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Chng CL, Lai OF, Seah LL, Yong KL, Chung YHW, Goh R, Lim CK. A combined transcriptomics and proteomics approach reveals S100A4 as a potential biomarker for Graves' orbitopathy. Front Genet 2024; 15:1342205. [PMID: 39359477 PMCID: PMC11445072 DOI: 10.3389/fgene.2024.1342205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 08/28/2024] [Indexed: 10/04/2024] Open
Abstract
Background There are no reliable biomarkers to identify Graves' disease patients who will develop severe Graves' orbitopathy (GO). We hypothesize that integrating various omics platforms can enhance our understanding of disease mechanisms and uncover potential biomarkers. This study aimed to (1) elucidate the differential gene expression profile of orbital fibroblasts in GO during early adipogenesis to better understand disease mechanisms and (2) compare tear protein profiles from our earlier study and the transcriptome profiles of orbital fibroblasts (OFs) to identify possible biomarkers of the disease. Methods OFs were grown from orbital adipose tissue obtained from nine GO patients (three for discovery and six for validation experiments). Total RNA was extracted from OFs on day 0 as the baseline for each sample and from differentiated OFs on days 4 and 8. Protein-protein interaction (PPI) analysis and functional enrichment analysis were also carried out. The differentially expressed genes (DEGs) from the RNA sequencing experiments were then compared to the full tear proteome profile from the author's previous study, which examined the tear protein changes of GO patients based on fold change > 1.6 or < -1.6. FDR < 0.05 was applied within all datasets. Further validation of S100 calcium-binding protein A4 (S100A4) downregulation in GO was performed via quantitative real-time PCR (qPCR). Results The whole transcriptomic analysis revealed 9 upregulated genes and 15 downregulated genes in common between the discovery and validation experiments. From the PPI network analysis, an interaction network containing six identified DEGs (ALDH2, MAP2K6, MT2A, SOCS3, S100A4, and THBD) was observed. The functional enrichment network analysis identified a set of genes related to oxysterol production. S100A4 was found to be consistently downregulated in both our transcriptome studies and the full-tear proteome profile from the author's previous study. Conclusion Our study identified several DEGs and potential gene pathways in GO patients, which concurred with the results of other studies. Tear S100A4 may serve as a biomarker for the propensity to develop thyroid eye disease (TED) in patients with autoimmune thyroid disease (AITD) before clinical manifestation and should be confirmed in future studies.
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Affiliation(s)
- Chiaw-Ling Chng
- Department of Endocrinology, Singapore General Hospital, Singapore, Singapore
| | - Oi Fah Lai
- Department of Clinical and Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Lay-Leng Seah
- Oculoplastic Department, Singapore National Eye Centre, Singapore, Singapore
| | - Kai-Ling Yong
- Oculoplastic Department, Singapore National Eye Centre, Singapore, Singapore
| | | | - Rochelle Goh
- Department of Clinical and Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Che Kang Lim
- Department of Clinical and Translational Research, Singapore General Hospital, Singapore, Singapore
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Vagefi MR, Idowu OO, Miller A, Doan T, Chen C, Hinterwirth A, Zhong L, Ahmad M, Ashraf DC, Grob SR, Kersten RC, Winn BJ. Metagenomic Deep Sequencing for Orbital Inflammatory Disease. Ocul Immunol Inflamm 2024; 32:718-721. [PMID: 37068263 PMCID: PMC10579447 DOI: 10.1080/09273948.2023.2199061] [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: 08/05/2022] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023]
Abstract
PURPOSE Orbital inflammatory disease (OID) is a heterogeneous group of immunologic disorders whose etiology is often non-specific despite routine investigation. In this proof-of-concept study, metagenomic deep sequencing (MDS) is applied to examine host gene expression in two subtypes of OID. METHODS Prospectively collected lacrimal gland tissue from patients with OID was processed for MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures. Proof-of-concept comparison was made between histologically confirmed samples of idiopathic dacryoadenitis and IgG4-related disease (IgG4-RD). RESULTS Twelve genes were identified to be differentially expressed between idiopathic dacryoadenitis and IgG4-RD. Differences in innate humoral immunity gene expression were observed. Several additional genes of interests were also found to be upregulated in idiopathic dacryoadenitis. CONCLUSIONS A unique transcriptome signature was found when comparing idiopathic dacryoadenitis to IgG4-RD. This suggests that MDS can identify differentially expressed genes in OID. Such insight could potentially provide a better understanding of host gene expression and the inflammatory pathways involved in OID.
