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Lyu P, Li F, Deng R, Wei Q, Lin B, Cheng L, Zhao B, Lu Z. Lnc-PIK3R1, transcriptionally suppressed by YY1, inhibits hepatocellular carcinoma progression via the Lnc-PIK3R1/miR-1286/GSK3β axis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167233. [PMID: 38744342 DOI: 10.1016/j.bbadis.2024.167233] [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: 01/29/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Hepatocellular carcinoma (HCC) poses a significant threat due to its highly aggressive and high recurrence characteristics, necessitating urgent advances in diagnostic and therapeutic approaches. Long non-coding RNAs exert vital roles in HCC tumorigenesis, however the mechanisms of their expression regulation and functions are not fully elucidated yet. Herein, we identify that a novel tumor suppressor 'lnc-PIK3R1' was significantly downregulated in HCC tissues, which was correlated with poor prognosis. Functionally, lnc-PIK3R1 played tumor suppressor roles to inhibit the proliferation and mobility of HCC cells, and to impede the distant implantation of xenograft in mice. Mechanistic studies revealed that lnc-PIK3R1 interacted with miR-1286 and alleviated the repression on GSK3B by miR-1286. Notably, pharmacological inhibition of GSK3β compromised the tumor suppression effect by lnc-PIK3R1, confirming their functional relevance. Moreover, we identified that oncogenic YY1 acts as a specific transcriptional repressor to downregulate the expression of lnc-PIK3R1 in HCC. In summary, this study highlights the tumor-suppressive effect of lnc-PIK3R1, and provides new insights into the regulation of GSK3β expression in HCC, which would benefit the development of innovative intervention strategies for HCC.
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Affiliation(s)
- Peng Lyu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Fengyue Li
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Runzhi Deng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Qiliang Wei
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Bingkai Lin
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Lei Cheng
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology, Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, PR China.
| | - Zhonglei Lu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, PR China.
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2
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Haybar H, Sarbazjoda E, Purrahman D, Mahmoudian-Sani MR, Saki N. The prognostic potential of long noncoding RNA XIST in cardiovascular diseases: a review. Per Med 2024:1-13. [PMID: 38889283 DOI: 10.1080/17410541.2024.2360380] [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: 08/26/2023] [Accepted: 05/23/2024] [Indexed: 06/20/2024]
Abstract
There is a significant mortality rate associated with cardiovascular disease despite advances in treatment. long Non-coding RNAs (lncRNAs) play a critical role in many biological processes and their dysregulation is associated with a wide range of diseases in which their downstream pathways are disrupted. A lncRNA X-inactive specific transcript (XIST) is well known as a factor that regulates the physiological process of chromosome dosage compensation for females. According to recent studies, lncRNA XIST is involved in a variety of cellular processes, including apoptosis, proliferation, invasion, metastasis, oxidative stress and inflammation, through molecular networks with microRNAs and their downstream targets in neoplastic and non-neoplastic diseases. Because these cellular processes play a role in the pathogenesis of cardiovascular diseases, we aim to investigate the role that lncRNA XIST plays in this process. Additionally, we wish to determine whether it is a prognostic factor or a potential therapeutic target in these diseases.
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Affiliation(s)
- Habib Haybar
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ehsan Sarbazjoda
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz,Iran
- Student Research Committee, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Daryush Purrahman
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz,Iran
| | - Mohammad Reza Mahmoudian-Sani
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz,Iran
| | - Najmaldin Saki
- Thalassemia & Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz,Iran
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3
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Yang S, Kim SH, Yang E, Kang M, Joo JY. Molecular insights into regulatory RNAs in the cellular machinery. Exp Mol Med 2024:10.1038/s12276-024-01239-6. [PMID: 38871819 DOI: 10.1038/s12276-024-01239-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 06/15/2024] Open
Abstract
It is apparent that various functional units within the cellular machinery are derived from RNAs. The evolution of sequencing techniques has resulted in significant insights into approaches for transcriptome studies. Organisms utilize RNA to govern cellular systems, and a heterogeneous class of RNAs is involved in regulatory functions. In particular, regulatory RNAs are increasingly recognized to participate in intricately functioning machinery across almost all levels of biological systems. These systems include those mediating chromatin arrangement, transcription, suborganelle stabilization, and posttranscriptional modifications. Any class of RNA exhibiting regulatory activity can be termed a class of regulatory RNA and is typically represented by noncoding RNAs, which constitute a substantial portion of the genome. These RNAs function based on the principle of structural changes through cis and/or trans regulation to facilitate mutual RNA‒RNA, RNA‒DNA, and RNA‒protein interactions. It has not been clearly elucidated whether regulatory RNAs identified through deep sequencing actually function in the anticipated mechanisms. This review addresses the dominant properties of regulatory RNAs at various layers of the cellular machinery and covers regulatory activities, structural dynamics, modifications, associated molecules, and further challenges related to therapeutics and deep learning.
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Affiliation(s)
- Sumin Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Sung-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Eunjeong Yang
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea
| | - Mingon Kang
- Department of Computer Science, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jae-Yeol Joo
- Department of Pharmacy, College of Pharmacy, Hanyang University, Ansan, Gyeonggi-do, 15588, Republic of Korea.
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4
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Li S, Wang M, Liu B, Lv Y, Man J, Liang M, Qiao H. Analysis of lncRNA-miRNA-mRNA interactions identified a novel biomarker LINC00657 to improve prognosis prediction of papillary thyroid carcinoma. Int Immunopharmacol 2024; 137:112432. [PMID: 38865751 DOI: 10.1016/j.intimp.2024.112432] [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: 03/04/2024] [Revised: 05/21/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most common type of thyroid cancer. Identification of novel biomarkers can potentially help explore the underlying molecular mechanisms of PTC. Long non-coding RNAs (lncRNAs) are involved in cancer development. However, understanding the role of lncRNA in PTC remains challenging. METHODS Based on the competitive endogenous RNA (ceRNA) theory, we constructed a comprehensive PTC-related lncRNA-miRNA-mRNA network using data from The Cancer Genome Atlas. To evaluate the prognostic power, we performed survival analysis for patients with PTC with low and high lncRNA expression levels, and examined the relationship between lncRNA and immune-related functions. RESULTS We identified a hub node, long intergenic non-coding RNA, LINC00657, as a novel prognostic biomarker in PTC. LINC00657 was differentially expressed between tumor and adjacent normal samples. Low LINC00657 expression levels was significantly associated with better survival outcome. Our functional analyses showed that LINC00657 was related with infiltration of CD8+ T cell and macrophage; immune check point molecules; and immune metagenes such as IgG, LCK, MHC_I/II and etc. These results suggest that LINC00657 is an immune-related biomarker with potential clinical applicability. Additionally, cancer-related signaling pathway and high frequency of gene BRAF mutation were found in PTC samples with high LINC00657 expression level, which were consistent with previous findings. CONCLUSION LINC00657 is an immune-related biomarker that can potentially improve prognosis prediction in PTC. Our study provided new treatment target of PTC in clinical practice and offered the novel insights in elucidating the functional role of lncRNAs.
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Affiliation(s)
- Shuang Li
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China; Department of Endocrinology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Mingli Wang
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bing Liu
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yichen Lv
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianting Man
- The Fourth Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meihua Liang
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Hong Qiao
- Department of Endocrinology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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5
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Chen W, Wang S, Wei D, Zhai L, Liu L, Pan C, Han Z, Liu H, Zhong W, Jiang X. LncRNA ZFAS1 promotes invasion of medullary thyroid carcinoma by enhancing EPAS1 expression via miR-214-3p/UCHL1 axis. J Cell Commun Signal 2024; 18:e12021. [PMID: 38946718 PMCID: PMC11208124 DOI: 10.1002/ccs3.12021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 07/02/2024] Open
Abstract
lncRNA ZFAS1 was identified to facilitate thyroid cancer, but its role in medullary thyroid carcinoma (MTC) remains unknown. This study aimed to unravel the potential function of this lncRNA in MTC by investigating the involvement of the lncRNA ZFAS1 in a ceRNA network that regulates MTC invasion. Proliferation, invasion, and migration of cells were evaluated using EdU staining and Transwell assays. Immunoprecipitation (IP) assays, dual-fluorescence reporter, and RNA IP assays were employed to examine the binding interaction among genes. Nude mice were used to explore the role of lncRNA ZFAS1 in MTC in vivo. ZFAS1 and EPAS1 were upregulated in MTC. Silencing ZFAS1 inhibited MTC cell proliferation and invasion under hypoxic conditions, which reduced EPAS1 protein levels. UCHL1 knockdown increased EPAS1 ubiquitination. ZFAS1 positively regulated UCHL1 expression by binding to miR-214-3p. Finally, silencing ZFAS1 significantly repressed tumor formation and metastasis in MTC. LncRNA ZFAS1 promotes invasion of MTC by upregulating EPAS1 expression via the miR-214-3p/UCHL1 axis.
