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Chen X, Wang T, Guo W, Yan X, Kou H, Yu Y, Liu C, Gao W, Wang W, Wang R. Transcriptome reveals the roles and potential mechanisms of lncRNAs in the regulation of albendazole resistance in Haemonchus contortus. BMC Genomics 2024; 25:188. [PMID: 38368335 PMCID: PMC10873934 DOI: 10.1186/s12864-024-10096-6] [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: 10/06/2023] [Accepted: 02/07/2024] [Indexed: 02/19/2024] Open
Abstract
BACKGROUND Haemonchus contortus (H. contortus) is the most common parasitic nematode in ruminants and is prevalent worldwide. H. contortus resistance to albendazole (ABZ) hinders the efficacy of anthelmintic drugs, but little is known about the molecular mechanisms that regulate this of drug resistance. Recent research has demonstrated that long noncoding RNAs (lncRNAs) can exert significant influence as pivotal regulators of the emergence of drug resistance. RESULTS In this study, transcriptome sequencing was conducted on both albendazole-sensitive (ABZ-sensitive) and albendazole-resistant (ABZ-resistant) H. contortus strains, with three biological replicates for each group. The analysis of lncRNA in the transcriptomic data revealed that there were 276 differentially expressed lncRNA (DElncRNA) between strains with ABZ-sensitive and ABZ-resistant according to the criteria of |log2Foldchange|≥ 1 and FDR < 0.05. Notably, MSTRG.12969.2 and MSTRG.9827.1 exhibited the most significant upregulation and downregulation, respectively, in the resistant strains. The potential roles of the DElncRNAs included catalytic activity, stimulus response, regulation of drug metabolism, and modulation of the immune response. Moreover, we investigated the interactions between DElncRNAs and other RNAs, specifically MSTRG.12741.1, MSTRG.11848.1, MSTRG.5895.1, and MSTRG.14070.1, involved in regulating drug stimulation through cis/trans/antisense/lncRNA‒miRNA-mRNA interaction networks. This regulation leads to a decrease (or increase) in the expression of relevant genes, consequently enhancing the resistance of H. contortus to albendazole. Furthermore, through comprehensive analysis of competitive endogenous RNAs (ceRNAs) involved in drug resistance-related pathways, such as the mTOR signalling pathway and ABC transporter signalling pathway, the relevance of the MSTRG.2499.1-novel-m0062-3p-HCON_00099610 interaction was identified to mainly involve the regulation of catalytic activity, metabolism, ubiquitination and transcriptional regulation of gene promoters. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) validation indicated that the transcription profiles of six DElncRNAs and six DEmRNAs were consistent with those obtained by RNA-seq. CONCLUSIONS The results of the present study allowed us to better understand the changes in the lncRNA expression profile of ABZ-resistant H. contortus. In total, these results suggest that the lncRNAs MSTRG.963.1, MSTRG.12741.1, MSTRG.11848.1 and MSTRG.2499.1 play important roles in the development of ABZ resistance and can serve as promising biomarkers for further study.
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Affiliation(s)
- Xindi Chen
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Tengyu Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wenrui Guo
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Xu Yan
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Huilin Kou
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Yu Yu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Chunxia Liu
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, Inner Mongolia Municipality, China
| | - Wa Gao
- Inner Mongolia Key Laboratory of Tick-Borne Zoonotic Infectious Disease, Department of Medicine, Hetao College, Bayan Nur, 015000, Inner Mongolia Autonomous Region, China
| | - Wenlong Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
| | - Rui Wang
- Key Laboratory of Animal Disease Clinical Diagnosis and Treatment Technology, College of Veterinary Medicine, Inner Mongolia Agricultural University, Ordos Street, Hohhot, 010018, Inner Mongolia Municipality, China.
