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Bai R, Yin P, Xing Z, Wu S, Zhang W, Ma X, Gan X, Liang Y, Zang Q, Lei H, Wei Y, Zhang C, Dai B, Zheng Y. Investigation of GPR143 as a promising novel marker for the progression of skin cutaneous melanoma through bioinformatic analyses and cell experiments. Apoptosis 2024; 29:372-392. [PMID: 37945816 DOI: 10.1007/s10495-023-01913-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Skin cutaneous melanoma (SKCM) is an aggressive and life-threatening skin cancer. G-protein coupled receptor 143 (GPR143) belongs to the superfamily of G protein-coupled receptors. METHODS We used the TCGA, GTEx, CCLE, and the Human Protein Atlas databases to examine the mRNA and protein expression of GPR143. In addition, we performed a survival analysis and evaluated the diagnostic efficacy using the Receiver-Operating Characteristic (ROC) curve. Through CIBERSORT, R programming, TIMER, Gene Expression Profiling Interactive Analysis, Sangerbox, and Kaplan-Meier plotter database analyses, we explored the relationships between GPR143, immune infiltration, and gene marker expression of immune infiltrated cells. Furthermore, we investigated the proteins that potentially interact with GPR143 and their functions using R programming and databases including STRING, GeneMANIA, and GSEA. Meanwhile, the cBioPortal, UALCNA, and the MethSurv databases were used to examine the genomic alteration and methylation of GPR143 in SKCM. The Connectivity Map database was used to discover potentially effective therapeutic molecules against SKCM. Finally, we conducted cell experiments to investigate the potential role of GPR143 in SKCM. RESULTS We demonstrated a significantly high expression level of GPR143 in SKCM compared with normal tissues. High GPR143 expression and hypomethylation status of GPR143 were associated with a poorer prognosis. ROC analysis showed that the diagnostic efficacy of the GPR143 was 0.900. Furthermore, GPR143 expression was significantly correlated with immune infiltration in SKCM. We identified 20 neighbor genes and the pathways they enriched were anabolic process of pigmentation, immune regulation, and so on. Genomic alteration analysis revealed significantly different copy number variations related to GPR143 expression in SKCM, and shallow deletion could lead to high expression of GPR143. Ten potential therapeutic drugs against SKCM were identified. GPR143 knockdown inhibited melanoma cell proliferation, migration, and colony formation while promoting apoptosis. CONCLUSIONS Our findings suggest that GPR143 serves as a novel diagnostic and prognostic biomarker and is associated with the progression of SKCM.
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Affiliation(s)
- Ruimin Bai
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Pan Yin
- Department of Medicine, Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Zixuan Xing
- Department of Medicine, Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Shaobo Wu
- Department of Medicine, Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
| | - Wen Zhang
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Xinyu Ma
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Xinyi Gan
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Yuxia Liang
- Department of Imaging, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Qijuan Zang
- Department of Medicine, Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Hao Lei
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Yi Wei
- Department of Urology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Chaonan Zhang
- Department of Radiation Oncology, National Clinical Research Center for Cancer/Cancer Hospital, National Cancer Center, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100730, China
| | - Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
| | - Yan Zheng
- Department of Dermatology, the First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an, Shaanxi, 710061, China.
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Xu J, Zheng Y, Cheng L, Sun H, Yu X, Gu F, Song E. GPR143 mutations in an X-linked infantile nystagmus syndrome cohort in Southeast China. Mol Vis 2023; 29:234-244. [PMID: 38222445 PMCID: PMC10784212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/25/2023] [Indexed: 01/16/2024] Open
Abstract
Purpose Infantile nystagmus syndrome (INS), or congenital nystagmus (CN), refers to a group of ocular motor disorders characterized by rapid to-and-fro oscillations of the eyes. GPR143 is the causative gene of ocular albinism type 1 (OA1), which is a special type of INS that manifests as reduced vision, nystagmus, and iris and fundus hypopigmentation. Here, we explored the genetic spectrum of INS and the genotype-phenotype correlation. Methods A total of 98 families with INS from Southeast China were recruited for this study. A sample from each participant was subjected to PCR-based DNA direct sequencing of GPR143. Varied bioinformatics analysis was subsequently used in a mutation assessment. All participants received detailed ophthalmic examinations. Results Genetic analysis identified 11 GPR143 mutations in 11.2% (11/98) of the X-linked INS families. These included seven novel mutations (c.899 C>T, c.886-2 A>G, c.1A>G, c.633_643del CCTGTTCCAAA, c.162_198delCGCGGGCCCCGGGTCCCCCGCGACGTCCCCGCCGGCC, c.628C>A, and c.178_179insGGGTCCC) and four known mutations. Patients who carried a GPR143 mutation were found to present a typical or atypical phenotype of OA1. All patients with GPR143 mutations manifested foveal hypoplasia; thus, about 45.8% (11/24) of the families with total X-linked INS exhibited foveal hypoplasia. Conclusions We discovered seven novel mutations and four previously reported mutations of GPR143 in a cohort of families with X-linked INS and enlarged the Chinese genetic spectrum of INS. These findings offer new insights for developing genetic screening strategies and shed light on the importance of conducting genetic analysis in confirming the clinical diagnosis in unresolved patients and atypical phenotypes.