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Affiliation(s)
- Wenjing Chen
- Department of PathologyQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Shaoqing Wang
- Pathology of Qiqihar Medical CollegeQiqiharHeilongjiang ProvinceChina
| | - Dongmei Wei
- Department of Science and EducationQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Lili Zhai
- Department of PathologyQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Li Liu
- Department of CT RadiologyQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Chunlei Pan
- Department of General SurgeryQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Zhongshu Han
- Department of Critical Care MedicineQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Huiming Liu
- Department of PathologyQiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Wei Zhong
- Qiqihar First HospitalQiqiharHeilongjiang ProvinceChina
| | - Xin Jiang
- Department of OrthopaedicsThird Affiliated Hospital of Qiqihar Medical CollegeQiqiharHeilongjiang ProvinceChina
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6
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Liu Y, Ma TX, Fan PF, Wang Z, Wang Z, Li L. STAT3-induced lncRNA GNAS-AS1 accelerates keloid formation by mediating the miR-196a-5p/CXCL12/STAT3 axis in a feedback loop. Exp Dermatol 2024; 33:e15111. [PMID: 38840411 DOI: 10.1111/exd.15111] [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: 02/01/2024] [Revised: 04/16/2024] [Accepted: 04/28/2024] [Indexed: 06/07/2024]
Abstract
Keloids are pathological scar tissue resulting from skin trauma or spontaneous formation, often accompanied by itching and pain. Although GNAS antisense RNA 1 (GNAS-AS1) shows abnormal upregulation in keloids, the underlying molecular mechanism is unclear. The levels of genes and proteins in clinical tissues from patients with keloids and human keloid fibroblasts (HKFs) were measured using quantitative reverse transcription PCR, western blot and enzyme-linked immunosorbent assay. The features of HKFs, including proliferation and migration, were evaluated using cell counting kit 8 and a wound healing assay. The colocalization of GNAS-AS1 and miR-196a-5p in HKFs was measured using fluorescence in situ hybridization. The relationships among GNAS-AS1, miR-196a-5p and C-X-C motif chemokine ligand 12 (CXCL12) in samples from patients with keloids were analysed by Pearson correlation analysis. Gene interactions were validated by chromatin immunoprecipitation and luciferase reporter assays. GNAS-AS1 and CXCL12 expression were upregulated and miR-196a-5p expression was downregulated in clinical tissues from patients with keloids. GNAS-AS1 knockdown inhibited proliferation, migration, and extracellular matrix (ECM) accumulation of HKFs, all of which were reversed by miR-196a-5p downregulation. Signal transducer and activator of transcription 3 (STAT3) induced GNAS-AS1 transcription through GNAS-AS1 promoter interaction, and niclosamide, a STAT3 inhibitor, decreased GNAS-AS1 expression. GNAS-AS1 positively regulated CXCL12 by sponging miR-196-5p. Furthermore, CXCL12 knockdown restrained STAT3 phosphorylation in HKFs. Our findings revealed a feedback loop of STAT3/GNAS-AS1/miR-196a-5p/CXCL12/STAT3 that promoted HKF proliferation, migration and ECM accumulation and affected keloid progression.
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Affiliation(s)
- Yun Liu
- Department of Plastic and cosmetic Surgery, Hainan General Hospital (Hainan Affifiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Teng-Xiao Ma
- Department of Plastic and cosmetic Surgery, Hainan General Hospital (Hainan Affifiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Peng-Fei Fan
- Department of Plastic and cosmetic Surgery, Hainan General Hospital (Hainan Affifiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Ze Wang
- Hainan Medical University, Haikou, Hainan, China
| | - Zhe Wang
- Department of Plastic and cosmetic Surgery, Hainan General Hospital (Hainan Affifiliated Hospital of Hainan Medical University), Haikou, Hainan, China
| | - Lei Li
- Department of Plastic and cosmetic Surgery, Hainan General Hospital (Hainan Affifiliated Hospital of Hainan Medical University), Haikou, Hainan, China
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7
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Chu J, Newman J, Cho J. Molecular Mimicry of Transposable Elements in Plants. PLANT & CELL PHYSIOLOGY 2024:pcae058. [PMID: 38808931 DOI: 10.1093/pcp/pcae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/06/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators.
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Affiliation(s)
- Jie Chu
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, Beijing 200032, China
- University of Chinese Academy of Science, Beijing 100049, China
| | - Josephine Newman
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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8
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Pascual-García S, Martínez-Peinado P, Pujalte-Satorre C, Navarro-Sempere A, Esteve-Girbés J, López-Jaén AB, Javaloyes-Antón J, Cobo-Velacoracho R, Navarro-Blasco FJ, Sempere-Ortells JM. Exosomal Osteoclast-Derived miRNA in Rheumatoid Arthritis: From Their Pathogenesis in Bone Erosion to New Therapeutic Approaches. Int J Mol Sci 2024; 25:1506. [PMID: 38338785 PMCID: PMC10855630 DOI: 10.3390/ijms25031506] [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: 12/20/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease that causes inflammation, pain, and ultimately, bone erosion of the joints. The causes of this disease are multifactorial, including genetic factors, such as the presence of the human leukocyte antigen (HLA)-DRB1*04 variant, alterations in the microbiota, or immune factors including increased cytotoxic T lymphocytes (CTLs), neutrophils, or elevated M1 macrophages which, taken together, produce high levels of pro-inflammatory cytokines. In this review, we focused on the function exerted by osteoclasts on osteoblasts and other osteoclasts by means of the release of exosomal microRNAs (miRNAs). Based on a thorough revision, we classified these molecules into three categories according to their function: osteoclast inhibitors (miR-23a, miR-29b, and miR-214), osteoblast inhibitors (miR-22-3p, miR-26a, miR-27a, miR-29a, miR-125b, and miR-146a), and osteoblast enhancers (miR-20a, miR-34a, miR-96, miR-106a, miR-142, miR-199a, miR-324, and miR-486b). Finally, we analyzed potential therapeutic targets of these exosomal miRNAs, such as the use of antagomiRs, blockmiRs, agomiRs and competitive endogenous RNAs (ceRNAs), which are already being tested in murine and ex vivo models of RA. These strategies might have an important role in reestablishing the regulation of osteoclast and osteoblast differentiation making progress in the development of personalized medicine.
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Affiliation(s)
- Sandra Pascual-García
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | | | | | - Alicia Navarro-Sempere
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Jorge Esteve-Girbés
- Department of Legal Studies of the State, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Ana B. López-Jaén
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Juan Javaloyes-Antón
- Department of Physics, Systems Engineering and Signal Theory, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Raúl Cobo-Velacoracho
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
| | - Francisco J. Navarro-Blasco
- Department of Biotechnology, University of Alicante, 03690 San Vicente del Raspeig, Spain
- Rheumatology Unit, University General Hospital of Elche, 03203 Elche, Spain
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9
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Pengjie Y, Rong J, Pengfei N. miR-378a-5p exerts tumor-suppressive effects on esophageal squamous cell carcinoma after neoadjuvant immunotherapy by downregulating APOC1/CEP55. Sci Rep 2024; 14:305. [PMID: 38172247 PMCID: PMC10764758 DOI: 10.1038/s41598-023-50938-z] [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: 06/10/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Genetic assessment of tumors following neoadjuvant immunotherapy helps identifying targets that mediate anti-tumor immunity. In this study, we explored dysregulated RNAs in esophageal squamous cell carcinoma samples after neoadjuvant immunotherapy using deep sequencing and high-throughput screening. We identified 584 differentially expressed messenger RNAs (mRNAs), 67 differentially expressed microRNAs (miRNAs), and 1,047 differentially expressed long non-coding RNAs (lncRNAs) using differential expression analysis. Competing endogenous RNAs closely related to esophageal squamous cell carcinoma were selected via a combined Pearson's correlation test and weighted correlation network analysis. After validation using survival analysis and dry-lab and wet-lab-based studies, we identified the I-miR-378-5p-APOC1/CEP55 as a critical pathway for esophageal squamous cell carcinoma progression after neoadjuvant immunotherapy. Tumor immune infiltration analysis showed that APOC1 and CEP55 expression is associated with immune regulatory pathways and the function of multiple infiltrating immune cells. We investigated the mechanism of esophageal squamous carcinoma progression after neoadjuvant immunotherapy from the perspective of the mRNA-miRNA-lncRNA network. Furthermore, we identified accurate novel therapeutic targets and prognostic biomarkers, introduced novel perspectives to immunotherapy studies, and laid the foundation for the clinical treatment of patients with esophageal squamous carcinoma.