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Affiliation(s)
- M. Reza Vagefi
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Oluwatobi O. Idowu
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Amanda Miller
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Thuy Doan
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Cindi Chen
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Armin Hinterwirth
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Lina Zhong
- Francis I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Meleha Ahmad
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Davin C. Ashraf
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Seanna R. Grob
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Robert C. Kersten
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
| | - Bryan J. Winn
- Division of Oculofacial Plastic Surgery, Department of Ophthalmology, University of California San Francisco, San Francisco, CA
- Ophthalmology Section, Surgical Service, San Francisco Veterans Affairs Medical Center, 4150 Clement Street, San Francisco, CA 94121
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Ye Y, Dai L, Mugaanyi J, Fu W, Hu F. Novel insights into the pathogenesis of thyroid eye disease through ferroptosis-related gene signature and immune infiltration analysis. Aging (Albany NY) 2024; 16:6008-6034. [PMID: 38536014 PMCID: PMC11042930 DOI: 10.18632/aging.205685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/13/2024] [Indexed: 04/23/2024]
Abstract
Thyroid eye disease (TED) has brought great physical and mental trauma to patients worldwide. Although a few potential signaling pathways have been reported, knowledge of TED remains limited. Our objective is to explore the fundamental mechanism of TED and identify potential therapeutic targets using diverse approaches. To perform a range of bioinformatic analyses, such as identifying differentially expressed genes (DEGs), conducting enrichment analysis, establishing nomograms, analyzing weighted gene correlation network analysis (WGCNA), and studying immune infiltration, the datasets GSE58331, GSE105149, and GSE9340 were integrated. Further validation was conducted using qPCR, western blot, and immunohistochemistry techniques. Eleven ferroptosis-related DEGs derived from the lacrimal gland were originally screened. Their high diagnostic value was proven, and diagnostic prediction nomogram models with high accuracy and robustness were established by using machine learning. A total of 15 hub gene-related DEGs were identified by WGCNA. Through CIBERSORTx, we uncovered five immune cells highly correlated with TED and found several special associations between these immune cells and the above DEGs. Furthermore, EGR2 from the thyroid sample was revealed to be closely negatively correlated with most DEGs from the lacrimal gland. High expression of APOD, COPB2, MYH11, and MYCN, as well as CD4/CD8 T cells and B cells, was verified in the periorbital adipose tissues of TED patients. To summarize, we discovered a new gene signature associated with ferroptosis that has a critical impact on the development of TED and provides valuable insights into immune infiltration. These findings might highlight the new direction and therapeutic strategies of TED.
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Affiliation(s)
- Yunyan Ye
- Department of Ophthalmology, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China
| | - Lei Dai
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China
| | - Joseph Mugaanyi
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China
| | - Weina Fu
- Department of Ophthalmology, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China
| | - Feng Hu
- Department of Ophthalmology, Ningbo Medical Centre Lihuili Hospital, Ningbo University, Ningbo 315040, Zhejiang, China
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4
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Peng L, Zhang X, Du Y, Li F, Han J, Liu O, Dai S, Zhang X, Liu GE, Yang L, Zhou Y. New insights into transcriptome variation during cattle adipocyte adipogenesis by direct RNA sequencing. iScience 2023; 26:107753. [PMID: 37692285 PMCID: PMC10492216 DOI: 10.1016/j.isci.2023.107753] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/31/2023] [Accepted: 08/24/2023] [Indexed: 09/12/2023] Open
Abstract
We performed direct RNA sequencing (DRS) together with PCR-amplified cDNA long and short read sequencing for cattle adipocyte at different stages. We proved that the DRS was with advantages to avoid artificial transcripts and questionable exitrons. Totally, we obtained 68,124 transcripts with information of alternative splicing, poly (A) length and mRNA modification. The number of transcripts for adipogenesis was expanded by alternative splicing, which lead regulation mechanisms far more complex than ever known. We detected 891 differentially expressed genes (DEGs). However, 62.78% transcripts of DEGs were not significantly differentially expressed, and 248 transcripts showed opposite changing directions with their genes. The poly (A) tail became globally shorter in differentiated adipocyte than in primary adipocyte, and had a weak negative correlation with gene/transcript expression. Moreover, the study of different mRNA modifications implied their potential roles in gene expression and alternative splicing. Overall, our study promoted better understanding of adipogenesis mechanisms in cattle adipocytes.
