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Rani A. RAR-related orphan receptor alpha and the staggerer mice: a fine molecular story. Front Endocrinol (Lausanne) 2024; 14:1300729. [PMID: 38766309 PMCID: PMC11099308 DOI: 10.3389/fendo.2023.1300729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/15/2023] [Indexed: 05/22/2024] Open
Abstract
The retinoic acid-related orphan receptor alpha (RORα) protein first came into the limelight due to a set of staggerer mice, discovered at the Jackson Laboratories in the United States of America by Sidman, Lane, and Dickie (1962) and genetically deciphered by Hamilton et al. in 1996. These staggerer mice exhibited cerebellar defects, an ataxic gait, a stagger along with several other developmental abnormalities, compensatory mechanisms, and, most importantly, a deletion of 160 kilobases (kb), encompassing the RORα ligand binding domain (LBD). The discovery of the staggerer mice and the subsequent discovery of a loss of the LBD within the RORα gene of these mice at the genetic level clearly indicated that RORα's LBD played a crucial role in patterning during embryogenesis. Moreover, a chance study by Roffler-Tarlov and Sidman (1978) noted reduced concentrations of glutamic acid levels in the staggerer mice, indicating a possible role for the essence of a nutritionally balanced diet. The sequential organisation of the building blocks of intact genes, requires the nucleotide bases of deoxyribonucleic acid (DNA): purines and pyrimidines, both of which are synthesized, upon a constant supply of glutamine, an amino acid fortified in a balanced diet and a byproduct of the carbohydrate and lipid metabolic pathways. A nutritionally balanced diet, along with a metabolic "enzymatic machinery" devoid of mutations/aberrations, was essential in the uninterrupted transcription of RORα during embryogenesis. In addition to the above, following translation, a ligand-responsive RORα acts as a "molecular circadian regulator" during embryogenesis and not only is expressed selectively and differentially, but also promotes differential activity depending on the anatomical and pathological site of its expression. RORα is highly expressed in the central nervous system (CNS) and the endocrine organs. Additionally, RORα and the clock genes are core components of the circadian rhythmicity, with the expression of RORα fluctuating in a night-day-night sigmoidal pattern and undoubtedly serves as an endocrine-like, albeit "molecular-circadian regulator". Melatonin, a circadian hormone, along with tri-iodothyronine and some steroid hormones are known to regulate RORα-mediated molecular activity, with each of these hormones themselves being regulated rhythmically by the hypothalamic-pituitary axis (HPA). The HPA regulates the circadian rhythm and cyclical release of hormones, in a self-regulatory feedback loop. Irregular sleep-wake patterns affect circadian rhythmicity and the ability of the immune system to withstand infections. The staggerer mice with their thinner bones, an altered skeletal musculature, an aberrant metabolic profile, the ataxic gait and an underdeveloped cerebellar cortex; exhibited compensatory mechanisms, that not only allowed the survival of the staggerer mice, but also enhanced protection from microbial invasions and resistance to high-fat-diet induced obesity. This review has been compiled in its present form, more than 14 years later after a chromatin immunoprecipitation (ChIP) cloning and sequencing methodology helped me identify signal transducer and activator of transcription 5 (STAT5) target sequences, one of which was mapped to the first intron of the RORα gene. The 599-base-long sequence containing one consensus TTCNNNGAA (TTCN3GAA) gamma-activated sequence (GAS) and five other non-consensus TTN5AA sequences had been identified from the clones isolated from the STAT5 target sites (fragments) in human phytohemagglutinin-activated CD8+ T lymphocytes, during my doctoral studies between 2006 and 2009. Most importantly, preliminary studies noted a unique RORα expression profile, during a time-course study on the ribonucleic acid (RNA), extracted from human phytohemagglutinin (PHA) activated CD8+ T lymphocytes stimulated with interleukin-2 (IL-2). This review mainly focuses on the "staggerer mice" with one of its first roles materialising during embryogenesis, a molecular-endocrine mediated circadian-like regulatory process.