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Affiliation(s)
- Yang Pengjie
- Inner Mongolia Medical University, Jinshan Development Zone, Hohhot, 010110, Inner Mongolia Autonomous Region, China
- Thoracic Surgery Department, Peking University Cancer Hospital Inner Mongolia Hospital (Cancer Hospital Affiliated to Inner Mongolia Medical University), Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Jia Rong
- Inner Mongolia Medical University, Jinshan Development Zone, Hohhot, 010110, Inner Mongolia Autonomous Region, China
| | - Ning Pengfei
- Inner Mongolia Medical University, Jinshan Development Zone, Hohhot, 010110, Inner Mongolia Autonomous Region, China.
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10
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Li F, Wang Y, Wen M, Aizezi G, Yuan J, Zhou T, Shen G. NPHS2-6 drives cervical squamous cell carcinoma (CSCC) progression via hsa-miR-1323/SMC1B axis to activate PI3K-Akt pathway. Clin Transl Oncol 2024; 26:245-259. [PMID: 37322227 DOI: 10.1007/s12094-023-03248-9] [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: 04/05/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
PURPOSE A substantial amount of evidence demonstrates suggests that long non-coding RNAs (lncRNAs) play a key role in the progression of various malignancies, cervical squamous cell carcinoma (CSCC) included. In our study, we deeply investigated the role and molecular mechanism of lncRNA NPHS2-6 in CSCC. METHODS The expression level of gene and protein expression were measured by qRT-PCR and western blot. To test the cell proliferation and cell metastasis ability, we carried out the CCK-8 experiment, clone formation assay, transwell assay and wound healing, respectively. The interactivity among NPHS2-6, miR-1323 and SMC1B were co demonstrated using the bioinformatics tool, dual-luciferase reporter system, and RNA pulldown assay. The subcutaneous tumor model of nude mice was established to verify the results of previous studies at the in vivo. NPHS2-6 was upregulated in CSCC tissues and cells. RESULTS NPHS2-6 deficiency significantly inhibited CSCC cell growth and EMT in vitro. In addition, NPHS2-6 deficiency also inhibited the growth of CSCC xenograft tumors in mice in vivo. Importantly, NPHS2-6 was a competing endogenous RNA (ceRNA) to increases SMC1B levels by binding to miR-1323, leading to activate the PI3K/Akt pathway, thereby exacerbating tumorigenesis of CSCC. CONCLUSIONS In conclusion, NPHS2-6/miR-1323/SMC1B/PI3K/Akt signaling accelerates the progression of CSCC, providing a new direction for the treatment strategy of CSCC.
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Affiliation(s)
- Fen Li
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Yan Wang
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Mengke Wen
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Gulibiya Aizezi
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Jinrui Yuan
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Tongjunnan Zhou
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Guqun Shen
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China.
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11
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Wang Y, Wang J, Gruninger RJ, McAllister TA, Li M, Guan LL. Assessment of different enrichment methods revealed the optimal approach to identify bovine circRnas. RNA Biol 2024; 21:1-13. [PMID: 38797889 PMCID: PMC11135877 DOI: 10.1080/15476286.2024.2356334] [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] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Although circular RNAs (circRNAs) play important roles in regulating gene expression, the understanding of circRNAs in livestock animals is scarce due to the significant challenge to characterize them from a biological sample. In this study, we assessed the outcomes of bovine circRNA identification using six enrichment approaches with the combination of ribosomal RNAs removal (Ribo); linear RNAs degradation (R); linear RNAs and RNAs with structured 3' ends degradation (RTP); ribosomal RNAs coupled with linear RNAs elimination (Ribo-R); ribosomal RNA, linear RNAs and RNAs with poly (A) tailing elimination (Ribo-RP); and ribosomal RNA, linear RNAs and RNAs with structured 3' ends elimination (Ribo-RTP), respectively. RNA-sequencing analysis revealed that different approaches led to varied ratio of uniquely mapped reads, false-positive rate of identifying circRNAs, and the number of circRNAs per million clean reads (Padj <0.05). Out of 2,285 and 2,939 highly confident circRNAs identified in liver and rumen tissues, respectively, 308 and 260 were commonly identified from five methods, with Ribo-RTP method identified the highest number of circRNAs. Besides, 507 of 4,051 identified bovine highly confident circRNAs had shared splicing sites with human circRNAs. The findings from this work provide optimized methods to identify bovine circRNAs from cattle tissues for downstream research of their biological roles in cattle.
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Affiliation(s)
- Yixin Wang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Jian Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Robert J. Gruninger
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tim A. McAllister
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Mingzhou Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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12
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Li B, Feng C, Zhang W, Sun S, Yue D, Zhang X, Yang X. Comprehensive non-coding RNA analysis reveals specific lncRNA/circRNA-miRNA-mRNA regulatory networks in the cotton response to drought stress. Int J Biol Macromol 2023; 253:126558. [PMID: 37659489 DOI: 10.1016/j.ijbiomac.2023.126558] [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: 03/06/2023] [Revised: 07/29/2023] [Accepted: 08/20/2023] [Indexed: 09/04/2023]
Abstract
Root and leaf are essential organs of plants in sensing and responding to drought stress. However, comparative knowledge of non-coding RNAs (ncRNAs) of root and leaf tissues in the regulation of drought response in cotton is limited. Here, we used deep sequencing data of leaf and root tissues of drought-resistant and drought-sensitive cotton varieties for identifying miRNAs, lncRNAs and circRNAs. A total of 1531 differentially expressed (DE) ncRNAs was identified, including 77 DE miRNAs, 1393 DE lncRNAs and 61 DE circRNAs. The tissue-specific and variety-specific competing endogenous RNA (ceRNA) networks of DE lncRNA-miRNA-mRNA response to drought were constructed. Furthermore, the novel drought-responsive lncRNA 1 (DRL1), specifically and differentially expressed in root, was verified to positively affect phenotypes of cotton seedlings under drought stress, competitively binding to miR477b with GhNAC1 and GhSCL3. In addition, we also constructed another ceRNA network consisting of 18 DE circRNAs, 26 DE miRNAs and 368 DE mRNAs. Fourteen circRNA were characterized, and a novel molecular regulatory system of circ125- miR7484b/miR7450b was proposed under drought stress. Our findings revealed the specificity of ncRNA expression in tissue- and variety-specific patterns involved in the response to drought stress, and uncovered novel regulatory pathways and potentially effective molecules in genetic improvement for crop drought resistance.
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Affiliation(s)
- Baoqi Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
| | - Cheng Feng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Simin Sun
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China.