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Hong A, Cao M, Li D, Wang Y, Zhang G, Fang F, Zhao L, Wang Q, Lin T, Wang Y. Lnc-PKNOX1-1 inhibits tumor progression in cutaneous malignant melanoma by regulating NF-κB/IL-8 axis. Carcinogenesis 2023; 44:871-883. [PMID: 37843471 PMCID: PMC10818096 DOI: 10.1093/carcin/bgad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/28/2023] [Accepted: 10/15/2023] [Indexed: 10/17/2023] Open
Abstract
Cutaneous malignant melanoma is one of the most lethal cutaneous malignancies. Accumulating evidence has demonstrated the potential influence of long non-coding RNAs (lncRNAs) in biological behaviors of melanoma. Herein, we reported a novel lncRNA, lnc-PKNOX1-1 and systematically studied its functions and possible molecular mechanisms in melanoma. Reverse transcription-quantitative PCR assay showed that lnc-PKNOX1-1 was significantly decreased in melanoma cells and tissues. Low lnc-PKNOX1-1 expression was significantly correlated with invasive pathological type and Breslow thickness of melanoma. In vitro and in vivo experiments showed lnc-PKNOX1-1 dramatically inhibited melanoma cell proliferation, migration and invasion. Mechanically, protein microarray analysis suggested that interleukin-8 (IL-8) was negatively regulated by lnc-PKNOX1-1 in melanoma, which was confirmed by western blot and ELISA. Western blot analysis also showed that lnc-PKNOX1-1 could promote p65 phosphorylation at Ser536 in melanoma. Subsequent rescue assays proved IL-8 overexpression could partly reverse the tumor-suppressing function of lnc-PKNOX1-1 overexpression in melanoma cells, indicating that lnc-PKNOX1-1 suppressed the development of melanoma by regulating IL-8. Taken together, our study demonstrated the tumor-suppressing ability of lnc-PKNOX1-1 in melanoma, suggesting its potential as a novel diagnostic biomarker and therapeutic target for melanoma.
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Affiliation(s)
- Anlan Hong
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Meng Cao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Dongqing Li
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yixin Wang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Guoqiang Zhang
- Department of Dermatology, the First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fang Fang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Liang Zhao
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Qiang Wang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Tong Lin
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | - Yan Wang
- Hospital for Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
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Zhou W, Xu X, Cen Y, Chen J. The role of lncRNAs in the tumor microenvironment and immunotherapy of melanoma. Front Immunol 2022; 13:1085766. [PMID: 36601121 PMCID: PMC9806239 DOI: 10.3389/fimmu.2022.1085766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Melanoma is one of the most lethal tumors with highly aggressive and metastatic properties. Although immunotherapy and targeted therapy have certain therapeutic effects in melanoma, a significant proportion of patients still have drug resistance after treatment. Recent studies have shown that long noncoding RNAs (lncRNAs) are widely recognized as regulatory factors in cancer. They can regulate numerous cellular processes, including cell proliferation, metastasis, epithelial-mesenchymal transition (EMT) progression and the immune microenvironment. The role of lncRNAs in malignant tumors has received much attention, whereas the relationship between lncRNAs and melanoma requires further investigation. Our review summarizes tumor suppressive and oncogenic lncRNAs closely related to the occurrence and development of melanoma. We summarize the role of lncRNAs in the immune microenvironment, immunotherapy and targeted therapy to provide new targets and therapeutic methods for clinical treatment.