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Affiliation(s)
- Aradhana Rani
- Medical Biochemistry, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Pondicherry, India
- Human Resource Development and Management, Indian Institute of Technology (IIT) Kharagpur, West Bengal, India
- Immunology, King’s College London, London, United Kingdom
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Guo J, Zhang H, Lin W, Lu L, Su J, Chen X. Signaling pathways and targeted therapies for psoriasis. Signal Transduct Target Ther 2023; 8:437. [PMID: 38008779 PMCID: PMC10679229 DOI: 10.1038/s41392-023-01655-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/10/2023] [Accepted: 09/14/2023] [Indexed: 11/28/2023] Open
Abstract
Psoriasis is a common, chronic, and inflammatory skin disease with a high burden on individuals, health systems, and society worldwide. With the immunological pathologies and pathogenesis of psoriasis becoming gradually revealed, the therapeutic approaches for this disease have gained revolutionary progress. Nevertheless, the mechanisms of less common forms of psoriasis remain elusive. Furthermore, severe adverse effects and the recurrence of disease upon treatment cessation should be noted and addressed during the treatment, which, however, has been rarely explored with the integration of preliminary findings. Therefore, it is crucial to have a comprehensive understanding of the mechanisms behind psoriasis pathogenesis, which might offer new insights for research and lead to more substantive progress in therapeutic approaches and expand clinical options for psoriasis treatment. In this review, we looked to briefly introduce the epidemiology, clinical subtypes, pathophysiology, and comorbidities of psoriasis and systematically discuss the signaling pathways involving extracellular cytokines and intracellular transmission, as well as the cross-talk between them. In the discussion, we also paid more attention to the potential metabolic and epigenetic mechanisms of psoriasis and the molecular mechanistic cascades related to its comorbidities. This review also outlined current treatment for psoriasis, especially targeted therapies and novel therapeutic strategies, as well as the potential mechanism of disease recurrence.
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Affiliation(s)
- Jia Guo
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Hanyi Zhang
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Wenrui Lin
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Lixia Lu
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
| | - Xiang Chen
- Department of Dermatology, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, Hunan, China.
- National Engineering Research Center of Personalized Diagnostic and Therapeutic Technology, Changsha, 410008, Hunan, China.
- Hunan Key Laboratory of Skin Cancer and Psoriasis, Changsha, 410008, Hunan, China.
- Hunan Engineering Research Center of Skin Health and Disease, Changsha, 410008, Hunan, China.
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Park KC, Kim J, Lee A, Lim JS, Kim KI. Alleviation of imiquimod-induced psoriasis-like symptoms in Rorα-deficient mouse skin. BMB Rep 2023; 56:296-301. [PMID: 36698281 PMCID: PMC10230014 DOI: 10.5483/bmbrep.2022-0169] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/15/2022] [Accepted: 01/25/2023] [Indexed: 11/26/2023] Open
Abstract
Retinoic acid receptor-related orphan receptor α (RORα) plays a vital role in various physiological processes, including metabolism, cancer, circadian rhythm, cerebellar development, and inflammation. Although RORα is expressed in the skin, its role in skin physiology remains poorly elucidated. Herein, Rorα was expressed in the basal and suprabasal layers of the epidermis; however, keratinocyte-specific Rorα deletion did not impact normal epidermal formation. Under pathophysiological conditions, Rorα-deficient mice exhibited alleviated psoriasis-like symptoms, including relatively intact epidermal stratification, reduced keratinocyte hyperproliferation, and low-level expression of inflammatory cytokines in keratinocytes. Unexpectedly, the splenic population of Th17 cells was significantly lower in keratinocytespecific RORα deficient mice than in the control. Additionally, Rorα-deficiency reduced imiquimod-induced activation of nuclear factor-κB and STAT3 in keratinocytes. Therefore, we expect that RORα inhibitors act on immune cells and keratinocytes to suppress the onset and progression of psoriasis.as an adjuvant for cancer immunotherapy. [BMB Reports 2023; 56(5): 296-301].