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13
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Pan J, Xie X, Sheng J, Ju C, Sun S, Cui F, Zhai W, Ming L. Construction and identification of lncRNA/circRNA-coregulated ceRNA networks in gemcitabine-resistant bladder carcinoma. Carcinogenesis 2023; 44:847-858. [PMID: 37787763 DOI: 10.1093/carcin/bgad065] [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: 05/01/2023] [Revised: 08/24/2023] [Accepted: 10/02/2023] [Indexed: 10/04/2023] Open
Abstract
OBJECTIVES To explore the regulatory networks that underlie the development of chemoresistance in bladder cancer. METHODS We analyzed profiles of differentially expressed long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), microRNAs (miRNAs) and messenger RNA (mRNAs) in gemcitabine-resistant/sensitive bladder cancer cells using next-generation sequencing data. RESULTS Hundreds of differentially expressed lncRNAs and miRNAs and thousands of circRNAs and mRNAs were identified. Bioinformatics analysis revealed the chromosomal localizations, classification and coexpression of mRNAs, as well as candidates for cis and trans regulation by lncRNAs. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed mRNAs and circRNAs indicated important functional roles of coregulated RNAs, thus establishing competing endogenous RNA (ceRNA) and protein-protein interactions networks that may underlie chemoresistance in bladder cancer. We demonstrated that lncRNA LINP1 can act as a ceRNA by inhibiting miR-193a-5p to increase TP73 expression; and that lncRNA ESRG and hsa_circ_0075881 can simultaneously bind miR-324-3p to increase ST6GAL1 expression. Modulation of ceRNA network components using ablation and overexpression approaches contributed to gemcitabine resistance in bladder cancer cells. CONCLUSIONS These results elucidate mechanisms by which lncRNAs and circRNAs coregulate the development of bladder cancer cell resistance to gemcitabine, thus laying the foundation for future research to identify biomarkers and disease targets.
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Affiliation(s)
- Jingjing Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Xiaojuan Xie
- Shaanxi Center for Clinical Laboratory, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Jinxiu Sheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Chenxi Ju
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Shuaijie Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, China
| | - Fangfang Cui
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Wen Zhai
- Department of Medical Genetics, Northwest Women's and Children's Hospital, Xi'an, China
| | - Liang Ming
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, China
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14
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Haybar H, Sadati NS, Purrahman D, Mahmoudian-Sani MR, Saki N. lncRNA TUG1 as potential novel biomarker for prognosis of cardiovascular diseases. Epigenomics 2023; 15:1273-1290. [PMID: 38088089 DOI: 10.2217/epi-2023-0242] [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] [Indexed: 01/05/2024] Open
Abstract
Globally, cardiovascular diseases (CVDs) are among the leading causes of death. In light of the high prevalence and mortality of CVDs, it is imperative to understand the molecules involved in CVD pathogenesis and the signaling pathways that they initiate. This may facilitate the development of more precise and expedient diagnostic techniques, the identification of more effective prognostic molecules and the identification of potential therapeutic targets. Numerous studies have examined the role of lncRNAs, such as TUG1, in CVD pathogenesis in recent years. According to this review article, TUG1 can be considered a biomarker for predicting the prognosis of CVD.
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Affiliation(s)
- Habib Haybar
- Atherosclerosis Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Narjes Sadat Sadati
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Daryush Purrahman
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Reza Mahmoudian-Sani
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Najmaldin Saki
- Thalassemia and Hemoglobinopathy Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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15
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Brito VGB, Bell-Hensley A, McAlinden A. MicroRNA-138: an emerging regulator of skeletal development, homeostasis, and disease. Am J Physiol Cell Physiol 2023; 325:C1387-C1400. [PMID: 37842749 PMCID: PMC10861148 DOI: 10.1152/ajpcell.00382.2023] [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] [Received: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Noncoding microRNAs are powerful epigenetic regulators of cellular processes by their ability to target and suppress expression of numerous protein-coding mRNAs. This multitargeting function is a unique and complex feature of microRNAs. It is now well-described that microRNAs play important roles in regulating the development and homeostasis of many cell/tissue types, including those that make up the skeletal system. In this review, we focus on microRNA-138 (miR-138) and its effects on regulating bone and cartilage cell differentiation and function. In addition to its reported role as a tumor suppressor, miR-138 appears to function as an inhibitor of osteoblast differentiation. This review provides additional information on studies that have attempted to alter miR-138 expression in vivo as a means to dampen ectopic calcification or alter bone mass. However, a review of the published literature on miR-138 in cartilage reveals a number of contradictory and inconclusive findings with respect to regulating chondrogenesis and chondrocyte catabolism. This highlights the need for more research in understanding the role of miR-138 in cartilage biology and disease. Interestingly, a number of studies in other systems have reported miR-138-mediated effects in dampening inflammation and pain responses. Future studies will reveal if a multifunctional role of miR-138 involving suppression of ectopic bone, inflammation, and pain will be beneficial in skeletal conditions such as osteoarthritis and heterotopic ossification.
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Affiliation(s)
- Victor Gustavo Balera Brito
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Austin Bell-Hensley
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, Missouri, United States
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, Missouri, United States
- Department of Cell Biology & Physiology, Washington University School of Medicine, St. Louis, Missouri, United States
- Shriners Hospital for Children, St. Louis, Missouri, United States
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16
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Piergiorge RM, da Silva Francisco Junior R, de Vasconcelos ATR, Santos-Rebouças CB. Multi-layered transcriptomic analysis reveals a pivotal role of FMR1 and other developmental genes in Alzheimer's disease-associated brain ceRNA network. Comput Biol Med 2023; 166:107494. [PMID: 37769462 DOI: 10.1016/j.compbiomed.2023.107494] [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: 05/08/2023] [Revised: 09/05/2023] [Accepted: 09/15/2023] [Indexed: 09/30/2023]
Abstract
Alzheimer's disease (AD) is an increasingly neurodegenerative disorder that causes progressive cognitive decline and memory impairment. Despite extensive research, the underlying causes of late-onset AD (LOAD) are still in progress. This study aimed to establish a network of competing regulatory interactions involving circular RNAs (circRNAs), microRNAs (miRNAs), RNA-binding proteins (RBPs), and messenger RNAs (mRNAs) connected to LOAD. A systematic analysis of publicly available expression data was conducted to identify integrated differentially expressed genes (DEGs) from the hippocampus of LOAD patients. Subsequently, gene co-expression analysis identified modules comprising highly expressed DEGs that act cooperatively. The competition between co-expressed DEGs and miRNAs/RBPs and the simultaneous interactions between circRNA and miRNA/RBP revealed a complex ceRNA network responsible for post-transcriptional regulation in LOAD. Hippocampal expression data for miRNAs, circRNAs, and RBPs were used to filter relevant relationships for AD. An integrated topological score was used to identify the highly connected hub gene, from which a brain core ceRNA subnetwork was generated. The Fragile X Messenger Ribonucleoprotein 1 (FMR1) coding for the RBP FMRP emerged as the prominent driver gene in this subnetwork. FMRP has been previously related to AD but not in a ceRNA network context. Also, the substantial number of neurodevelopmental genes in the ceRNA subnetwork and their related biological pathways strengthen that AD shares common pathological mechanisms with developmental conditions. Our results enhance the current knowledge about the convergent ceRNA regulatory pathways underlying AD and provide potential targets for identifying early biomarkers and developing novel therapeutic interventions.
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Affiliation(s)
- Rafael Mina Piergiorge
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Cíntia Barros Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
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17
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Ratre P, Nazeer N, Bhargava A, Thareja S, Tiwari R, Raghuwanshi VS, Mishra PK. Design and Fabrication of a Nanobiosensor for the Detection of Cell-Free Circulating miRNAS-LncRNAS-mRNAS Triad Grid. ACS OMEGA 2023; 8:40677-40684. [PMID: 37953834 PMCID: PMC10637347 DOI: 10.1021/acsomega.3c05718] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023]
Abstract
The increased understanding of the competitive endogenous RNA (ceRNA) network in the onset and development of breast cancers has suggested their use as promising disease biomarkers. Keeping these RNAs as molecular targets, we designed and developed an optical nanobiosensor for specific detection of the miRNAs-LncRNAs-mRNAs triad grid in circulation. The sensor was formulated using three quantum dots (QDs), i.e., QD-705, QD-525, and GQDs. These QDs were surface-activated and modified with a target-specific probe. The results suggested the significant ability of the developed nanobiosensor to identify target RNAs in both isolated and plasma samples. Apart from the higher specificity and applicability, the assessment of the detection limit showed that the sensor could detect the target up to 1 fg concentration. After appropriate validation, the developed nanobiosensor might prove beneficial to characterizing and detecting aberrant disease-specific cell-free circulating miRNAs-lncRNAs-mRNAs.
