proteins and enzymes from the short-chain dehydrogenase/reductase and aldehyde dehydrogenase gene families. Serum retinol binding-protein delivers all-trans-retinol (vitamin A) from blood to cells through two membrane receptors, Stra6 and Rbpr2. Stra6 and Rbpr2 convey retinol to cellular retinol binding-protein type 1 (Crbp1). Holo-Crbp1 delivers retinol to lecithin: retinol acyl transferase (Lrat) for esterification and storage. Lrat channels retinol directly into its active site from holo-Crbp1 by protein-protein interaction. The ratio apo-Crbp1/holo-Crbp1 directs flux of retinol into and out of retinyl esters, through regulating esterification vs ester hydrolysis. Multiple retinol dehydrogenases (Rdh1, Rdh10, Dhrs9, Rdhe2, Rdhe2s) channel retinol from holo-Crbp1 to generate retinal for ATRA biosynthesis. β-Carotene oxidase type 1 generates retinal from carotenoids, delivered by the scavenger receptor-B1. Retinal reductases (Dhrs3, Dhrs4, Rdh11) reduce retinal into retinol, thereby restraining ATRA biosynthesis. Retinal dehydrogenases (Raldh1, 2, 3) dehydrogenate retinal irreversibly into ATRA. ATRA regulates its own concentrations by inducing Lrat and ATRA degradative enzymes. ATRA exhibits hormesis. Its effects relate to its concentration as an inverted J-shaped curve, transitioning from beneficial in the "goldilocks" zone to toxicity, as concentrations increase. Hormesis has distorted understanding physiological effects of ATRA post-nataly using chow-diet fed, ATRA-dosed animal models. Cancer, immune deficiency and metabolic abnormalities result from mutations and/or insufficiency in Crbp1 and retinoid metabolizing enzymes.
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Affiliation(s)
- Joseph L Napoli
- Graduate Program in Metabolic Biology, Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States.
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31
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Roberts C. Regulating Retinoic Acid Availability during Development and Regeneration: The Role of the CYP26 Enzymes. J Dev Biol 2020; 8:jdb8010006. [PMID: 32151018 PMCID: PMC7151129 DOI: 10.3390/jdb8010006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
This review focuses on the role of the Cytochrome p450 subfamily 26 (CYP26) retinoic acid (RA) degrading enzymes during development and regeneration. Cyp26 enzymes, along with retinoic acid synthesising enzymes, are absolutely required for RA homeostasis in these processes by regulating availability of RA for receptor binding and signalling. Cyp26 enzymes are necessary to generate RA gradients and to protect specific tissues from RA signalling. Disruption of RA homeostasis leads to a wide variety of embryonic defects affecting many tissues. Here, the function of CYP26 enzymes is discussed in the context of the RA signalling pathway, enzymatic structure and biochemistry, human genetic disease, and function in development and regeneration as elucidated from animal model studies.
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Affiliation(s)
- Catherine Roberts
- Developmental Biology of Birth Defects, UCL-GOS Institute of Child Health, 30 Guilford St, London WC1N 1EH, UK;
- Institute of Medical and Biomedical Education St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
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Maguire M, Larsen MC, Vezina CM, Quadro L, Kim YK, Tanumihardjo SA, Jefcoate CR. Cyp1b1 directs Srebp-mediated cholesterol and retinoid synthesis in perinatal liver; Association with retinoic acid activity during fetal development. PLoS One 2020; 15:e0228436. [PMID: 32027669 PMCID: PMC7004353 DOI: 10.1371/journal.pone.0228436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cytochrome P450 1b1 (Cyp1b1) deletion and dietary retinol deficiency during pregnancy (GVAD) affect perinatal liver functions regulated by Srebp. Cyp1b1 is not expressed in perinatal liver but appears in the E9.5 embryo, close to sites of retinoic acid (RA) signaling. Hypothesis Parallel effects of Cyp1b1 and retinol on postnatal Srebp derive from effects in the developing liver or systemic signaling. Approach Cluster postnatal increases in hepatic genes in relation to effects of GVAD or Cyp1b1 deletion. Sort expression changes in relation to genes regulated by Srebp1 and Srebp2.Test these treatments on embryos at E9.5, examining changes at the site of liver initiation. Use in situ hybridization to resolve effects on mRNA distributions of Aldh1a2 and Cyp26a1 (RA homeostasis); Hoxb1 and Pax6 (RA targets). Assess mice lacking Lrat and Rbp4 (DKO mice) that severely limits retinol supply to embryos. Results At birth, GVAD and Cyp1b1 deletion stimulate gene markers of hepatic stellate cell (HSC) activation but also suppress Hamp. These treatments then selectively prevent the postnatal onset of genes that synthesize cholesterol (Hmgcr, Sqle) and fatty acids (Fasn, Scd1), but also direct cholesterol transport (Ldlr, Pcsk9, Stard4) and retinoid synthesis (Aldh1a1, Rdh11). Extensive support by Cyp1b1 is implicated, but with distinct GVAD interventions for Srebp1 and Srebp2. At E9.5, Cyp1b1 is expressed in the septum transversum mesenchyme (STM) with β-carotene oxygenase (Bco1) that generates retinaldehyde. STM provides progenitors for the HSC and supports liver expansion. GVAD and Cyp1b1-/- do not affect RA-dependent Hoxb1 and Pax6. In DKO embryos, RA-dependent Cyp26a1 is lost but Hoxb1 is sustained with Cyp1b1 at multiple sites. Conclusion Cyp1b1-/- suppresses genes supported by Srebp. GVAD effects distinguish Srebp1 and Srebp2 mediation. Srebp regulation overlaps appreciably in cholesterol and retinoid homeostasis. Bco1/Cyp1b1 partnership in the STM may contribute to this later liver regulation.