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Affiliation(s)
- Lingwei Peng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolian Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqin Du
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jiazheng Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Oujin Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shoulu Dai
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiang Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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5
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Hu J, Zhou S, Guo W. Construction of the coexpression network involved in the pathogenesis of thyroid eye disease via bioinformatics analysis. Hum Genomics 2022; 16:38. [PMID: 36076300 PMCID: PMC9461120 DOI: 10.1186/s40246-022-00412-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
Background Thyroid eye disease (TED) is the most common orbital pathology that occurs in up to 50% of patients with Graves’ disease. Herein, we aimed at discovering the possible hub genes and pathways involved in TED based on bioinformatical approaches. Results The GSE105149 and GSE58331 datasets were downloaded from the Gene Expression Omnibus (GEO) database and merged for identifying TED-associated modules by weighted gene coexpression network analysis (WGCNA) and local maximal quasi-clique merger (lmQCM) analysis. EdgeR was run to screen differentially expressed genes (DEGs). Transcription factor (TF), microRNA (miR) and drug prediction analyses were performed using ToppGene suite. Function enrichment analysis was used to investigate the biological function of genes. Protein–protein interaction (PPI) analysis was performed based on the intersection between the list of genes obtained by WGCNA, lmQCM and DEGs, and hub genes were identified using the MCODE plugin. Based on the overlap of 497 genes retrieved from the different approaches, a robust TED coexpression network was constructed and 11 genes (ATP6V1A, PTGES3, PSMD12, PSMA4, METAP2, DNAJA1, PSMA1, UBQLN1, CCT2, VBP1 and NAA50) were identified as hub genes. Key TFs regulating genes in the TED-associated coexpression network, including NFRKB, ZNF711, ZNF407 and MORC2, and miRs including hsa-miR-144, hsa-miR-3662, hsa-miR-12136 and hsa-miR-3646, were identified. Genes in the coexpression network were enriched in the biological processes including proteasomal protein catabolic process and proteasome-mediated ubiquitin-dependent protein catabolic process and the pathways of endocytosis and ubiquitin-mediated proteolysis. Drugs perturbing genes in the coexpression network were also predicted and included enzyme inhibitors, chlorodiphenyl and finasteride. Conclusions For the first time, TED-associated coexpression network was constructed and key genes and their functions, as well as TFs, miRs and drugs, were predicted. The results of the present work may be relevant in the treatment and diagnosis of TED and may boost molecular studies regarding TED. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-022-00412-0.
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Affiliation(s)
- Jinxing Hu
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
| | - Shan Zhou
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China. .,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China.
| | - Weiying Guo
- Department of Endocrinology, HwaMei Hospital, University of Chinese Academy of Sciences, 41 Northwest Street Zhejiang Province, Ningbo, 315010, China.,Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315010, China
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6
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Bai XJ, Chu XJ, Yang T, Tong BD, Qi X, Peng YY, Li Y, Wang LJ, Li YP. Changes of mRNA expression underlying orbital adipogenesis in thyroid-associated orbitopathy. Arch Med Sci 2022; 18:1708-1715. [PMID: 36457984 PMCID: PMC9710284 DOI: 10.5114/aoms/153478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/03/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Xiao Jing Bai
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Department of Ophthalmology, the Aier Eye Hospital of Shanxi Province, Taiyuan, Shanxi Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Xiao Jing Chu
- Department of Ophthalmology, the Aier Eye Hospital of Shanxi Province, Taiyuan, Shanxi Province, China
| | - Tao Yang
- College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Bo Ding Tong
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Xin Qi
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Yang Yang Peng
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Yuan Li
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Lu Jue Wang
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
| | - Yun Ping Li
- Department of Ophthalmology, the Second Xiangya Hospital of Central South University, Changsha, Hunan Province, China
- Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan Province, China
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7