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Affiliation(s)
- Pooja Ratre
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Nazim Nazeer
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Arpit Bhargava
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
- Faculty
of Science, Ram Krishna Dharmarth Foundation
University, Bhopal 462030, India
| | - Suresh Thareja
- Department
of Pharmaceutical Sciences and Natural Products, Central University of Punjab, Bathinda 151001, India
| | - Rajnarayan Tiwari
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Vinay Singh Raghuwanshi
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
| | - Pradyumna Kumar Mishra
- Division
of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental
Health, Bhopal 462030, India
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18
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Chorostecki U, Bologna NG, Ariel F. The plant noncoding transcriptome: a versatile environmental sensor. EMBO J 2023; 42:e114400. [PMID: 37735935 PMCID: PMC10577639 DOI: 10.15252/embj.2023114400] [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] [Received: 04/28/2023] [Revised: 08/11/2023] [Accepted: 08/21/2023] [Indexed: 09/23/2023] Open
Abstract
Plant noncoding RNA transcripts have gained increasing attention in recent years due to growing evidence that they can regulate developmental plasticity. In this review article, we comprehensively analyze the relationship between noncoding RNA transcripts in plants and their response to environmental cues. We first provide an overview of the various noncoding transcript types, including long and small RNAs, and how the environment modulates their performance. We then highlight the importance of noncoding RNA secondary structure for their molecular and biological functions. Finally, we discuss recent studies that have unveiled the functional significance of specific long noncoding transcripts and their molecular partners within ribonucleoprotein complexes during development and in response to biotic and abiotic stress. Overall, this review sheds light on the fascinating and complex relationship between dynamic noncoding transcription and plant environmental responses, and highlights the need for further research to uncover the underlying molecular mechanisms and exploit the potential of noncoding transcripts for crop resilience in the context of global warming.
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Affiliation(s)
- Uciel Chorostecki
- Faculty of Medicine and Health SciencesUniversitat Internacional de CatalunyaBarcelonaSpain
| | - Nicolas G. Bologna
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UBBarcelonaSpain
| | - Federico Ariel
- Instituto de Agrobiotecnologia del Litoral, CONICET, FBCBUniversidad Nacional del LitoralSanta FeArgentina
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19
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Wu C, Xu Q, Li J, Qin C, Tulafu H, Liu W, Lu Q, Zheng W, Fu X. Regulation of cashmere fineness traits by noncoding RNA in Jiangnan cashmere goats. BMC Genomics 2023; 24:604. [PMID: 37821834 PMCID: PMC10566132 DOI: 10.1186/s12864-023-09531-x] [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: 01/16/2023] [Accepted: 07/24/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Cashmere has long been used as the raw material for wool textiles. The diameter of the cashmere fibre determines its quality and economic value. However, the regulatory role of noncoding RNAs (ncRNAs) in cashmere fineness remains unclear, especially regarding the interaction between ncRNAs and coding RNAs. RESULTS Transcriptome sequencing was used to identify the expression profiles of long noncoding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs) in the skin tissues of Jiangnan cashmere goats with different cashmere fineness levels. Integration analysis of ncRNA and coding RNA was performed in combination with previous research results. The results showed that 16,437 lncRNAs, 2234 circRNAs, and 1322 miRNAs were identified in 8 skin samples of cashmere goats. A total of 403 differentially expressed (DE) lncRNAs, 62 DE circRNAs and 30 DE miRNAs were identified in the skin tissues of the fine groups (Fe) and coarse groups (Ce). We predicted the target gene of DE lncRNA, the target gene of DE miRNA and the host gene of DE circRNA. Based on functional annotation and enrichment analysis of target genes, we found that DE lncRNAs could be involved in regulating the fineness traits of cashmere. The most potential lncRNAs were MSTRG.42054.1, MSTRG.18602.3, and MSTRG.2199.13. CONCLUSIONS The data from this study enriched the cashmere goat noncoding RNA database and helped to supplement the annotation of the goat genome. The results provided a new direction for the breeding of cashmere characters.
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Affiliation(s)
- Cuiling Wu
- School of Life Sciences, Xinjiang Normal University, Urumqi, China
| | - Qin Xu
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Jianying Li
- Key Laboratory of Special Environmental Medicine, Xinjiang Military General Hospital, Urumqi, China
| | - Chongkai Qin
- Aksu Prefecture Animal Husbandry Technology Extension Center, Aksu, China
| | - Hanikezi Tulafu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Wenna Liu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Qingwei Lu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wenxin Zheng
- Xinjiang Uygur Autonomous Region Breeding sheep and wool Cashmere Quality Safety Supervision and Inspection Center, Institute of Animal Husbandry Quality Standard, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China.
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat (XJYS1105), Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.
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20
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Li Y, Zhang JK, Yu ZT, Jiang JW, Tang H, Tu GL, Xia Y. LncRNA XIST Exacerbates Oxygen-Glucose Deprivation/Reoxygenation-Induced Cerebral Injury Through the miR-25-3p/TRAF3 Axis. Mol Neurobiol 2023; 60:6109-6120. [PMID: 37422573 DOI: 10.1007/s12035-023-03450-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 06/15/2023] [Indexed: 07/10/2023]
Abstract
Ischemic stroke causes lethal damage to the brain. Identifying key regulators of OGD/R-induced cerebral injury is important for developing novel therapies for ischemic stroke. HMC3 and SH-SY5Y cells were treated with OGD/R as an in vitro ischemic stroke model. Cell viability and apoptosis were determined via CCK-8 assay and flow cytometry. Inflammatory cytokines were examined by ELISA. Luciferase activity was measured for evaluating the interaction of XIST, miR-25-3p, and TRAF3. Bcl-2, Bax, Bad, cleaved-caspase 3, total caspase 3, and TRAF3 were detected via western blotting. HMC3 and SH-SY5Y cells showed increased XIST expression and decreased miR-25-3p expression following OGD/R. Importantly, silencing of XIST and overexpression of miR-25-3p reduced apoptosis and inflammatory response following OGD/R. Furthermore, XIST worked as a miR-25-3p sponge, and miR-25-3p targeted TRAF3 to suppress its expression. Moreover, the knockdown of TRAF3 ameliorated OGD/R-induced injury. Loss of XIST-mediated protective effects was reversed by overexpression of TRAF3. LncRNA XIST exacerbates OGD/R-induced cerebral damage via sponging miR-25-3p and enhancing TRAF3 expression.
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Affiliation(s)
- You Li
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China
| | - Ji-Kun Zhang
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China
| | - Zheng-Tao Yu
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China.
| | - Jun-Wen Jiang
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China
| | - Hong Tang
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China
| | - Guo-Long Tu
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China
| | - Ying Xia
- Department of Neurosurgery, Affiliated Haikou Hospital at Xiangya Medical College, Central South University, No. 43, People's Avenue, Meilan District, Haikou, 570208, Hainan Province, People's Republic of China.
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21
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Choudhuri S. Long noncoding RNAs: biogenesis, regulation, function, and their emerging significance in toxicology. Toxicol Mech Methods 2023; 33:541-551. [PMID: 36992569 DOI: 10.1080/15376516.2023.2197489] [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: 01/22/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023]
Abstract
The repertoire of regulatory noncoding RNAs (ncRNAs) has been enriched by the inclusion of long noncoding RNA (lncRNA) that are longer than 200 nt. Some of the currently known lncRNAs, were reported in the 1990s before the term lncRNA was introduced. These lncRNAs have diverse regulatory functions including regulation of transcription via interactions with proteins and RNAs, chromatin remodeling, translation, posttranslational protein modification, protein trafficking and cell signaling. Predictably, the dysregulation of lncRNA expression due to exposure to toxicants may precipitate adverse health consequences. Dysregulation of lncRNAs has also been implicated in various adverse human health outcomes. There is an increasing agreement that lncRNA expression profiling data needs to be closely examined to determine whether their altered expression can be used as biomarkers of toxicity as well as adverse human health outcomes. This review summarizes the biogenesis, regulation, function of lncRNA and their emerging significance in toxicology and disease conditions. Because our understanding of the lncRNA-toxicity relationship is still evolving, this review discusses this developing field using some examples.