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Affiliation(s)
- Meghan Maguire
- Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI
| | | | - Chad M. Vezina
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI
| | - Loredana Quadro
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey
| | - Youn-Kyung Kim
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey
| | | | - Colin R. Jefcoate
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI
- * E-mail:
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Sirbu IO, Chiş AR, Moise AR. Role of carotenoids and retinoids during heart development. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1865:158636. [PMID: 31978553 DOI: 10.1016/j.bbalip.2020.158636] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/15/2020] [Accepted: 01/16/2020] [Indexed: 02/08/2023]
Abstract
The nutritional requirements of the developing embryo are complex. In the case of dietary vitamin A (retinol, retinyl esters and provitamin A carotenoids), maternal derived nutrients serve as precursors to signaling molecules such as retinoic acid, which is required for embryonic patterning and organogenesis. Despite variations in the composition and levels of maternal vitamin A, embryonic tissues need to generate a precise amount of retinoic acid to avoid congenital malformations. Here, we summarize recent findings regarding the role and metabolism of vitamin A during heart development and we survey the association of genes known to affect retinoid metabolism or signaling with various inherited disorders. A better understanding of the roles of vitamin A in the heart and of the factors that affect retinoid metabolism and signaling can help design strategies to meet nutritional needs and to prevent birth defects and disorders associated with altered retinoid metabolism. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Affiliation(s)
- Ioan Ovidiu Sirbu
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania; Timisoara Institute of Complex Systems, V. Lucaciu 18, 300044 Timisoara, Romania.
| | - Aimée Rodica Chiş
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Alexander Radu Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada; Department of Chemistry and Biochemistry, Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON P3E 2C6, Canada.
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Belyaeva OV, Adams MK, Popov KM, Kedishvili NY. Generation of Retinaldehyde for Retinoic Acid Biosynthesis. Biomolecules 2019; 10:biom10010005. [PMID: 31861321 PMCID: PMC7022914 DOI: 10.3390/biom10010005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/14/2019] [Accepted: 12/16/2019] [Indexed: 12/11/2022] Open
Abstract
The concentration of all-trans-retinoic acid, the bioactive derivative of vitamin A, is critically important for the optimal performance of numerous physiological processes. Either too little or too much of retinoic acid in developing or adult tissues is equally harmful. All-trans-retinoic acid is produced by the irreversible oxidation of all-trans-retinaldehyde. Thus, the concentration of retinaldehyde as the immediate precursor of retinoic acid has to be tightly controlled. However, the enzymes that produce all-trans-retinaldehyde for retinoic acid biosynthesis and the mechanisms responsible for the control of retinaldehyde levels have not yet been fully defined. The goal of this review is to summarize the current state of knowledge regarding the identities of physiologically relevant retinol dehydrogenases, their enzymatic properties, and tissue distribution, and to discuss potential mechanisms for the regulation of the flux from retinol to retinaldehyde.
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Affiliation(s)
- Olga V. Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
- Correspondence: ; Tel.: +1-205-996-4024
| | - Mark K. Adams
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA;
| | - Kirill M. Popov
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
| | - Natalia Y. Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA; (K.M.P.); (N.Y.K.)
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Carotenoid metabolism at the intestinal barrier. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1865:158580. [PMID: 31794861 DOI: 10.1016/j.bbalip.2019.158580] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/17/2022]
Abstract
Carotenoids exert a rich variety of physiological functions in mammals and are beneficial for human health. These lipids are acquired from the diet and metabolized to apocarotenoids, including retinoids (vitamin A and its metabolites). The small intestine is a major site for their absorption and bioconversion. From here, carotenoids and their metabolites are distributed within the body in triacylglycerol-rich lipoproteins to support retinoid signaling in peripheral tissues and photoreceptor function in the eyes. In recent years, much progress has been made in identifying carotenoid metabolizing enzymes, transporters, and binding proteins. A diet-responsive regulatory network controls the activity of these components and adapts carotenoid absorption and bioconversion to the bodily requirements of these lipids. Genetic variability in the genes encoding these components alters carotenoid homeostasis and is associated with pathologies. We here summarize the advanced state of knowledge about intestinal carotenoid metabolism and its impact on carotenoid and retinoid homeostasis of other organ systems, including the eyes, liver, and immune system. The implication of the findings for science-based intake recommendations for these essential dietary lipids is discussed. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.