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Affiliation(s)
- Koog Chan Park
- Research Institute of Women’s Health, Sookmyung Women
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women’s University, Seoul 04310, Korea
| | - Jiwon Kim
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women’s University, Seoul 04310, Korea
| | - Aram Lee
- Research Institute of Women’s Health, Sookmyung Women
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women’s University, Seoul 04310, Korea
| | - Jong-Seok Lim
- Research Institute of Women’s Health, Sookmyung Women
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women’s University, Seoul 04310, Korea
| | - Keun Il Kim
- Research Institute of Women’s Health, Sookmyung Women
- Department of Biological Sciences, Cellular Heterogeneity Research Center, Sookmyung Women’s University, Seoul 04310, Korea
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Loers JU, Vermeirssen V. SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks. BMC Bioinformatics 2022; 23:363. [PMID: 36064320 PMCID: PMC9442970 DOI: 10.1186/s12859-022-04908-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/24/2022] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Representing the complex interplay between different types of biomolecules across different omics layers in multi-omics networks bears great potential to gain a deep mechanistic understanding of gene regulation and disease. However, multi-omics networks easily grow into giant hairball structures that hamper biological interpretation. Module detection methods can decompose these networks into smaller interpretable modules. However, these methods are not adapted to deal with multi-omics data nor consider topological features. When deriving very large modules or ignoring the broader network context, interpretability remains limited. To address these issues, we developed a SUbgraph BAsed mulTi-OMIcs Clustering framework (SUBATOMIC), which infers small and interpretable modules with a specific topology while keeping track of connections to other modules and regulators. RESULTS SUBATOMIC groups specific molecular interactions in composite network subgraphs of two and three nodes and clusters them into topological modules. These are functionally annotated, visualized and overlaid with expression profiles to go from static to dynamic modules. To preserve the larger network context, SUBATOMIC investigates statistically the connections in between modules as well as between modules and regulators such as miRNAs and transcription factors. We applied SUBATOMIC to analyze a composite Homo sapiens network containing transcription factor-target gene, miRNA-target gene, protein-protein, homologous and co-functional interactions from different databases. We derived and annotated 5586 modules with diverse topological, functional and regulatory properties. We created novel functional hypotheses for unannotated genes. Furthermore, we integrated modules with condition specific expression data to study the influence of hypoxia in three cancer cell lines. We developed two prioritization strategies to identify the most relevant modules in specific biological contexts: one considering GO term enrichments and one calculating an activity score reflecting the degree of differential expression. Both strategies yielded modules specifically reacting to low oxygen levels. CONCLUSIONS We developed the SUBATOMIC framework that generates interpretable modules from integrated multi-omics networks and applied it to hypoxia in cancer. SUBATOMIC can infer and contextualize modules, explore condition or disease specific modules, identify regulators and functionally related modules, and derive novel gene functions for uncharacterized genes. The software is available at https://github.com/CBIGR/SUBATOMIC .
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Affiliation(s)
- Jens Uwe Loers
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG), Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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Yu Y, Zhu T. RAR-Related Orphan Receptor: An Accelerated Preeclampsia Progression by Activating the JAK/STAT3 Pathway. Yonsei Med J 2022; 63:554-563. [PMID: 35619579 PMCID: PMC9171667 DOI: 10.3349/ymj.2022.63.6.554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/13/2022] [Accepted: 02/09/2022] [Indexed: 11/27/2022] Open
Abstract
PURPOSE To investigate the effect and underlying mechanism of RAR related orphan receptor A (RORA) on preeclampsia (PE). MATERIALS AND METHODS Differentially expressed genes (DEGs) in four datasets were obtained by using the Venn diagram method. RORA mRNA and protein expressions were detected by qRT-PCR, western blot, and immunohistochemistry. HTR-8/SVneo cell viability, proliferation, invasion, migration, and angiogenesis were detected by CCK-8 assay, EdU assay, Transwell, wound healing assay, and tube formation assay, respectively. The concentration of Ang-1 in cells was assessed using available ELISA kit. Epithelial-mesenchymal transition, proliferation, and angiogenesis-related proteins were detected by western blot. GSEA analysis were performed for common DEGs, and the expression of enriched pathway-related proteins was also detected. RESULTS The expression of RORA was increased in PE tissue and HTR-8/SVneo cells. Silencing RORA could promote the migration, invasion, epithelial-mesenchymal transition, proliferation, and angiogenesis of hypoxia-treated HTR-8/SVneo cells. Mechanistically, RORA contributed to the deterioration of PE by activating the JAK2/STAT3 signaling pathway to promote cell proliferation, migration, invasion, and angiogenesis. CONCLUSION RORA was up-regulated in PE and affected HTR-8/SVneo cell proliferation, invasion, migration, apoptosis, and angiogenesis via the JAK2/STAT3 signaling pathway. This provided a novel strategy for the prevention and treatment of PE.