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Liu S, Fan Y, Li K, Zhang H, Wang X, Ju R, Huang L, Duan M, Zhou F. Integration of lncRNAs, Protein-Coding Genes and Pathology Images for Detecting Metastatic Melanoma. Genes (Basel) 2022; 13:genes13101916. [PMID: 36292801 PMCID: PMC9602061 DOI: 10.3390/genes13101916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022] Open
Abstract
Melanoma is a lethal skin disease that develops from moles. This study aimed to integrate multimodal data to predict metastatic melanoma, which is highly aggressive and difficult to treat. The proposed EnsembleSKCM method evaluated the prediction performances of long noncoding RNAs (lncRNAs), protein-coding messenger genes (mRNAs) and pathology images (images) for metastatic melanoma. Feature selection was used to screen for metastatic biomarkers in the lncRNA and mRNA datasets. The integrated EnsembleSKCM model was built based on the weighted results of the lncRNA-, mRNA- and image-based models. EnsembleSKCM achieved 0.9444 in the prediction accuracy of metastatic melanoma and outperformed the single-modal prediction models based on the lncRNA, mRNA and image data. The experimental data suggest the importance of integrating the complementary information from the three data modalities. WGCNA was used to analyze the relationship of molecular-level features and image features, and the results show connections between them. Another cohort was used to validate our prediction.
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Affiliation(s)
- Shuai Liu
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Yusi Fan
- College of Software, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Kewei Li
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Haotian Zhang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Xi Wang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Ruofei Ju
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Meiyu Duan
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Fengfeng Zhou
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun 130012, China
- Correspondence: ; Tel./Fax: +86-431-8516-6024
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Zhang K, Qi Y, Wang M, Chen Q. Long non-coding RNA HIF1A-AS2 modulates the proliferation, migration, and phenotypic switch of aortic smooth muscle cells in aortic dissection via sponging microRNA-33b. Bioengineered 2022; 13:6383-6395. [PMID: 35212609 PMCID: PMC8974049 DOI: 10.1080/21655979.2022.2041868] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aortic dissection (AD), also known as aortic dissecting aneurysm, is one of the most common and dangerous cardiovascular diseases with high morbidity and mortality. This study was aimed to investigate the functional role of long non-coding RNA Hypoxia-inducible factor 1 alpha-antisense RNA 2 (lncRNA HIF1A-AS2) in AD. An in vitro model of AD was established by platelet-derived growth factor-BB (PDGF-BB)-mediated human aortic Smooth Muscle Cells (SMCs). HIF1A-AS2 expression in human AD tissues was determined by quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH) assays, followed by investigation of biological roles of HIF1A-AS2 in AD development by Cell Counting Kit-8 (CCK-8), immunofluorescence, and transwell assays. Additionally, the correlation between HIF1A-AS2, miR-33b, and high mobility group AT-hook2 (HMGA2) were identified by RNA immunoprecipitation (RIP), RNA pull-down and luciferase reporter assays. Results showed that HIF1A-AS2 was obviously increased, while the contractile-phenotype markers of vascular SMCs were significantly decreased in human AD tissues, when compared to normal tissues. Inhibition of HIF1A-AS2 attenuated SMCs proliferation and migration, whereas enhanced the phenotypic switch under the stimulation of PDGF-BB. Results from RIP, RNA pull-down and luciferase reporter assays demonstrated that miR-33b directly bound with HIF1A-AS2, and HIF1A-AS2 silencing suppressed the expression of HMGA2, which was induced by miR-33b inhibitor. In conclusion, knockdown of HIF1A-AS2 suppressed the proliferation and migration, while promoted the phenotypic switching of SMCs through miR-33b/HMGA2 axis, which laid a theoretical foundation for understanding the development of AD and shed light on a potential target for AD treatment.
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Affiliation(s)
- Kai Zhang
- Department of Cardiac Surgery, Tianjin Chest Hospital, Tianjin, China.,Department of Cardiac ICU, Tianjin Chest HospitalTianjin, China , Tianjin China
| | - Yujuan Qi
- Department of Cardiac ICU, Tianjin Chest Hospital, Tianjin, China
| | - Meng Wang
- Department of Cardiac Surgery, Tianjin Chest Hospital, Tianjin, China
| | - Qingliang Chen
- Department of Cardiac Surgery, Tianjin Chest Hospital, Tianjin, China.,Department of Cardiac ICU, Tianjin Chest HospitalTianjin, China , Tianjin China
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