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Wang S, Yu J, Kane MA, Moise AR. Modulation of retinoid signaling: therapeutic opportunities in organ fibrosis and repair. Pharmacol Ther 2019; 205:107415. [PMID: 31629008 DOI: 10.1016/j.pharmthera.2019.107415] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/17/2019] [Indexed: 02/08/2023]
Abstract
The vitamin A metabolite, retinoic acid, is an important signaling molecule during embryonic development serving critical roles in morphogenesis, organ patterning and skeletal and neural development. Retinoic acid is also important in postnatal life in the maintenance of tissue homeostasis, while retinoid-based therapies have long been used in the treatment of a variety of cancers and skin disorders. As the number of people living with chronic disorders continues to increase, there is great interest in extending the use of retinoid therapies in promoting the maintenance and repair of adult tissues. However, there are still many conflicting results as we struggle to understand the role of retinoic acid in the multitude of processes that contribute to tissue injury and repair. This review will assess our current knowledge of the role retinoic acid signaling in the development of fibroblasts, and their transformation to myofibroblasts, and of the potential use of retinoid therapies in the treatment of organ fibrosis.
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Affiliation(s)
- Suya Wang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Jianshi Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA.
| | - Alexander R Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada; Departments of Chemistry and Biochemistry, and Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, P3E 2C6, Canada.
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37
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Wu L, Belyaeva OV, Adams MK, Klyuyeva AV, Lee SA, Goggans KR, Kesterson RA, Popov KM, Kedishvili NY. Mice lacking the epidermal retinol dehydrogenases SDR16C5 and SDR16C6 display accelerated hair growth and enlarged meibomian glands. J Biol Chem 2019; 294:17060-17074. [PMID: 31562240 DOI: 10.1074/jbc.ra119.010835] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/24/2019] [Indexed: 12/18/2022] Open
Abstract
Retinol dehydrogenases catalyze the rate-limiting step in the biosynthesis of retinoic acid, a bioactive lipid molecule that regulates the expression of hundreds of genes by binding to nuclear transcription factors, the retinoic acid receptors. Several enzymes exhibit retinol dehydrogenase activities in vitro; however, their physiological relevance for retinoic acid biosynthesis in vivo remains unclear. Here, we present evidence that two murine epidermal retinol dehydrogenases, short-chain dehydrogenase/reductase family 16C member 5 (SDR16C5) and SDR16C6, contribute to retinoic acid biosynthesis in living cells and are also essential for the oxidation of retinol to retinaldehyde in vivo Mice with targeted knockout of the more catalytically active SDR16C6 enzyme have no obvious phenotype, possibly due to functional redundancy, because Sdr16c5 and Sdr16c6 exhibit an overlapping expression pattern during later developmental stages and in adulthood. Mice that lack both enzymes are viable and fertile but display accelerated hair growth after shaving and also enlarged meibomian glands, consistent with a nearly 80% reduction in the retinol dehydrogenase activities of skin membrane fractions from the Sdr16c5/Sdr16c6 double-knockout mice. The up-regulation of hair-follicle stem cell genes is consistent with reduced retinoic acid signaling in the skin of the double-knockout mice. These results indicate that the retinol dehydrogenase activities of murine SDR16C5 and SDR16C6 enzymes are not critical for survival but are responsible for most of the retinol dehydrogenase activity in skin, essential for the regulation of the hair-follicle cycle, and required for the maintenance of both sebaceous and meibomian glands.
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Affiliation(s)
- Lizhi Wu
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Mark K Adams
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Seung-Ah Lee
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Robert A Kesterson
- Department of Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Kirill M Popov
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama 35294
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Wang S, Moise AR. Recent insights on the role and regulation of retinoic acid signaling during epicardial development. Genesis 2019; 57:e23303. [PMID: 31066193 PMCID: PMC6682438 DOI: 10.1002/dvg.23303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 12/18/2022]
Abstract
The vitamin A metabolite, retinoic acid, carries out essential and conserved roles in vertebrate heart development. Retinoic acid signals via retinoic acid receptors (RAR)/retinoid X receptors (RXRs) heterodimers to induce the expression of genes that control cell fate specification, proliferation, and differentiation. Alterations in retinoic acid levels are often associated with congenital heart defects. Therefore, embryonic levels of retinoic acid need to be carefully regulated through the activity of enzymes, binding proteins and transporters involved in vitamin A metabolism. Here, we review evidence of the complex mechanisms that control the fetal uptake and synthesis of retinoic acid from vitamin A precursors. Next, we highlight recent evidence of the role of retinoic acid in orchestrating myocardial compact zone growth and coronary vascular development.