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Affiliation(s)
- Ying Yu
- Department of Obstetrics, Zhangqiu District People's Hospital, Jinan, Shandong, China
| | - Tongyu Zhu
- Department of Obstetrics, 960th Hospital of the Joint Logistics Support Force of the Chinese People's Liberation Army, Jinan, Shandong, China.
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6
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Xiao W, Geng W, Zhou M, Xu J, Wang S, Huang Q, Sun Y, Li Y, Yang G, Jin Y. POU6F1 cooperates with RORA to suppress the proliferation of lung adenocarcinoma by downregulation HIF1A signaling pathway. Cell Death Dis 2022; 13:427. [PMID: 35504868 PMCID: PMC9065044 DOI: 10.1038/s41419-022-04857-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/08/2022] [Accepted: 04/13/2022] [Indexed: 12/14/2022]
Abstract
Lung adenocarcinoma (LUAD) represents the most frequently diagnosed histological subtype of non-small cell lung cancer with the highest mortality worldwide. Transcriptional dysregulation is a hallmark of nearly all kinds of cancers. In the study, we identified that the POU domain, class 6, transcription factor 1 (POU6F1), a member of the POU family of transcription factors, was closely associated with tumor stage and death in LUAD. We revealed that POU6F1 was downregulated in LUAD tissues and downregulated POU6F1 was predictive of an unfavorable prognosis in LUAD patients. In vitro assays, including CCK8, soft agar, transwell, clone formation, wound-healing assay, and nude mouse xenograft model all revealed that POU6F1 inhibited the growth and invasion of LUAD cells. Mechanistically, POU6F1 bound and stabilized retinoid-related orphan receptor alpha (RORA) to exert the transcriptional inhibition of hypoxia-inducible factor 1-alpha (HIF1A) and alter the expression of HIF1A signaling pathway-associated genes, including ENO1, PDK1, and PRKCB, thereby leading to the suppression of LUAD cells. Collectively, these results demonstrated the suppressive role of POU6F1/RORA in the progression of LUAD and may potentially be used as a target for the treatment of LUAD.