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Kim DW, Taneja K, Hoang T, Santiago CP, McCulley TJ, Merbs SL, Mahoney NR, Blackshaw S, Rajaii F. Transcriptomic Profiling of Control and Thyroid-Associated Orbitopathy (TAO) Orbital Fat and TAO Orbital Fibroblasts Undergoing Adipogenesis. Invest Ophthalmol Vis Sci 2021; 62:24. [PMID: 34269815 PMCID: PMC8297424 DOI: 10.1167/iovs.62.9.24] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Purpose Orbital fat hyperplasia commonly occurs in thyroid-associated orbitopathy (TAO). To understand molecular mechanisms underlying orbital adipogenesis, we used transcriptomics to compare gene expression in controls and patients with TAO, as well as in orbital fibroblasts (OFs) undergoing adipogenic differentiation. Methods We performed bulk RNA sequencing (RNA-Seq) on intraconal orbital fat from controls and patients with TAO. We treated cultured OFs derived from patients with TAO with adipogenic media to induce adipogenesis. We used single nucleus RNA-Seq (snRNA-Seq) to profile treated and control OFs, identifying genes that are dynamically expressed during orbital adipogenesis in vitro, and compared these results to data from control and TAO orbital fat. Results Gene expression profiles in control and TAO orbital fat are distinct. Signaling pathways including PI3K-Akt signaling, cAMP signaling, AGE-RAGE signaling, regulation of lipolysis, and thyroid hormone signaling are enriched in orbital fat isolated from patients with TAO. SnRNA-Seq of orbital fibroblasts undergoing adipogenesis reveals differential expression of the adipocyte-specific genes FABP4/5, APOE, PPARG, and ADIPOQ during adipogenic differentiation. The insulin-like growth factor-1 receptor and Wnt signaling pathways appear to be enriched early in adipogenesis. Gene modules that are enriched in TAO orbital fat are upregulated in orbital adipocytes during differentiation in vitro, whereas genes that are enriched in control orbital fat are enriched in undifferentiated OFs. Conclusions We identified pathways enriched in TAO orbital fat, and dynamic changes in gene expression that occur during adipogenic differentiation of orbital fibroblasts. These findings may help guide functional studies of genes and pathways critical for orbital adipogenesis.
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Affiliation(s)
- Dong Won Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Kamil Taneja
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Thanh Hoang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Clayton P Santiago
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Timothy J McCulley
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Shannath L Merbs
- Department of Ophthalmology and Visual Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States
| | - Nicholas R Mahoney
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.,Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Fatemeh Rajaii
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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8
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Tu W, Yao J, Mei Z, Jiang X, Shi Y. Microarray Data of Lacrimal Gland Implicates Dysregulated Protein Processing in Endoplasmic Reticulum in Graves' Ophthalmopathy. Front Endocrinol (Lausanne) 2020; 11:571151. [PMID: 33613444 PMCID: PMC7888479 DOI: 10.3389/fendo.2020.571151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
Graves' ophthalmopathy (GO) has become one of the most common orbital diseases. Although some evidences announced the potential mechanism of pathological changes in extraocular muscle and orbital adipose tissue, little is known about that in lacrimal enlargement of GO patients. Thus, gene expression profiles of lacrimal gland derived from GO patients and normal controls were investigated using the microarray datasets of GSE105149 and GSE58331. The raw data and annotation files of GSE105149 and GSE58331 were downloaded from Gene Expression Omnibus (GEO) database. Bioinformatics including differentially expressed genes (DEGs), Gene Ontology, Kyoto Encyclopedia of Gene and Genome (KEGG) pathway, protein-protein interaction (PPI) network construction, hub gene identification, and gene set variation analysis (GSVA) were successively performed. A total of 173 overlapping DEGs in GSE105149 and GSE58331 were screened out, including 20 up-regulated and 153 down-regulated genes. Gene Ontology, KEGG and GSVA analyses of these DEGs showed that the most significant mechanism was closely associated with endoplasmic reticulum (ER). Moreover, we identified 40 module genes and 13 hub genes which were also enriched in the ER-associated terms and pathways. Among the hub genes, five genes including HSP90AA1, HSP90B1, DNAJC10, HSPA5, and CANX may be involved in the dysfunction of protein processing in ER. Taken together, our observations revealed a dysregulated gene network which is essential for protein processing in ER in GO patients. These findings provided a potential mechanism in the progression of lacrimal enlargement in GO patients, as a new insight into GO pathogenesis.