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Affiliation(s)
- Suya Wang
- Department of Cardiology, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Alexander R. Moise
- Medical Sciences Division, Northern Ontario School of Medicine, Sudbury, ON P3E 2C6, Canada
- Departments of Chemistry and Biochemistry, and Biology and Biomolecular Sciences Program, Laurentian University, Sudbury, ON, P3E 2C6 Canada
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, KS, 66045, USA
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Kim EW, De Leon A, Jiang Z, Radu RA, Martineau AR, Chan ED, Bai X, Su WL, Montoya DJ, Modlin RL, Liu PT. Vitamin A Metabolism by Dendritic Cells Triggers an Antimicrobial Response against Mycobacterium tuberculosis. mSphere 2019; 4:e00327-19. [PMID: 31167948 PMCID: PMC6553556 DOI: 10.1128/msphere.00327-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/12/2019] [Indexed: 12/24/2022] Open
Abstract
Epidemiological evidence correlates low serum vitamin A (retinol) levels with increased susceptibility to active tuberculosis (TB); however, retinol is biologically inactive and must be converted into its bioactive form, all-trans retinoic acid (ATRA). Given that ATRA triggers a Niemann-Pick type C2 (NPC2)-dependent antimicrobial response against Mycobacterium tuberculosis, we investigated the mechanism by which the immune system converts retinol into ATRA at the site of infection. We demonstrate that granulocyte-macrophage colony-stimulating factor (GM-CSF)-derived dendritic cells (DCs), but not macrophages, express enzymes in the vitamin A metabolic pathway, including aldehyde dehydrogenase 1 family, member a2 (ALDH1A2) and short-chain dehydrogenase/reductase family, member 9 (DHRS9), enzymes capable of the two-step conversion of retinol into ATRA, which is subsequently released from the cell. Additionally, mRNA and protein expression levels of ALDH1A2 and DC marker CD1B were lower in tuberculosis lung tissues than in normal lung. The conditioned medium from DCs cultured with retinol stimulated antimicrobial activity from M. tuberculosis-infected macrophages, as well as the expression of NPC2 in monocytes, which was blocked by specific inhibitors, including retinoic acid receptor inhibitor (RARi) or N,N-diethylaminobenzaldehyde (DEAB), an ALDH1A2 inhibitor. These results indicate that metabolism of vitamin A by DCs transactivates macrophage antimicrobial responses.IMPORTANCE Tuberculosis (TB) is the leading cause of death by a single infectious agent worldwide. One factor that contributes to the success of the microbe is the deficiency in immunomodulatory nutrients, such as vitamin A (retinol), which are prevalent in areas where TB is endemic. Clinical trials show that restoration of systemic retinol levels in active TB patients is ineffective in mitigating the disease; however, laboratory studies demonstrate that activation of the vitamin A pathway in Mycobacterium tuberculosis-infected macrophages triggers an antimicrobial response. Therefore, the goal of this study was to determine the link between host retinol levels and retinoic acid-mediated antimicrobial responses against M. tuberculosis By combining established in vitro models with in situ studies of lung tissue from TB patients, this study demonstrates that the innate immune system utilizes transcellular metabolism leading to activation between dendritic cells and macrophages as a means to combat the pathogen.
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Affiliation(s)
- Elliot W Kim
- Department of Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
- UCLA and Orthopaedic Hospital Department of Orthopaedic Surgery, The Orthopaedic Hospital Research Center, Los Angeles, Los Angeles, California, USA
| | - Avelino De Leon
- Division of Dermatology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Zhichun Jiang
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Roxana A Radu
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Adrian R Martineau
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Edward D Chan
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, Colorado, USA
| | - Xiyuan Bai
- Department of Medicine and Academic Affairs, National Jewish Health, Denver, Colorado, USA
| | - Wen-Lin Su
- Division of Pulmonary and Critical Care Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei, Taiwan
| | - Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Robert L Modlin
- Division of Dermatology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Philip T Liu
- Division of Dermatology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- UCLA and Orthopaedic Hospital Department of Orthopaedic Surgery, The Orthopaedic Hospital Research Center, Los Angeles, Los Angeles, California, USA
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Perl E, Waxman JS. Reiterative Mechanisms of Retinoic Acid Signaling during Vertebrate Heart Development. J Dev Biol 2019; 7:jdb7020011. [PMID: 31151214 PMCID: PMC6631158 DOI: 10.3390/jdb7020011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/25/2019] [Accepted: 05/28/2019] [Indexed: 01/07/2023] Open
Abstract
Tightly-regulated levels of retinoic acid (RA) are critical for promoting normal vertebrate development. The extensive history of research on RA has shown that its proper regulation is essential for cardiac progenitor specification and organogenesis. Here, we discuss the roles of RA signaling and its establishment of networks that drive both early and later steps of normal vertebrate heart development. We focus on studies that highlight the drastic effects alternative levels of RA have on early cardiomyocyte (CM) specification and cardiac chamber morphogenesis, consequences of improper RA synthesis and degradation, and known effectors downstream of RA. We conclude with the implications of these findings to our understanding of cardiac regeneration and the etiologies of congenital heart defects.
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Affiliation(s)
- Eliyahu Perl
- Molecular and Developmental Biology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Joshua S Waxman
- The Heart Institute and Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, USA.