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Affiliation(s)
- Supratim Choudhuri
- Division of Food Ingredients, Office of Food Additive Safety, U.S. Food and Drug Administration, College Park, MD, USA
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22
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth PA, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. BIOINFORMATICS ADVANCES 2023; 3:vbad093. [PMID: 37485422 PMCID: PMC10359604 DOI: 10.1093/bioadv/vbad093] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long noncoding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (i) identifies circRNAs via backsplicing junctions detected in RNA-seq data, (ii) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (iii) performs differential expression analysis, (iv) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (v) predicts miRNA binding sites on circRNAs, (vi) systematically investigates potential circRNA-miRNA sponging events, (vii) creates a network of competing endogenous RNAs and (viii) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues, where we identified two distinct types of circRNAs characterized by a specific ratio of the number of the binding site to the length of the transcript. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability and implementation https://github.com/biomedbigdata/circRNA-sponging. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | | | | | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Freising D-85354, Germany
| | - Jakub Jankowski
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hye Kyung Lee
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jan Baumbach
- Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla A Furth
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study, Technical University of Munich, Garching D-85748, Germany
- Laboratory of Genetics and Physiology, National Institute of Diabetes, Digestive, and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Markus List
- To whom correspondence should be addressed. or
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Lee KH, Hwang HJ, Im YJ, Nam AR, Lee JW, Cho JY. New oncogenic functions of LINE1 retroelement as a ceRNA for tumor suppressive microRNA miR-126 on ENPP5. PLoS One 2023; 18:e0286814. [PMID: 37352273 PMCID: PMC10289412 DOI: 10.1371/journal.pone.0286814] [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: 01/30/2023] [Accepted: 05/23/2023] [Indexed: 06/25/2023] Open
Abstract
Retroelements (REs) had been considered 'Junk' until the encyclopedia of DNA elements (ENCODE) project demonstrated that most genome is functional. Although the function of retroelements has been reported in diverse cancers including human breast cancer (HBC) and subtypes, only a few studies have suggested the putative functions of REs via their random genome integration. A canine mammary tumor (CMT) has been highlighted due to the similarities in molecular and pathophysiology with HBC. This study investigated the putative roles of REs common in both HBC and CMT. The human LINE and HERV-K sequences harbor many miRNAs responsive elements (MREs) for tumor-suppressive miRNA such as let-7. We also observed that various MREs are exist in the ERV and LINE highly expressed in the transcriptome data of CMT as well as HBC sets. MREs against miR-126 were highly expressed in both HBC and CMT while the levels of miR-126 were down-regulated. Oppositely, the expression of miR-126 target genes was significantly up-regulated in the cancers. Moreover, cancer patients with an increased level of miR-126 showed better overall survival. The expression of ENPP5, a putative miR-126 target gene, was downregulated by miR-126 mimic. Importantly, overexpression of LINE fragment significantly suppressed miR-126 function on the target gene expression. We propose the functional role of REs expression in tumorigenesis as competing endogenous RNAs (ceRNA) against tumor-suppressive miRNAs. This study provided pieces of evidence that LINE expression, even partial and fragmented, have a regulatory function in ENPP5 gene expression via the competition with miR-126.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Hyeon-Ji Hwang
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Yeo-Jin Im
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - A-Reum Nam
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jeong-Woon Lee
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, BK21 Plus and Research Institute for Veterinary Science, School of Veterinary Medicine, Seoul National University, Seoul, Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, Republic of Korea
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24
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Wang D, Xie D, Zhang J, Cai B, Yang B, Zhou L, Huang X. Comprehensive analysis of the coding and non-coding RNA transcriptome expression profiles of hippocampus tissue in tx-J animal model of Wilson's disease. Sci Rep 2023; 13:9252. [PMID: 37286730 DOI: 10.1038/s41598-023-36503-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/05/2023] [Indexed: 06/09/2023] Open
Abstract
Wilson's disease (WD) is an autosomal recessive disorder with a genetic basis. The predominant non-motor symptom of WD is cognitive dysfunction, although the specific genetic regulatory mechanism remains unclear. Tx-J mice, with an 82% sequence homology of the ATP7B gene to the human gene, are considered the most suitable model for WD. This study employs deep sequencing to investigate the differences in RNA transcript profiles, both coding and non-coding, as well as the functional characteristics of the regulatory network involved in WD cognitive impairment. The cognitive function of tx-J mice was evaluated using the Water Maze Test (WMT). Long non-coding RNA (lncRNA), circular RNA (circRNA), and messenger RNA (mRNA) profiles were analyzed in the hippocampal tissue of tx-J mice to identify differentially expressed RNAs (DE-RNAs). Subsequently, the DE-RNAs were used to construct protein-protein interaction (PPI) networks, as well as DE-circRNAs and lncRNAs-associated competing endogenous RNA (ceRNA) expression networks, and coding-noncoding co-expression (CNC) networks. To elucidate their biological functions and pathways, the PPI and ceRNA networks were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. A total of 361 differentially expressed mRNAs (DE-mRNAs), comprising 193 up-regulated and 168 down-regulated mRNAs, 2627 differentially expressed long non-coding RNAs (DE-lncRNAs), consisting of 1270 up-regulated and 1357 down-regulated lncRNAs, and 99 differentially expressed circular RNAs (DE-circRNAs), consisting of 68 up-regulated and 31 down-regulated circRNAs, were observed in the tx-J mice group when compared to the control mice group. Gene Ontology (GO) and pathway analyses revealed that DE-mRNAs were enriched in cellular processes, calcium signaling pathways, and mRNA surveillance pathways. In contrast, the DE-circRNAs-associated competing endogenous RNA (ceRNA) network was enriched for covalent chromatin modification, histone modification, and axon guidance, whereas the DE-lncRNAs-associated ceRNA network was enriched for dendritic spine, regulation of cell morphogenesis involved in differentiation, and mRNA surveillance pathway. The study presented the expression profiles of lncRNA, circRNA, and mRNA in the hippocampal tissue of tx-J mice. Furthermore, the study constructed PPI, ceRNA, and CNC expression networks. The findings are significant in comprehending the function of regulatory genes in WD associated with cognitive impairment. These results also offer valuable information for the diagnosis and treatment of WD.
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Affiliation(s)
- Dan Wang
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Daojun Xie
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China.
| | - Juan Zhang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Biao Cai
- College of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, No. 1 Qianjiang Road, Xinzhan District, Hefei, 230012, People's Republic of China
| | - Bo Yang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Lei Zhou
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
| | - Xiaofeng Huang
- Encephalopathy Center, The First Affiliated Hospital of Anhui University of Chinese Medicine, No. 117 Meishan Road, Shushan District, Hefei, 230031, People's Republic of China
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25
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Shan W, Li S, Yin Z. Identification of canonical pyroptosis-related genes, associated regulation axis, and related traditional Chinese medicine in spinal cord injury. Front Aging Neurosci 2023; 15:1152297. [PMID: 37273650 PMCID: PMC10232751 DOI: 10.3389/fnagi.2023.1152297] [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: 01/27/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Neuroinflammation plays an important role in spinal cord injury (SCI), and pyroptosis is inflammatory-related programmed cell death. Although neuroinflammation induced by pyroptosis has been reported in SCI, there is a lack of systematic research on SCI pyroptosis and its regulation mechanism. The purpose of this study was to systematically analyze the expression of pyroptosis-related genes (PRGs) in different SCI models and associated regulation axis by bioinformatics methods. We downloaded raw counts data of seven high-throughput sequencings and two microarray datasets from the GEO database, classified by species (rat and mouse) and SCI modes (moderate contusive model, aneurysm clip impact-compression model, and hemisection model), including mRNAs, miRNAs, lncRNAs, and circRNAs, basically covering the acute, subacute and chronic stages of SCI. We performed differential analysis by R (DEseq2) or GEO2R and found that the AIM2/NLRC4/NLRP3 inflammasome-related genes, GSDMD, IL1B, and IL18, were highly expressed in SCI. Based on the canonical NLRP3 inflammasome-mediated pyroptosis-related genes (NLRP3/PRGs), we constructed transcription factors (TFs)-NLRP3/PRGs, miRNAs- Nlrp3/PRGs and lncRNAs/circRNAs/mRNAs-miRNA- Nlrp3/PRGs (ceRNA) networks. In addition, we also predicted Traditional Chinese medicine (TCM) and small, drug-like molecules with NLRP3/PRGs as potential targets. Finally, 39 up-regulated TFs were identified, which may regulate at least two of NLRP3/PRGs. A total of 7 down-regulated miRNAs were identified which could regulate Nlrp3/PRGs. ceRNA networks were constructed including 23 lncRNAs, 3 cicrRNAs, 6 mRNAs, and 44 miRNAs. A total of 24 herbs were identified which may with two NLRP3/PRGs as potential targets. It is expected to provide new ideas and therapeutic targets for the treatment of SCI.
