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Wang Y, Zou B, Zhang Y, Zhang J, Li S, Yu B, An Z, Li L, Cui S, Zhang Y, Yao J, Shi X, Liu J. Comprehensive Long-Read Sequencing Analysis Discloses the Transcriptome Features of Papillary Thyroid Microcarcinoma. J Clin Endocrinol Metab 2024; 109:1263-1274. [PMID: 38038628 DOI: 10.1210/clinem/dgad695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/14/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
CONTEXT Papillary thyroid microcarcinoma (PTMC) is the most common type of thyroid cancer. It has been shown that lymph node metastasis is associated with poor prognosis in patients with PTMC. OBJECTIVE We aim to characterize the PTMC transcriptome landscape and identify the candidate transcripts that are associated with lateral neck lymph node metastasis of PTMC. METHODS We performed full-length transcriptome sequencing in 64 PTMC samples. Standard bioinformatic pipelines were applied to characterize and annotate the full-length expression profiles of 2 PTMC subtypes. Functional open reading frame (ORF) annotation of the known and novel transcripts were predicted by HMMER, DeepLoc, and DeepTMHMM tools. Candidate transcripts associated with the pN1b subtype were identified after transcript quantification and differential gene expression analyses. RESULTS We found that skipping exons accounted for the more than 27.82% of the alternative splicing events. At least 42.56% of the discovered transcripts were novel isoforms of annotated genes. A total of 39 193 ORFs in novel transcripts and 18 596 ORFs in known transcripts were identified. Distribution patterns of the characterized transcripts in functional domain, subcellular localization, and transmembrane structure were predicted. In total, 1033 and 1204 differentially expressed genes were identified in the pN0 and pN1b groups, respectively. Moreover, novel isoforms of FRMD3, NOD1, and SHROOM4 were highlighted for their association with pN1b subtype. CONCLUSION Our data provided the global transcriptome landscape of PTMC and also revealed the novel isoforms that associated with PTMC aggressiveness.
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Affiliation(s)
- Yanqiang Wang
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Binbin Zou
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Yanyan Zhang
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jin Zhang
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Shujing Li
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Bo Yu
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Zhekun An
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Lei Li
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Siqian Cui
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Yutong Zhang
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jiali Yao
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Xiuzhi Shi
- Key Laboratory of Cellular Physiology of the Ministry of Education (Shanxi Medical University), Translational Medicine Research Center, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi 030001, China
| | - Jing Liu
- Department of Thyroid Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001, China
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Ma M, Ciren D, Feng M, Zhen L, Jin G. Gentiana macrophylla flavonoids from Tibetan medicine decreases circ_0059665 to alleviate the progression of non-small cell lung cancer under hypoxia. Thorac Cancer 2024; 15:77-88. [PMID: 37993113 PMCID: PMC10761625 DOI: 10.1111/1759-7714.15165] [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: 08/18/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Gentiana macrophylla Pall. is a traditional Tibetan medicinal herb possessing antinociceptive and anti-inflammatory activities. Circular RNAs (circRNAs) have been identified to be involved in the tumorigenesis of non-small cell lung cancer (NSCLC). Here, this study focused on investigating the function and mechanism of Gentiana macrophylla flavonoids (GF) and circ_0059665 in NSCLC progression. METHODS The contents of mRNA and protein were detected using qRT-PCR and western blotting analysis. Cell proliferative and invasive abilities were evaluated by cell counting kit-8, EdU, colony formation and transwell assays, respectively. M2 macrophage polarization was analyzed by flow cytometry. RESULTS GF treatment suppressed NSCLC cell proliferation, invasion and M2 macrophage polarization under hypoxic conditions. Circ_0059665 was highly expressed in NSCLC tissues and cells. Its expression was increased under hypoxic conditions but was reduced following GF treatment. Furthermore, circ_0059665 overexpression reversed the anticancer effects of GF on NSCLC cells under hypoxic conditions. Mechanistically, circ_0059665 acted as a sponge for miR-512-5p to regulate NOVA2 expression. Hypoxia decreased miR-512-5p levels, and increased NOVA2 levels in NSCLC cells, while these tendencies were abolished after GF treatment. Circ_0059665 silencing inhibited NSCLC cell proliferation, invasion and M2 macrophage polarization in hypoxic environments, which were counteracted by NOVA2 overexpression. Moreover, NOVA2 upregulation reversed the suppressive effects of GF on NSCLC cells with hypoxia treatment. In addition, GF impeded NSCLC tumor growth in vivo via suppressing circ_0059665. CONCLUSION GF treatment in hypoxic environments suppressed NSCLC cell proliferation, invasion and M2 macrophage polarization via the circ_0059665/miR-512-5p/NOVA2 axis.
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Affiliation(s)
- Mi Ma
- University of Tibetan MedicineLhasaChina
| | | | | | - Luo Zhen
- University of Tibetan MedicineLhasaChina
| | - Guilin Jin
- University of Tibetan MedicineLhasaChina
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