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Affiliation(s)
- Wenjing Xiao
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Wei Geng
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Mei Zhou
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Juanjuan Xu
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Sufei Wang
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Qi Huang
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Yice Sun
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Yumei Li
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
| | - Guanghai Yang
- grid.33199.310000 0004 0368 7223Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Yang Jin
- grid.33199.310000 0004 0368 7223Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, Wuhan, 430022 Hubei China
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Yu X, Megens HJ, Mengistu SB, Bastiaansen JWM, Mulder HA, Benzie JAH, Groenen MAM, Komen H. Genome-wide association analysis of adaptation to oxygen stress in Nile tilapia (Oreochromis niloticus). BMC Genomics 2021; 22:426. [PMID: 34107887 PMCID: PMC8188787 DOI: 10.1186/s12864-021-07486-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Background Tilapia is one of the most abundant species in aquaculture. Hypoxia is known to depress growth rate, but the genetic mechanism by which this occurs is unknown. In this study, two groups consisting of 3140 fish that were raised in either aerated (normoxia) or non-aerated pond (nocturnal hypoxia). During grow out, fish were sampled five times to determine individual body weight (BW) gains. We applied a genome-wide association study to identify SNPs and genes associated with the hypoxic and normoxic environments in the 16th generation of a Genetically Improved Farmed Tilapia population. Results In the hypoxic environment, 36 SNPs associated with at least one of the five body weight measurements (BW1 till BW5), of which six, located between 19.48 Mb and 21.04 Mb on Linkage group (LG) 8, were significant for body weight in the early growth stage (BW1 to BW2). Further significant associations were found for BW in the later growth stage (BW3 to BW5), located on LG1 and LG8. Analysis of genes within the candidate genomic region suggested that MAPK and VEGF signalling were significantly involved in the later growth stage under the hypoxic environment. Well-known hypoxia-regulated genes such as igf1rb, rora, efna3 and aurk were also associated with growth in the later stage in the hypoxic environment. Conversely, 13 linkage groups containing 29 unique significant and suggestive SNPs were found across the whole growth period under the normoxic environment. A meta-analysis showed that 33 SNPs were significantly associated with BW across the two environments, indicating a shared effect independent of hypoxic or normoxic environment. Functional pathways were involved in nervous system development and organ growth in the early stage, and oocyte maturation in the later stage. Conclusions There are clear genotype-growth associations in both normoxic and hypoxic environments, although genome architecture involved changed over the growing period, indicating a transition in metabolism along the way. The involvement of pathways important in hypoxia especially at the later growth stage indicates a genotype-by-environment interaction, in which MAPK and VEGF signalling are important components. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07486-5.
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Affiliation(s)
- Xiaofei Yu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.
| | - Hendrik-Jan Megens
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Samuel Bekele Mengistu
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.,School of Animal and Range Sciences, College of Agriculture, Hawassa University, Hawassa, Ethiopia
| | - John W M Bastiaansen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Han A Mulder
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - John A H Benzie
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Martien A M Groenen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
| | - Hans Komen
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands
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Identification of the Potential Biomarkers Involved in the Human Oral Mucosal Wound Healing: A Bioinformatic Study. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/6695245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Objective. To identify the key genetic and epigenetic mechanisms involved in the wound healing process after injury of the oral mucosa. Materials and Methods. Gene expression profiling datasets pertaining to rapid wound healing of oral mucosa were identified using the Gene Expression Omnibus (GEO) database. Differential gene expression analysis was performed to identify differentially expressed genes (DEGs) during oral mucosal wound healing. Next, functional enrichment analysis was performed to identify the biological processes (BPs) and signaling pathways relevant to these DEGs. A protein-protein interaction (PPI) network was constructed to identify hub DEGs. Interaction networks were constructed for both miRNA-target DEGs and DEGs-transcription factors. A DEGs-chemical compound interaction network and a miRNA-small molecular interaction network were also constructed. Results. DEGs were found significantly enriched in several signaling pathways including arachidonic acid metabolism, cell cycle, p53, and ECM-receptor interaction. Hub genes, GABARAPL1, GABARAPL2, HDAC5, MAP1LC3A, AURKA, and PLK1, were identified via PPI network analysis. Two miRNAs, miR-34a-5p and miR-335-5p, were identified as pivotal players in the miRNA-target DEGs network. Four transcription factors FOS, PLAU, BCL6, and RORA were found to play key roles in the TFs-DEGs interaction network. Several chemical compounds including Valproic acid, Doxorubicin, Nickel, and tretinoin and small molecular drugs including atorvastatin, 17β-estradiol, curcumin, and vitamin D3 were noted to influence oral mucosa regeneration by regulating the expression of healing-associated DEGs/miRNAs. Conclusion. Genetic and epigenetic mechanisms and specific drugs were identified as significant molecular mechanisms and entities relevant to oral mucosal healing. These may be valuable potential targets for experimental research.