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Affiliation(s)
- Wenshan Shan
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Shuang Li
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- The Key Laboratory of Microbiology and Parasitology of Anhui Province, Anhui Medical University, Hefei, Anhui, China
| | - Zongsheng Yin
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
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26
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Zhou Q, Shu X, Chai Y, Liu W, Li Z, Xi Y. The non-coding competing endogenous RNAs in acute myeloid leukemia: biological and clinical implications. Biomed Pharmacother 2023; 163:114807. [PMID: 37150037 DOI: 10.1016/j.biopha.2023.114807] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/28/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023] Open
Abstract
Acute myeloid leukemia (AML) is a hematologic carcinoma that has seen a considerable improvement in patient prognosis because of genetic diagnostics and molecularly-targeted therapies. Nevertheless, recurrence and drug resistance remain significant obstacles to leukemia treatment. It is critical to investigate the underlying molecular mechanisms and find solutions. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), circular RNAs, long non-coding RNAs, and pseudogenes, have been found to be crucial components in driving cancer. The competing endogenous RNA (ceRNA) mechanism has expanded the complexity of miRNA-mediated gene regulation. A great deal of literature has shown that ncRNAs are essential to the biological functions of the ceRNA network (ceRNET). NcRNAs can compete for the same miRNA response elements to influence miRNA-target RNA interactions. Recent evidence suggests that ceRNA might be a potential biomarker and therapeutic strategy. So far, however, there have been no comprehensive studies on ceRNET about AML. What is not yet clear is the clinical application of ceRNA in AML. This study attempts to summarize the development of research on the related ceRNAs in AML and the roles of ncRNAs in ceRNET. We also briefly describe the mechanisms of ceRNA and ceRNET. What's more significant is that we explore the clinical value of ceRNAs to provide accurate diagnostic and prognostic biomarkers as well as therapeutic targets. Finally, limitations and prospects are considered.
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Affiliation(s)
- Qi Zhou
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Xiaojun Shu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Vascular Surgery, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yihong Chai
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Wenling Liu
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China
| | - Zijian Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China
| | - Yaming Xi
- The First Clinical Medical College of Lanzhou University, Lanzhou, Gansu, China; Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu, China.
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27
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Di Mauro G, Frontini F, Torreggiani E, Iaquinta MR, Caselli A, Mazziotta C, Esposito V, Mazzoni E, Libener R, Grosso F, Maconi A, Martini F, Bononi I, Tognon M. Epigenetic investigation into circulating microRNA 197-3p in sera from patients affected by malignant pleural mesothelioma and workers ex-exposed to asbestos. Sci Rep 2023; 13:6501. [PMID: 37081052 PMCID: PMC10119131 DOI: 10.1038/s41598-023-33116-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/07/2023] [Indexed: 04/22/2023] Open
Abstract
The epigenetic role of microRNAs is established at both physiological and pathological levels. Dysregulated miRNAs and their targets appear to be a promising approach for innovative anticancer therapies. In our previous study, circulating miR-197-3p tested dysregulated in workers ex-exposed to asbestos (WEA). Herein, an epigenetic investigation on this circulating miRNA was carried out in sera from malignant pleural mesothelioma (MPM) patients. MiR-197-3p was quantified in MPM (n = 75) sera and comparatively analyzed to WEA (n = 75) and healthy subject (n = 75) sera, using ddPCR and RT-qPCR techniques. Clinicopathological characteristics, occupational, non-occupational information and overall survival (OS) were evaluated in correlation studies. MiR-197-3p levels, analyzed by ddPCR, were significantly higher in MPM than in WEA cohort, with a mean copies/µl of 981.7 and 525.01, respectively. Consistently, RT-qPCR showed higher miR-197-3p levels in sera from MPM with a mean copies/µl of 603.7, compared to WEA with 336.1 copies/µl. OS data were significantly associated with histologic subtype and pleurectomy. Circulating miR-197-3p is proposed as a new potential biomarker for an early diagnosis of the MPM onset. Indeed, miR-197-3p epigenetic investigations along with chest X-ray, computed tomography scan and spirometry could provide relevant information useful to reach an early and effective diagnosis for MPM.
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Affiliation(s)
- Giulia Di Mauro
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Francesca Frontini
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Elena Torreggiani
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Maria Rosa Iaquinta
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Andrea Caselli
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Chiara Mazziotta
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Valentina Esposito
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Elisa Mazzoni
- Department of Chemical, Pharmaceutical and Agricultural Sciences-DOCPAS, University of Ferrara, 44121, Ferrara, Italy
| | - Roberta Libener
- Research Training and Innovation Infrastructure - Department of Integrated Research and Innovation Activities (DAIRI), AO SS. Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy
| | - Federica Grosso
- Mesothelioma Unit, AO SS. Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy
| | - Antonio Maconi
- Research Training and Innovation Infrastructure - Department of Integrated Research and Innovation Activities (DAIRI), AO SS. Antonio e Biagio e Cesare Arrigo, 15121, Alessandria, Italy
| | - Fernanda Martini
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy
| | - Ilaria Bononi
- Department of Translational Medicine and for Romagna, University of Ferrara, 70, Fossato di Mortara Street, 44121, Ferrara, Italy.
| | - Mauro Tognon
- Department of Medical Sciences, Laboratories of Cell Biology and Molecular Genetics, School of Medicine, University of Ferrara, 64B, Fossato di Mortara Street, 44121, Ferrara, Italy.
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28
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Kattner AA. When it doesn't run in the blood(vessels) - events involved in vascular disorders. Biomed J 2023; 46:100591. [PMID: 37059363 DOI: 10.1016/j.bj.2023.03.004] [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: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/16/2023] Open
Abstract
In the current issue of the Biomedical Journal the underlying pathology of hemodynamic compromise in acute small subcortical infarction are elucidated. A follow-up study in patients with childhood Kawasaki disease is presented, as well as an insight into the gradually decreasing antigen expression in cases of acute myeloid leukemia. Furthermore this issue provides an exciting update concerning COVID-19 and the use of CRISPR-Cas, a review about computational approaches in the research of kidney stone formation, factors connected to central precocious puberty, and why a rock star of paleogenetics recently received a Nobel Prize. Additionally, this issue contains an article proposing the repurposing of the lung cancer drug Capmatinib, a study of how the gut microbiome develops in neonates, an impulse about the role of the transmembrane protein TMED3 in esophageal carcinoma, and the revelation about how competing endogenous RNA influences ischemic stroke. Lastly, genetic reasons for male infertility are discussed, as well as the relation between non-alcoholic fatty liver disease and chronic kidney disease.
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Zhou H, Huang J, Wang F. Increased transcription of hsa_circ_0000644 upon RUNX family transcription factor 3 downregulation participates in the malignant development of bladder cancer. Cell Signal 2023; 104:110590. [PMID: 36627006 DOI: 10.1016/j.cellsig.2023.110590] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
BACKGROUND Studies are ongoing to examine the versatile functions of circular RNAs (circRNAs) in human diseases. This research investigates the effects of hsa_circ_0000644 (circ_644) and its related molecules on the malignant behavior of bladder cancer (BCa) cells. METHODS Abundant bioinformatics analyses were performed to screen the key circRNA and its related molecules in BCa. Tumor tissues and the para-tumorous tissues were collected from 58 patients with BCa. Expression of RUNX family transcription factor 3 (RUNX3), circ_644, microRNA-143-3p (miR-143-3p), and musashi RNA binding protein 2 (MSI2) in BCa tissues or cells was determined. Molecular interactions were confirmed by chromatin immunoprecipitation, RNA pull-down, and luciferase assays. Gain and loss-of function assays were performed using two BCa cell lines (T24 and HT1376). RESULTS Circ_644 was highly expressed whereas RUNX3, which could suppress circ_644 transcription, was lowly expressed in BCa tissues and cells. Upregulation of RUNX3 suppressed proliferation, colony formation, migration and invasion, and tumorigenicity of BCa cells and induced cell cycle arrest. However, the tumor-suppressive effects of RUNX3 were blocked by circ_644 upregulation. Circ_644 served as a sponge for miR-143-3p, and miR-143-3p bound to MSI2 mRNA. The rescue experiments showed that miR-143-3p inhibition or MSI2 overexpression restored the malignant behaviors of BCa cells induced by circ_644 knockdown or RUNX3 overexpression. CONCLUSION This study demonstrates that transcriptional activation of circ_644 upon RUNX3 downregulation drives the malignant development of BCa through the miR-143-3p/MSI2 axis. RUNX3 restoration or specific inhibition of circ_644 or MSI2 may help block BCa progression.