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Wu L, Kedishvili NY, Belyaeva OV. Retinyl esters are elevated in progeny of retinol dehydrogenase 11 deficient dams. Chem Biol Interact 2019; 302:117-122. [PMID: 30731079 DOI: 10.1016/j.cbi.2019.01.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/03/2019] [Accepted: 01/31/2019] [Indexed: 11/29/2022]
Abstract
Retinol dehydrogenase 11 (RDH11) is an NADPH-dependent retinaldehyde reductase that was previously reported to function in the visual cycle. Recently, we have shown that RDH11 contributes to the maintenance of retinol levels in extraocular tissues under conditions of vitamin A deficiency or reduced vitamin A availability. RDH11 is also expressed in the embryo. Rdh11 knockout animals do not display embryonic defects and appear to develop normally to the adult stage, but the exact function of RDH11 during development is not yet known. In contrast to RDH11-null mice, animals that lack dehydrogenase/reductase 3 (DHRS3), the enzyme that functions as a retinaldehyde reductase and is essential for the maintenance of retinoid homeostasis during embryogenesis, rarely survive until birth. Here, we investigated whether inactivation of RDH11 together with DHRS3 exacerbates the severity of retinoid homeostasis disruption in embryos that lack both enzymes compared to DHRS3-null mice. The results of this study indicate that in vitamin A sufficient animals, the loss of RDH11 in addition to DHRS3 does not appear to significantly impact the total levels of retinoic acid, free retinol, or retinyl esters in Rdh11-/-/Dhrs3-/-embryos in comparison to Dhrs3-/- embryos. Surprisingly, Rdh11-/- single gene knockout embryos obtained from breeding of Rdh11-/- dams display elevated levels of embryonic retinyl esters compared to wild type embryos. The mechanism of the maternal effect of Rdh11 status on fetal retinoid stores remains to be elucidated.
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Affiliation(s)
- Lizhi Wu
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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Zemanová L, Navrátilová H, Andrýs R, Šperková K, Andrejs J, Kozáková K, Meier M, Möller G, Novotná E, Šafr M, Adamski J, Wsól V. Initial characterization of human DHRS1 (SDR19C1), a member of the short-chain dehydrogenase/reductase superfamily. J Steroid Biochem Mol Biol 2019; 185:80-89. [PMID: 30031147 DOI: 10.1016/j.jsbmb.2018.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 07/05/2018] [Accepted: 07/17/2018] [Indexed: 11/28/2022]
Abstract
Many enzymes from the short-chain dehydrogenase/reductase superfamily (SDR) have already been well characterized, particularly those that participate in crucial biochemical reactions in the human body (e.g. 11β-hydroxysteroid dehydrogenase 1, 17β-hydroxysteroid dehydrogenase 1 or carbonyl reductase 1). Several other SDR enzymes are completely or almost completely uncharacterized, such as DHRS1 (also known as SDR19C1). Based on our in silico and experimental approaches, DHRS1 is described as a likely monotopic protein that interacts with the membrane of the endoplasmic reticulum. The highest expression level of DHRS1 protein was observed in human liver and adrenals. The recombinant form of DHRS1 was purified using the detergent n-dodecyl-β-D-maltoside, and DHRS1 was proven to be an NADPH-dependent reductase that is able to catalyse the in vitro reductive conversion of some steroids (estrone, androstene-3,17-dione and cortisone), as well as other endogenous substances and xenobiotics. The expression pattern and enzyme activities fit to a role in steroid and/or xenobiotic metabolism; however, more research is needed to fully clarify the exact biological function of DHRS1.
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Affiliation(s)
- Lucie Zemanová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic.
| | - Hana Navrátilová
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Rudolf Andrýs
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Rokitanskeho 62, 500 03 Hradec Kralove, Czech Republic
| | - Kristýna Šperková
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Jiří Andrejs
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Klára Kozáková
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Marc Meier
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Gabriele Möller
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Eva Novotná
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
| | - Miroslav Šafr
- Institute of Legal Medicine, Faculty of Medicine in Hradec Králové, Charles University and University Hospital in Hradec Králové, Sokolská 581, 500 05 Hradec Kralove, Czech Republic
| | - Jerzy Adamski
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany; Lehrstuhl für Experimentelle Genetik, Technische Universität München, 85350 Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
| | - Vladimír Wsól
- Department of Biochemical Sciences, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovskeho 1203, 500 05 Hradec Kralove, Czech Republic
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43
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Wang S, Huang W, Castillo HA, Kane MA, Xavier-Neto J, Trainor PA, Moise AR. Alterations in retinoic acid signaling affect the development of the mouse coronary vasculature. Dev Dyn 2018; 247:976-991. [PMID: 29806219 DOI: 10.1002/dvdy.24639] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 05/08/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND During the final stages of heart development the myocardium grows and becomes vascularized by means of paracrine factors and cell progenitors derived from the epicardium. There is evidence to suggest that retinoic acid (RA), a metabolite of vitamin A, plays an important role in epicardial-based developmental programming. However, the consequences of altered RA-signaling in coronary development have not been systematically investigated. RESULTS We explored the developmental consequences of altered RA-signaling in late cardiogenic events that involve the epicardium. For this, we used a model of embryonic RA excess based on mouse embryos deficient in the retinaldehyde reductase DHRS3, and a complementary model of embryonic RA deficiency based on pharmacological inhibition of RA synthesis. We found that alterations in embryonic RA signaling led to a thin myocardium and aberrant coronary vessel formation and remodeling. Both excess, and deficient RA-signaling are associated with reductions in ventricular coverage and density of coronary vessels, altered vessel morphology, and impaired recruitment of epicardial-derived mural cells. Using a combined transcriptome and proteome profiling approach, we found that RA treatment of epicardial cells influenced key signaling pathways relevant for cardiac development. CONCLUSIONS Epicardial RA-signaling plays critical roles in the development of the coronary vasculature needed to support myocardial growth. Developmental Dynamics 247:976-991, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Suya Wang