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miR-155 Contributes to Normal Keratinocyte Differentiation and Is Upregulated in the Epidermis of Psoriatic Skin Lesions. Int J Mol Sci 2020; 21:ijms21239288. [PMID: 33291448 PMCID: PMC7731132 DOI: 10.3390/ijms21239288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/19/2020] [Accepted: 12/03/2020] [Indexed: 12/14/2022] Open
Abstract
The role of microRNAs (miRNAs) during keratinocyte (KC) differentiation and in skin diseases with epidermal phenotypes has attracted strong interest over the past few years. However, combined mRNA and miRNA expression analyses to elucidate the intricate mRNA–miRNA networks of KCs at different stages of differentiation have not been performed yet. In the present study, we investigated the dynamics of miRNA and mRNA expression during KC differentiation in vitro and in normal and psoriatic epidermis. While we identified comparable numbers of up- and downregulated mRNAs (49% and 51%, respectively), miRNAs were predominantly upregulated (76% vs 24%) during KC differentiation. Further bioinformatics analyses suggested an important inhibitory role for miR-155 in KC differentiation, as it was repressed during KC differentiation in normal skin but strongly upregulated in the epidermis of psoriatic skin lesions. Mimicking the inflammatory milieu of psoriatic skin in vitro, we could show that the pro-inflammatory cytokines IL17, IL1β and INFγ synergistically upregulated miR-155 expression in KCs. Forced over-expression of miR-155 in human in vitro skin models specifically reduced the expression of loricrin (LOR) in KCs, indicating that miR-155 interferes with the establishment of a normal epidermal barrier. Together, our data indicate that downregulation of miR-155 during KC differentiation is a crucial step for epidermal barrier formation. Furthermore, its strong upregulation in psoriatic lesions suggests a contributing role of miR-155 in the altered keratinocyte differentiation observed in psoriasis. Therefore, miR-155 represents as a potential target for treating psoriatic skin lesions.
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Yang HZ, Zhou XH. Mechanism for hypoxia inducible factor-1α to promote immune escape and therapeutic tolerance in hepatocellular carcinoma under hypoxic microenvironment. Shijie Huaren Xiaohua Zazhi 2020; 28:904-913. [DOI: 10.11569/wcjd.v28.i18.904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The liver is the largest immune organ in the body, and immunologic tolerance and escape mechanisms play an important role in hepatocellular carcinoma (HCC) development. HCC has a complex tumor microenvironment (TME), and it is necessary to study the mechanism that causes HCC cells to escape the body immune surveillance and produce therapeutic resistance in HCC clinical treatment. Hypoxia inducible factor-1α (HIF-1α) is a transcription factor that contains α subunits regulated by hypoxia. Tumor cells highly express HIF-1α in a hypoxic environment, which participates in the processes of tumor cell proliferation and metastasis, microvascular production, immune escape, and therapeutic tolerance, ultimately promoting tumorigenesis and development. In this paper, we will elaborate on the mechanisms by which HCC cells activate HIF-1α expression to promote hypoxic adaptation in cancer cells and regulate immune escape and treatment tolerance in hypoxic TME.
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Affiliation(s)
- Huan-Zhen Yang
- Graduate School of Youjiang Medical College for Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Xi-Han Zhou
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical College Nationalities, Baise 533000, Guangxi Zhuang Autonomous Region, China
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Pamenter ME, Hall JE, Tanabe Y, Simonson TS. Cross-Species Insights Into Genomic Adaptations to Hypoxia. Front Genet 2020; 11:743. [PMID: 32849780 PMCID: PMC7387696 DOI: 10.3389/fgene.2020.00743] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 06/22/2020] [Indexed: 12/13/2022] Open
Abstract
Over millions of years, vertebrate species populated vast environments spanning the globe. Among the most challenging habitats encountered were those with limited availability of oxygen, yet many animal and human populations inhabit and perform life cycle functions and/or daily activities in varying degrees of hypoxia today. Of particular interest are species that inhabit high-altitude niches, which experience chronic hypobaric hypoxia throughout their lives. Physiological and molecular aspects of adaptation to hypoxia have long been the focus of high-altitude populations and, within the past decade, genomic information has become increasingly accessible. These data provide an opportunity to search for common genetic signatures of selection across uniquely informative populations and thereby augment our understanding of the mechanisms underlying adaptations to hypoxia. In this review, we synthesize the available genomic findings across hypoxia-tolerant species to provide a comprehensive view of putatively hypoxia-adaptive genes and pathways. In many cases, adaptive signatures across species converge on the same genetic pathways or on genes themselves [i.e., the hypoxia inducible factor (HIF) pathway). However, specific variants thought to underlie function are distinct between species and populations, and, in most cases, the precise functional role of these genomic differences remains unknown. Efforts to standardize these findings and explore relationships between genotype and phenotype will provide important clues into the evolutionary and mechanistic bases of physiological adaptations to environmental hypoxia.