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Affiliation(s)
- Jingling Xu
- Department of Ophthalmology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
- Eye Hospital of Wenzhou Medical University Wenzhou China
| | - Yihan Zheng
- Eye Hospital of Wenzhou Medical University Wenzhou China
| | - Lulu Cheng
- Eye Department in People's Hospital of Longgang District, Shenzhen, China
| | - Huihui Sun
- Eye Department of Children Hosptial in Hebei Province, Shijiazhuang, China
| | - Xinping Yu
- Eye Hospital of Wenzhou Medical University Wenzhou China
| | - Feng Gu
- Eye Hospital of Wenzhou Medical University Wenzhou China
| | - E Song
- Department of Ophthalmology, Lixiang Eye Hospital of Soochow University, Suzhou, Jiangsu, China
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Jara E, Peñagaricano F, Armstrong E, Menezes C, Tardiz L, Rodons G, Iriarte A. Identification of Long Noncoding RNAs Involved in Eyelid Pigmentation of Hereford Cattle. Front Genet 2022; 13:864567. [PMID: 35601493 PMCID: PMC9114348 DOI: 10.3389/fgene.2022.864567] [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: 01/28/2022] [Accepted: 04/20/2022] [Indexed: 12/05/2022] Open
Abstract
Several ocular pathologies in cattle, such as ocular squamous cell carcinoma and infectious keratoconjunctivitis, have been associated with low pigmentation of the eyelids. The main objective of this study was to analyze the transcriptome of eyelid skin in Hereford cattle using strand-specific RNA sequencing technology to characterize and identify long noncoding RNAs (lncRNAs). We compared the expression of lncRNAs between pigmented and unpigmented eyelids and analyzed the interaction of lncRNAs and putative target genes to reveal the genetic basis underlying eyelid pigmentation in cattle. We predicted 4,937 putative lncRNAs mapped to the bovine reference genome, enriching the catalog of lncRNAs in Bos taurus. We found 27 differentially expressed lncRNAs between pigmented and unpigmented eyelids, suggesting their involvement in eyelid pigmentation. In addition, we revealed potential links between some significant differentially expressed lncRNAs and target mRNAs involved in the immune response and pigmentation. Overall, this study expands the catalog of lncRNAs in cattle and contributes to a better understanding of the biology of eyelid pigmentation.
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Affiliation(s)
- Eugenio Jara
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Eileen Armstrong
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Claudia Menezes
- Laboratorio de Endocrinología y Metabolismo Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Lucía Tardiz
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Gastón Rodons
- Unidad de Genética y Mejora Animal, Departamento de Producción Animal, Facultad de Veterinaria, Universidad de La República, Montevideo, Uruguay
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- *Correspondence: Andrés Iriarte,
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Wang XF, Chen H, Huang PJ, Feng ZK, Hua ZQ, Feng X, Han F, Xu XT, Shen RJ, Li Y, Jin ZB, Yu HY. Genotype-Phenotype Analysis and Mutation Spectrum in a Cohort of Chinese Patients With Congenital Nystagmus. Front Cell Dev Biol 2021; 9:627295. [PMID: 33732697 PMCID: PMC7958879 DOI: 10.3389/fcell.2021.627295] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022] Open
Abstract
Purpose: Congenital nystagmus (CN) is a genetically and clinically heterogeneous ocular disorder that manifests as involuntary, periodic oscillations of the eyes. To date, only FRMD7 and GPR143 have been reported to be responsible for causing CN. Here, we aimed to identify the disease-causing mutations and describe the clinical features in the affected members in our study. Methods: All the subjects underwent a detailed ophthalmic examination. Direct sequencing of all coding exons and splice site regions in FRMD7 and GPR143 and a mutation assessment were performed in each patient. Results: We found 14 mutations in 14/37 (37.8%) probands, including nine mutations in the FRMD7 gene and five mutations in the GPR143 gene, seven of which are novel, including c.284G>A(R95K), c.964C>T(P322S), c.284+10T>G, c.901T>C (Y301H), and c.2014_2023delTCACCCATGG(S672Pfs*12) in FRMD7, and c.250+1G>C, and c.485G>A (W162*) in GPR143. The mutation detection rate was 87.5% (7/8) of familial vs. 24.1% (7/29) of sporadic cases. Ten mutations in 24 (41.7%) non-syndromic subjects and 4 mutations in 13(30.8%) syndromic subjects were detected. A total of 77.8% (7/9) of mutations in FRMD7 were concentrated within the FERM and FA domains, while all mutations in GPR143 were located in exons 1, 2, 4 and 6. We observed that visual acuity tended to be worse in the GPR143 group than in the FRMD7 group, and no obvious difference in other clinical manifestations was found through comparisons in different groups of patients. Conclusions: This study identified 14 mutations (seven novel and seven known) in eight familial and 29 sporadic patients with congenital nystagmus, expanding the mutational spectrum and validating FRMD7 and GPR143 as mutation hotspots. These findings also revealed a significant difference in the screening rate between different groups of participants, providing new insights for the strategy of genetic screening and early clinical diagnosis of CN.
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Affiliation(s)
- Xiao-Fang Wang
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Hui Chen
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Peng-Juan Huang
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhuo-Kun Feng
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zi-Qi Hua
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiang Feng
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Fang Han
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiao-Tao Xu
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ren-Juan Shen
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Huan-Yun Yu
- School of Ophthalmology and Optometry, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
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