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - Hozana A Castillo
- Brazilian Biosciences National Laboratory, LNBio, Rua Giuseppe Máximo Scolfaro, Polo II de Alta Tecnologia de Campinas, Campinas, SP, Brazil
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland
| | - José Xavier-Neto
- Conselho Nacional do Desenvolvimnto Científico e Tecnológico (Cnpq) CEP 01414000 Cerqueira Cesar Sao Paulo, Sao Paulo, Brazil
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas
| | - Alexander R Moise
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas.,Northern Ontario School of Medicine, Biomolecular Sciences Program and Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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44
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Belyaeva OV, Wu L, Shmarakov I, Nelson PS, Kedishvili NY. Retinol dehydrogenase 11 is essential for the maintenance of retinol homeostasis in liver and testis in mice. J Biol Chem 2018; 293:6996-7007. [PMID: 29567832 DOI: 10.1074/jbc.ra117.001646] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/20/2018] [Indexed: 11/06/2022] Open
Abstract
Retinol dehydrogenase 11 (RDH11) is a microsomal short-chain dehydrogenase/reductase that recognizes all-trans- and cis-retinoids as substrates and prefers NADPH as a cofactor. Previous work has suggested that RDH11 contributes to the oxidation of 11-cis-retinol to 11-cis-retinaldehyde during the visual cycle in the eye's retinal pigment epithelium. However, the role of RDH11 in metabolism of all-trans-retinoids remains obscure. Here, we report that microsomes isolated from the testes and livers of Rdh11-/- mice fed a regular diet exhibited a 3- and 1.7-fold lower rate of all-trans-retinaldehyde conversion to all-trans-retinol, respectively, than the microsomes of WT littermates. Testes and livers of Rdh11-/- mice fed a vitamin A-deficient diet had ∼35% lower levels of all-trans-retinol than those of WT mice. Furthermore, the conversion of β-carotene to retinol via retinaldehyde as an intermediate appeared to be impaired in the testes of Rdh11-/-/retinol-binding protein 4-/-(Rbp4-/-) mice, which lack circulating holo RBP4 and rely on dietary supplementation with β-carotene for maintenance of their retinoid stores. Together, these results indicate that in mouse testis and liver, RDH11 functions as an all-trans-retinaldehyde reductase essential for the maintenance of physiological levels of all-trans-retinol under reduced vitamin A availability.
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Affiliation(s)
- Olga V Belyaeva
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Lizhi Wu
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Igor Shmarakov
- the Department of Medicine, Columbia University, New York, New York 21007
| | - Peter S Nelson
- the Departments of Urology and Medicine, University of Washington, Seattle, Washington 98195, and.,the Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Natalia Y Kedishvili
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294,
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45
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Wang S, Yu J, Jones JW, Pierzchalski K, Kane MA, Trainor PA, Xavier-Neto J, Moise AR. Retinoic acid signaling promotes the cytoskeletal rearrangement of embryonic epicardial cells. FASEB J 2018; 32:3765-3781. [PMID: 29447006 DOI: 10.1096/fj.201701038r] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
All- trans-retinoic acid (RA), a vitamin A metabolite, is an important signaling molecule required for the proper development of the heart. The epicardium is the main source of RA in the embryonic heart, yet the cardiogenic functions of epicardial-produced RA are not fully understood. Here, we investigated the roles of RA signaling in the embryonic epicardium using in vivo and in vitro models of excess or deficiency of RA. Our results suggested that RA signaling facilitates the cytoskeletal rearrangement required for the epicardial-to-mesenchymal transition of epicardial cells. In vivo treatment with an inhibitor of RA synthesis delayed the migration of epicardial-derived precursor cells (EPDCs) into the myocardium; the opposite was seen in the case of dehydrogenase/reductase superfamily (DHRS)3-deficient embryos, a mouse model of RA excess. Analysis of the behavior of epicardial cells exposed to RA receptor agonists or inhibitors of RA synthesis in vitro revealed that appropriate levels of RA are important in orchestrating the platelet-derived growth factor-induced loss of epithelial character, cytoskeletal remodeling, and migration, necessary for the infiltration of the myocardium by EPDCs. To understand the molecular mechanisms by which RA regulates epicardial cytoskeletal rearrangement, we used a whole transcriptome profiling approach, which in combination with pull-down and inhibition assays, demonstrated that the Ras homolog gene family, member A (RhoA) pathway is required for the morphologic changes induced by RA in epicardial cells. Collectively, these data demonstrate that RA regulates the cytoskeletal rearrangement of epicardial cells via a signaling cascade that involves the RhoA pathway.-Wang, S., Yu, J., Jones, J. W., Pierzchalski, K., Kane, M. A., Trainor, P. A., Xavier-Neto, J., Moise, A. R. Retinoic acid signaling promotes the cytoskeletal rearrangement of embryonic epicardial cells.