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Affiliation(s)
- Matthew E. Pamenter
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Brain and Mind Research Institute, University of Ottawa, Ottawa, ON, Canada
| | - James E. Hall
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Yuuka Tanabe
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Tatum S. Simonson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, United States
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12
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Retinoic acid signalling adjusts tight junction permeability in response to air-liquid interface conditions. Cell Signal 2020; 65:109421. [DOI: 10.1016/j.cellsig.2019.109421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/14/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022]
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Brożyna AA, Jóźwicki W, Jetten AM, Slominski AT. On the relationship between VDR, RORα and RORγ receptors expression and HIF1-α levels in human melanomas. Exp Dermatol 2019; 28:1036-1043. [PMID: 31287590 DOI: 10.1111/exd.14002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
We analysed the correlation between the expression of HIF-1α (hypoxia-inducible factor 1 alpha), the nuclear receptors: VDR (vitamin D receptor), RORα (retinoic acid receptor-related orphan receptor alpha), and RORγ and CYP24A1 (cytochrome P450 family 24 subfamily A member 1) and CYP27B1 (cytochrome P450 family 27 subfamily B member 1), enzymes involved in vitamin D metabolism. In primary and metastatic melanomas, VDR negatively correlated with nuclear HIF-1α expression (r = -.2273, P = .0302; r = -.5081, P = .0011). Furthermore, the highest HIF-1α expression was observed in pT3-pT4 VDR-negative melanomas. A comparative analysis of immunostained HIF-1α and CYP27B1 and CYP24A1 showed lack of correlation between these parameters both in primary tumors and melanoma metastases. In contrast, RORα expression correlated positively with nuclear HIF-1α expression in primary and metastatic lesions (r = .2438, P = .0175; r = .3662, P = .0166). Comparable levels of HIF-1α expression pattern was observed in localized and advanced melanomas. RORγ in primary melanomas correlated also positively with nuclear HIF-1α expression (r = .2743, P = .0129). HIF-1α expression was the lowest in localized RORγ-negative melanomas. In addition, HIF-1α expression correlated with RORγ-positive lymphocytes in melanoma metastases. We further found that in metastatic lymph nodes FoxP3 immunostaining correlated positively with HIF-1α and RORγ expression in melanoma cells (r = .3667; P = .0327; r = .4208, P = .0129). In summary, our study indicates that the expression of VDR, RORα and RORγ in melanomas is related to hypoxia and/or HIF1-α activity, which also affects FoxP3 expression in metastatic melanoma. Therefore, the hypoxia can affect tumor biology by changing nuclear receptors expression and molecular pathways regulated by nuclear receptors and immune responses.