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Affiliation(s)
- Wenling Tu
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, China
| | - Jia Yao
- Research and Development Center, Chengdu SuAn Technology Co., Ltd, Chengdu, China
| | - Zhanjun Mei
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Xue Jiang
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
| | - Yuhong Shi
- Department of Nuclear Medicine, The Second Affiliated Hospital of Chengdu Medical College, China National Nuclear Corporation 416 Hospital, Chengdu, China
- *Correspondence: Yuhong Shi,
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9
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Zhang W, Xu L, Luo T, Zhao B, Wu F, Li X. Immune-related gene expression profiles of hypothermia adipocytes: Implications for Bell's palsy. Oral Dis 2019; 25:1652-1663. [PMID: 31127963 DOI: 10.1111/odi.13126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To identify immune-related gene expression profiles of adipocytes under low temperatures with RNA sequencing as a model for Bell's palsy implications. METHODS Adipocytes were harvested from the white adipose tissue of male Sprague-Dawley rats and cultured under different acute-grade cold exposure conditions of 30, 20, and 10°C, and their genomes were sequenced for RNA sequencing analysis. The differentially expressed genes (DEGs) were validated with reverse transcription polymerase chain reaction. RESULTS In total, 55 (35 upregulated and 20 downregulated), 121 (76 upregulated and 45 downregulated), and 92 (64 upregulated and 28 downregulated) DEGs were identified under 30, 20, and 10°C compared with the control, respectively. KEGG and GO analysis revealed that the DEGs were considerably enriched in immune-related pathways (leukocyte transendothelial migration and platelet activation) and infection (bacterial invasion of epithelial cells and Salmonella infection). The levels of key inflammatory chemokines (CSF1, CXCL1, CCL2, and CCL7) were enhanced after cold exposure. CONCLUSION These findings broaden our understanding of the immune responses to cold exposure in adipocytes. The molecular profiles of adipocyte immune function will help clarify the potential mechanism impacting myelin, which might contribute to the development of strategies to control Bell's palsy.
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Affiliation(s)
- Wenjuan Zhang
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China
| | - Lei Xu
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China
| | - Tingting Luo
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China.,The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory for Oral Biomedical Engineering of Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Bin Zhao
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China
| | - Feng Wu
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China
| | - Xianqi Li
- School and Hospital of Stomatology, Shanxi Medical University, Taiyuan, China.,Department of Oral and Maxillofacial Surgery, Matsumoto Dental University, Shiojiri, Japan
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10
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T2-relaxation mapping and fat fraction assessment to objectively quantify clinical activity in thyroid eye disease: an initial feasibility study. Eye (Lond) 2018; 33:235-243. [PMID: 30538310 DOI: 10.1038/s41433-018-0304-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 11/16/2018] [Indexed: 11/08/2022] Open
Abstract
Imaging in thyroid eye disease (TED) is used to exclude other diagnoses, assess for apical crowding and plan surgery. But to quantify TED activity objectively, subjective clinical scoring assessments remain the norm. Magnetic resonance imaging (MRI) T2-relaxation times correlate with extra-ocular muscle (EOM) inflammation, but are confounded by signal from fat. We investigated whether T2-relaxation mapping in combination with fat fraction (FF) measurements could quantify disease activity in EOMs objectively. Sixty-two TED patients and six controls were enroled for coronal short tau inversion recovery (STIR), T2 multi-echo fast-spin echo and multi-echo fast-gradient echo MRI of the orbits. STIR signal intensity ratios (SIRs), T2-relaxation times and percentage FF were derived for inferior, lateral, superior and medial recti bilaterally. Twelve patients were re-scanned following immunosuppressive treatment. The results found a positive correlation for all subjects between T2 and SIR (p < 0.001), but only mean T2 differed significantly between patients and controls (p < 0.001). We measured FF in EOMs for the first time and found it greater in TED (p < 0.001). There was also a significant reduction in mean T2 after treatment, with a corresponding reduction in the clinical activity score (CAS) in almost all patients. We show that T2-relaxation times differentiate between normal and inflamed EOMs and are responsive to treatment. Combined, uniquely, with FF measurement in EOMs, an objective, quantitative marker of inflammation in TED-affected muscles could be derived. T2-relaxation times mirrored improvements in CAS after treatment, occasionally preceding them. Rarely, they diverged, suggesting limitations in the CAS as a disease burden marker.
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