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Dobrzycka M, Sulewska A, Biecek P, Charkiewicz R, Karabowicz P, Charkiewicz A, Golaszewska K, Milewska P, Michalska-Falkowska A, Nowak K, Niklinski J, Konopińska J. miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives. Int J Mol Sci 2023; 24:14699. [PMID: 37834147 PMCID: PMC10572595 DOI: 10.3390/ijms241914699] [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: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glaucoma through discussing their potential as biomarkers for early detection and diagnosis; offering insights into molecular pathways and mechanisms; and discussing their potential utility with respect to personalized medicine, their therapeutic potential, and non-invasive monitoring. Limitations, such as variability, small sample sizes, sample specificity, and limited accessibility to ocular tissues, are also addressed, underscoring the need for robust protocols and collaboration. Reproducibility and validation are crucial to establish the credibility of miRNA research findings, and the integration of bioinformatics tools for miRNA database creation is a valuable component of a comprehensive approach to investigate miRNA aberrations in patients with glaucoma. Overall, miRNA research in glaucoma has provided significant insights into the molecular mechanisms of the disease, offering potential biomarkers, diagnostic tools, and therapeutic targets. However, addressing challenges such as variability and limited tissue accessibility is essential, and further investigations and validation will contribute to a deeper understanding of the functional significance of miRNAs in glaucoma.
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Affiliation(s)
- Margarita Dobrzycka
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Przemyslaw Biecek
- Faculty of Mathematics and Information Science, Warsaw University of Technology, 00-662 Warsaw, Poland;
| | - Radoslaw Charkiewicz
- Center of Experimental Medicine, Medical University of Bialystok, 15-369 Bialystok, Poland;
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Piotr Karabowicz
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | - Angelika Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Kinga Golaszewska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
| | - Patrycja Milewska
- Biobank, Medical University of Bialystok, 15-269 Bialystok, Poland; (P.K.); (P.M.); (A.M.-F.)
| | | | - Karolina Nowak
- Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Bialystok, 15-269 Bialystok, Poland; (A.S.); (A.C.); (J.N.)
| | - Joanna Konopińska
- Department of Ophthalmology, Medical University of Bialystok, 15-276 Bialystok, Poland; (M.D.); (K.G.)
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Yue P, Zhang H, Tong X, Peng T, Tang P, Gao T, Guo J. Genome-wide identification and expression profiling of thes MAPK, MAPKK, and MAPKKK gene families in Ophiocordyceps sinensis. Gene 2022; 807:145930. [PMID: 34461151 DOI: 10.1016/j.gene.2021.145930] [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: 04/26/2021] [Revised: 08/19/2021] [Accepted: 08/25/2021] [Indexed: 11/04/2022]
Abstract
Mitogen-activated protein kinase (MAPK) cascades have a universal cell signaling mechanism in eukaryotes. A typical MAPK signal transduction module comprises three kinds of sequentially phosphorylated protein kinases: MAPK, Mitogen-activated protein kinase kinase (MAPKK), and Mitogen-activated protein kinase kinase kinase (MAPKKK). However, little is known regarding the genes involved in MAPK cascades in Ophiocordyceps sinensis. Nine genes (three MAPK, three MAPKK, and three MAPKKK) were identified in this study. The MAPK, MAPKK, and MAPKKK genes were divided into three subfamilies, according to the phylogenetic analysis. TEY and TGY represented the activation domains of the MAPKs; the corresponding domains in MAPKKs were SDIWS and SDVWS, and those in the MAPKKs were GSVFYWMAPEV and GTPMYMSPEV. Transcription data analysis and quantitative real-time polymerase chain reaction showed that the MAPK cascade was related to the growth of the fruiting body. This is the first study to report a genome-wide identification of the MAPK, MAPKK, and MAPKK gene families in O. sinensis.
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Affiliation(s)
- Pan Yue
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Han Zhang
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xinxin Tong
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ting Peng
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Pan Tang
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - TingHui Gao
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jinlin Guo
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, Key Laboratory of Standardization of Chinese Medicine, Ministry of Education, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China.
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Wan JN, Li Y, Guo T, Ji GY, Luo SZ, Ji KP, Cao Y, Tan Q, Bao DP, Yang RH. Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development. Front Microbiol 2021; 12:732458. [PMID: 34659161 PMCID: PMC8511702 DOI: 10.3389/fmicb.2021.732458] [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: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023] Open
Abstract
Phlebopus portentosus (Berk. and Broome) Boedijin, a widely consumed mushroom in China and Thailand, is the first species in the order Boletaceae to have been industrially cultivated on a large scale. However, to date, the lignocellulose degradation system and molecular basis of fruiting body development in P. portentosus have remained cryptic. In the present study, genome and transcriptome sequencing of P. portentosus was performed during the mycelium (S), primordium (P), and fruiting body (F) stages. A genome of 32.74 Mb with a 48.92% GC content across 62 scaffolds was obtained. A total of 9,464 putative genes were predicted from the genome, of which the number of genes related to plant cell wall-degrading enzymes was much lower than that of some saprophytic mushrooms with specific ectomycorrhizal niches. Principal component analysis of RNA-Seq data revealed that the gene expression profiles at all three stages were different. The low expression of plant cell wall-degrading genes also confirmed the limited ability to degrade lignocellulose. The expression profiles also revealed that some conserved and specific pathways were enriched in the different developmental stages of P. portentosus. Starch and sucrose metabolic pathways were enriched in the mycelium stage, while DNA replication, the proteasome and MAPK signaling pathways may be associated with maturation. These results provide a new perspective for understanding the key pathways and hub genes involved in P. portentosus development.
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Affiliation(s)
- Jia-Ning Wan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yan Li
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Ting Guo
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guang-Yan Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Shun-Zhen Luo
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Kai-Ping Ji
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Yang Cao
- Hongzhen Agricultural Science and Technology Co. Ltd., Jinghong, China
| | - Qi Tan
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Da-Peng Bao
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Rui-Heng Yang
- Key Laboratory of Agricultural Genetics and Breeding of Shanghai, Key Laboratory of Edible Fungal Resources and Utilization (South), National Engineering Research Center of Edible Fungi, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, China
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