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Affiliation(s)
- Anna A Brożyna
- Department of Human Biology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Toruń, Poland.,Department of Tumor Pathology and Pathomorphology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Jóźwicki
- Department of Tumor Pathology and Pathomorphology, Oncology Centre - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland.,Department of Tumor Pathology and Pathomorphology, Faculty of Health Sciences, Nicolaus Copernicus University Collegium Medicum in Bydgoszcz, Bydgoszcz, Poland
| | - Anton M Jetten
- Cell Biology Section, Inflammation, Immunity and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Andrzej T Slominski
- Department of Dermatology, Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, USA.,Laboratory Service of the VA Medical Center, Birmingham, AL, USA
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Human skin equivalents cultured under hypoxia display enhanced epidermal morphogenesis and lipid barrier formation. Sci Rep 2019; 9:7811. [PMID: 31127151 PMCID: PMC6534609 DOI: 10.1038/s41598-019-44204-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/02/2019] [Indexed: 12/17/2022] Open
Abstract
Human skin equivalents (HSEs) are three-dimensional cell models mimicking characteristics of native human skin (NHS) in many aspects. However, a limitation of HSEs is the altered in vitro morphogenesis and barrier formation. Differences between in vitro and in vivo skin could have been induced by suboptimal cell culture conditions, of which the level of oxygen in vitro (20%) is much higher than in vivo (0.5-8%). Our aim is to study how external oxygen levels affect epidermal morphogenesis and barrier formation in HSEs. In the present study, fibroblast and keratinocyte monocultures, and HSEs were generated under 20% (normoxia) and 3% (hypoxia) oxygen level. In all cultures under hypoxia, expression of hypoxia-inducible factor target genes was increased. Characterization of HSEs generated under hypoxia using immunohistochemical analyses of morphogenesis biomarkers revealed a reduction in epidermal thickness, reduced proliferation, similar early differentiation, and an attenuated terminal differentiation program compared to normoxia, better mimicking NHS. The stratum corneum ceramide composition was studied with liquid chromatography coupled to mass spectrometry. Under hypoxia, HSEs exhibited a ceramide composition that more closely resembles that of NHS. Consequently, the lipid organization was improved. In conclusion, epidermal morphogenesis and barrier formation in HSEs reconstructed under hypoxia better mimics that of NHS.
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Sun Y, Wang P, Li H, Dai J. BMAL1 and CLOCK proteins in regulating UVB-induced apoptosis and DNA damage responses in human keratinocytes. J Cell Physiol 2018; 233:9563-9574. [PMID: 29943823 PMCID: PMC6185778 DOI: 10.1002/jcp.26859] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 05/22/2018] [Indexed: 12/15/2022]
Abstract
A diverse array of biological processes are under circadian controls. In mouse skin, ultraviolet ray (UVR)-induced apoptosis and DNA damage responses are time-of-day dependent, which are controlled by core clock proteins. This study investigates the roles of clock proteins in regulating UVB responses in human keratinocytes (HKCs). We found that the messenger RNA expression of brain and muscle ARNT-like 1 (BMAL1) and circadian locomotor output cycles kaput (CLOCK) genes is altered by low doses (5 mJ/cm2 ) of UVB in the immortalized HaCat HKCs cell line. Although depletion of BMAL1 or CLOCK has no effect on the activation of Rad3-related protein kinases-checkpoint kinase 1-p53 mediated DNA damage checkpoints, it leads to suppression of UVB-stimulated apoptotic responses, and downregulation of UVB-elevated expression of DNA damage marker γ-H2AX and cell cycle inhibitor p21. Diminished apoptotic responses are also observed in primary HKCs depleted of BMAL1 or CLOCK after UVB irradiation. While CLOCK depletion shows a suppressive effect on UVB-induced p53 protein accumulation, depletion of either clock gene triggers early keratinocyte differentiation of HKCs at their steady state. These results suggest that UVB-induced apoptosis and DNA damage responses are controlled by clock proteins, but via different mechanisms in the immortalized human adult low calcium temperature and primary HKCs. Given the implication of UVB in photoaging and photocarcinogenesis, mechanistic elucidation of circadian controls on UVB effects in human skin will be critical and beneficial for prevention and treatment of skin cancers and other skin-related diseases.
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Affiliation(s)
- Yang Sun
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072 P. R. China
| | - Peiling Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072 P. R. China
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, Madison, WI 53705 USA
| | - Hongyu Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072 P. R. China
| | - Jun Dai
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072 P. R. China
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin, Madison, WI 53705 USA
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