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Affiliation(s)
- Suya Wang
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas, USA
| | - Jianshi Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Jace W Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Keely Pierzchalski
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, Missouri, USA.,Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - José Xavier-Neto
- Conselho Nacional do Desenvolvimento Científico e Tecnológico (CNPq) Sao Paulo, Brazil; and
| | - Alexander R Moise
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Kansas, Lawrence, Kansas, USA.,Northern Ontario School of Medicine, Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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Abstract
Multiple binding and transport proteins facilitate many aspects of retinoid biology through effects on retinoid transport, cellular uptake, metabolism, and nuclear delivery. These include the serum retinol binding protein sRBP (aka Rbp4), the plasma membrane sRBP receptor Stra6, and the intracellular retinoid binding-proteins such as cellular retinol-binding proteins (CRBP) and cellular retinoic acid binding-proteins (CRABP). sRBP transports the highly lipophilic retinol through an aqueous medium. The major intracellular retinol-binding protein, CRBP1, likely enhances efficient retinoid use by providing a sink to facilitate retinol uptake from sRBP through the plasma membrane or via Stra6, delivering retinol or retinal to select enzymes that generate retinyl esters or retinoic acid, and protecting retinol/retinal from excess catabolism or opportunistic metabolism. Intracellular retinoic acid binding-proteins (CRABP1 and 2, and FABP5) seem to have more diverse functions distinctive to each, such as directing retinoic acid to catabolism, delivering retinoic acid to specific nuclear receptors, and generating non-canonical actions. Gene ablation of intracellular retinoid binding-proteins does not cause embryonic lethality or gross morphological defects. Metabolic and functional defects manifested in knockouts of CRBP1, CRBP2 and CRBP3, however, illustrate their essentiality to health, and in the case of CRBP2, to survival during limited dietary vitamin A. Future studies should continue to address the specific molecular interactions that occur between retinoid binding-proteins and their targets and their precise physiologic contributions to retinoid homeostasis and function.
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Affiliation(s)
- Joseph L Napoli
- Graduate Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, 119 Morgan Hall, 94720, Berkeley, CA, USA.
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47
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McKeown MR, Corces MR, Eaton ML, Fiore C, Lee E, Lopez JT, Chen MW, Smith D, Chan SM, Koenig JL, Austgen K, Guenther MG, Orlando DA, Lovén J, Fritz CC, Majeti R. Superenhancer Analysis Defines Novel Epigenomic Subtypes of Non-APL AML, Including an RARα Dependency Targetable by SY-1425, a Potent and Selective RARα Agonist. Cancer Discov 2017; 7:1136-1153. [PMID: 28729405 PMCID: PMC5962349 DOI: 10.1158/2159-8290.cd-17-0399] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 06/22/2017] [Accepted: 07/18/2017] [Indexed: 01/11/2023]
Abstract
We characterized the enhancer landscape of 66 patients with acute myeloid leukemia (AML), identifying 6 novel subgroups and their associated regulatory loci. These subgroups are defined by their superenhancer (SE) maps, orthogonal to somatic mutations, and are associated with distinct leukemic cell states. Examination of transcriptional drivers for these epigenomic subtypes uncovers a subset of patients with a particularly strong SE at the retinoic acid receptor alpha (RARA) gene locus. The presence of a RARA SE and concomitant high levels of RARA mRNA predisposes cell lines and ex vivo models to exquisite sensitivity to a selective agonist of RARα, SY-1425 (tamibarotene). Furthermore, only AML patient-derived xenograft (PDX) models with high RARA mRNA were found to respond to SY-1425. Mechanistically, we show that the response to SY-1425 in RARA-high AML cells is similar to that of acute promyelocytic leukemia treated with retinoids, characterized by the induction of known retinoic acid response genes, increased differentiation, and loss of proliferation.Significance: We use the SE landscape of primary human AML to elucidate transcriptional circuitry and identify novel cancer vulnerabilities. A subset of patients were found to have an SE at RARA, which is predictive for response to SY-1425, a potent and selective RARα agonist, in preclinical models, forming the rationale for its clinical investigation in biomarker-selected patients. Cancer Discov; 7(10); 1136-53. ©2017 AACR.See related commentary by Wang and Aifantis, p. 1065.This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
| | - M Ryan Corces
- Program in Cancer Biology, Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center Stanford University School of Medicine, Stanford, California
| | | | - Chris Fiore
- Syros Pharmaceuticals, Cambridge, Massachusetts
| | - Emily Lee
- Syros Pharmaceuticals, Cambridge, Massachusetts
| | | | | | | | - Steven M Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Julie L Koenig
- Program in Cancer Biology, Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center Stanford University School of Medicine, Stanford, California
| | | | | | | | - Jakob Lovén
- Syros Pharmaceuticals, Cambridge, Massachusetts
| | | | - Ravindra Majeti
- Program in Cancer Biology, Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, and Ludwig Center Stanford University School of Medicine, Stanford, California.
- Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California
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48
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The role of retinol dehydrogenase 10 in the cone visual cycle. Sci Rep 2017; 7:2390. [PMID: 28539612 PMCID: PMC5443843 DOI: 10.1038/s41598-017-02549-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
Pigment regeneration is critical for the function of cone photoreceptors in bright and rapidly-changing light conditions. This process is facilitated by the recently-characterized retina visual cycle, in which Müller cells recycle spent all-trans-retinol visual chromophore back to 11-cis-retinol. This 11-cis-retinol is oxidized selectively in cones to the 11-cis-retinal used for pigment regeneration. However, the enzyme responsible for the oxidation of 11-cis-retinol remains unknown. Here, we sought to determine whether retinol dehydrogenase 10 (RDH10), upregulated in rod/cone hybrid retinas and expressed abundantly in Müller cells, is the enzyme that drives this reaction. We created mice lacking RDH10 either in cone photoreceptors, Müller cells, or the entire retina. In vivo electroretinography and transretinal recordings revealed normal cone photoresponses in all RDH10-deficient mouse lines. Notably, their cone-driven dark adaptation both in vivo and in isolated retina was unaffected, indicating that RDH10 is not required for the function of the retina visual cycle. We also generated transgenic mice expressing RDH10 ectopically in rod cells. However, rod dark adaptation was unaffected by the expression of RDH10 and transgenic rods were unable to use cis-retinol for pigment regeneration. We conclude that RDH10 is not the dominant retina 11-cis-RDH, leaving its primary function in the retina unknown.
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49
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Peroxisome Proliferator-Activated Receptor α Activation Is Not the Main Contributor to Teratogenesis Elicited by Polar Compounds from Oxidized Frying Oil. Int J Mol Sci 2017; 18:ijms18030510. [PMID: 28264465 PMCID: PMC5372526 DOI: 10.3390/ijms18030510] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/16/2017] [Accepted: 02/23/2017] [Indexed: 01/28/2023] Open
Abstract
We previously reported that polar compounds (PO) in cooking oil are teratogenic and perturbed retinoic acid (RA) metabolism. Considering PO as a potent peroxisome proliferator-activated receptor α (PPARα) activator, this study aimed to investigate the role of PPARα in PO-induced teratogenesis and disturbance of RA metabolism. Female PPARα knockout or wild type mice were mated with males of the same genotype. Pregnant mice were fed a diet containing 10% fat from either fresh oil (FO) or PO from gestational day1 to day18, and killed at day18. The PO diet significantly increased the incidence of teratogenesis and fetal RA concentrations, regardless of genotype. Though PPARα deficiency disturbed maternal RA homeostasis, itself did not contribute to teratogenesis as long as FO diet was given. The mRNA profile of genes involved in RA metabolism was differentially affected by diet or genotype in mothers and fetuses. Based on hepatic mRNA levels of genes involved in xenobiotic metabolism, we inferred that PO not only activated PPARα, but also altered transactivity of other xenobiotic receptors. We concluded that PO-induced fetal anomalies and RA accumulation were independent of PPARα activation.
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50
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Belyaeva OV, Adams MK, Wu L, Kedishvili NY. The antagonistically bifunctional retinoid oxidoreductase complex is required for maintenance of all- trans-retinoic acid homeostasis. J Biol Chem 2017; 292:5884-5897. [PMID: 28232491 DOI: 10.1074/jbc.m117.776914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/21/2017] [Indexed: 11/06/2022] Open
Abstract
All-trans-retinoic acid (RA), a bioactive derivative of vitamin A, exhibits diverse effects on gene transcription and non-genomic regulatory pathways. The steady-state levels of RA are therefore tightly controlled, but the mechanisms responsible for RA homeostasis are not fully understood. We report a molecular mechanism that allows cells to maintain a stable rate of RA biosynthesis by utilizing a biological circuit generated by a bifunctional retinoid oxidoreductive complex (ROC). We show that ROC is composed of at least two subunits of NAD+-dependent retinol dehydrogenase 10 (RDH10), which catalyzes the oxidation of retinol to retinaldehyde, and two subunits of NADPH-dependent dehydrogenase reductase 3 (DHRS3), which catalyzes the reduction of retinaldehyde back to retinol. RDH10 and DHRS3 also exist as homo-oligomers. When complexed, RDH10 and DHRS3 mutually activate and stabilize each other. These features of ROC ensure that the rate of RA biosynthesis in whole cells is largely independent of the concentration of the individual ROC components. ROC operates in various subcellular fractions including microsomes, mitochondria, and lipid droplets; however, lipid droplets display weaker mutual activation between RDH10 and DHRS3, suggesting reduced formation of ROC. Importantly, disruption of the ROC-generated circuit by a knockdown of DHRS3 results in an increased flux through the RA biosynthesis pathway and elevated RA levels despite the decrease in RDH10 protein destabilized by the absence of DHRS3, hence demonstrating a loss of control. Thus, the bifunctional nature of ROC provides the RA-based signaling system with robustness by safeguarding appropriate RA concentration despite naturally occurring fluctuations in RDH10 and DHRS3.
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Affiliation(s)
- Olga V Belyaeva
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Mark K Adams
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Lizhi Wu
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Natalia Y Kedishvili
- From the Department of Biochemistry and Molecular Genetics, Schools of Medicine and Dentistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
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