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Affiliation(s)
- Hao Zhou
- Department of Urology, The Second Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410001, Hunan, PR China
| | - Jiangbo Huang
- Department of Urology, The Second Affiliated Hospital of Hunan University of Chinese Medicine, Changsha 410001, Hunan, PR China
| | - Fang Wang
- Department of Medicine, Changsha Social Work College, Changsha 410004, Hunan, PR China.
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Zhu X, Song J, Wang M, Wang X, Lv L. Dysregulated ceRNA network modulated by copy number variation-driven lncRNAs in breast cancer: A comprehensive analysis. J Gene Med 2023; 25:e3471. [PMID: 36525372 DOI: 10.1002/jgm.3471] [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: 08/10/2022] [Revised: 11/09/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is a malignancy harmful to physical and mental health in women, with quite high mortality. Copy number variations (CNVs) are vital factors affecting the progression of breast cancer. Detecting CNVs in breast cancer to predict the prognosis of patients has become a promising approach to accurate treatment in recent years. The differential analysis was performed on CNVs of long noncoding RNAs (lncRNAs) as well as the expression of lncRNAs, microRNAs (miRNAs) and mRNAs in normal tissue and breast tumor tissue based on The Cancer Genome Atlas (TCGA) database. The CNV-driven lncRNAs were identified by the Kruskal-Wallis test. Meanwhile, a competitive endogenous RNA (ceRNA) network regulated by CNV-driven lncRNA was constructed. As the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed, the mRNAs in the dysregulated ceRNA network were mainly enriched in the biological functions and signaling pathways, including the Focal Adhesion-PI3K-Akt-mTOR-signaling pathway, the neuronal system, metapathway biotransformation Phase I and II and blood circulation, etc. The relationship between the CNVs of five lncRNAs and their gene expression in the ceRNA network was analyzed via a chi-square test, which confirmed that except for LINC00243, the expression of four lncRNAs was notably correlated with the CNVs. The survival analysis revealed that only the copy number gain of LINC00536 was evidently related to the poor prognosis of patients. The CIBERSORT algorithm showed that five lncRNAs were correlated with the abundance of immune cell infiltration and immune checkpoints. In a word, by analyzing CNV-driven lncRNAs and the ceRNA network regulated by these lncRNAs, this study explored the mechanism of breast cancer and provided novel insights into new biomarkers.
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Affiliation(s)
- Xiaotao Zhu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jialu Song
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingzheng Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Xiaohui Wang
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Lin Lv
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
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The Genes-Stemness-Secretome Interplay in Malignant Pleural Mesothelioma: Molecular Dynamics and Clinical Hints. Int J Mol Sci 2023; 24:ijms24043496. [PMID: 36834912 PMCID: PMC9963101 DOI: 10.3390/ijms24043496] [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: 01/23/2023] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
MPM has a uniquely poor somatic mutational landscape, mainly driven by environmental selective pressure. This feature has dramatically limited the development of effective treatment. However, genomic events are known to be associated with MPM progression, and specific genetic signatures emerge from the exceptional crosstalk between neoplastic cells and matrix components, among which one main area of focus is hypoxia. Here we discuss the novel therapeutic strategies focused on the exploitation of MPM genetic asset and its interconnection with the surrounding hypoxic microenvironment as well as transcript products and microvesicles representing both an insight into the pathogenesis and promising actionable targets.
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32
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Yang F, Wang M, Shi J, Xu G. IncRNA MALAT1 Regulates the Proliferation, Apoptosis, Migration, and Invasion of Osteosarcoma Cells by Targeting miR-873-5p/ROCK1. Crit Rev Eukaryot Gene Expr 2023; 33:67-79. [PMID: 36734858 DOI: 10.1615/critreveukaryotgeneexpr.2022044747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The malignant bone tumor osteosarcoma (OS) was one of the most aggressive tumors. Despite breakthroughs in treatment options for OS recently, the survival rate of patients with metastasis or reoccurring disease has remained unchanged over the last 25 years, at around 20%. lncRNA expression dysregulation is linked to carcinogenesis, advancement, and metastasis. Additionally, the fundamental mechanism of lncRNAs in regulating OS cell biological activity and progression is still being investigated. The expression of miR-873-5p and MALAT1 were detected by quantitative real-time polymerase chain reaction (qRT-PCR) in OS. The relationship between the expression level of MALAT1 and the survival rate of OS individuals was evaluated by the Kaplan-Meier plotter. The tumor cell's capability of proliferation was determined using the CCK-8. Transwell was used to test the migratory and invasive properties of tumor cells. ROCK1 protein expression was analyzed by western blot, while qRT-PCR was used to detect ROCK1 mRNA expression. Targeted genes of MALAT1 or miR-873-5p were predicted by StarBase2.0. The target association among miR-873-5p and MALAT1 or ROCK1 was confirmed using the luciferase assay. The relationship between ROCK1 and MALAT1 or miR-873-5p expression in OS was investigated using Spearman's correlation analysis. MALAT1 was up-regulated and was linked to a lower survival rate of patients in OS. The malignant behaviors of cells were inhibited by down-regulated MALAT1 in vitro. Dual-luciferase gene experiments confirmed the presence of MALAT1/miR-873-5p/ROCK1 axis. The up-regulated miR-873-5p blocked the promoted effects of MALAT1 on cell behaviors. Over-expressed MALAT1 promoted the malignant behaviors of cells by miR-873-5p/ROCK1 axis in OS.
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Affiliation(s)
- Fan Yang
- Department of Bone and Soft-Tissue Tumor, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, Shanxi, China
| | - Mao Wang
- Department of Bone and Soft-Tissue Tumor, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, Shanxi, China
| | - Junlong Shi
- Department of Bone and Soft-Tissue Tumor, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, Shanxi, China
| | - Gang Xu
- Department of Bone and Soft-Tissue Tumor, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, Shanxi, China
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Liu H, Chen Q, Zheng W, Zhou Y, Bai Y, Pan Y, Zhang J, Shao C. LncRNA CASC19 Enhances the Radioresistance of Nasopharyngeal Carcinoma by Regulating the miR-340-3p/FKBP5 Axis. Int J Mol Sci 2023; 24:ijms24033047. [PMID: 36769373 PMCID: PMC9917593 DOI: 10.3390/ijms24033047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Radioresistance remains a serious obstacle encountered in the radiotherapy of nasopharyngeal carcinoma (NPC). Both mRNAs and non-coding RNAs (ncRNAs), including long ncRNA (lncRNA) and microRNA (miRNA), play essential roles in radiosensitivity. However, the comprehensive expression profiles and competing endogenous RNA (ceRNA) regulatory networks among lncRNAs, miRNAs, and mRNAs in NPC radioresistance are still bewildering. In this study, we performed an RNA-sequencing (RNA-seq) assay in the radioresistant NPC cells CNE2R and its parental cells CNE2 to identify the differentially expressed lncRNAs, miRNAs, and mRNAs. The ceRNA networks containing lncRNAs, miRNAs, and mRNAs were predicted on the basis of the Pearson correlation coefficients and authoritative miRanda databases. In accordance with bioinformatic analysis of the data of the tandem mass tag (TMT) assay of CNE2R and CNE2 cells and the gene chip assay of radioresistant NPC samples in pre- and post-radiotherapy, the radioresistance-related signaling network of lncRNA CASC19, miR-340-3p, and FKBP5 was screened and further verified using an RT-qPCR assay. CASC19 was positively associated with FKBP5 expression while negatively correlated with miR-340-3p, and the target binding sites of CASC19/miR-340-3p and miR-340-3p/FKBP5 were confirmed using a dual-luciferase reporter assay. Moreover, using an mRFP-GFP-LC3 maker, it was found that autophagy contributed to the radioresistance of NPC. MiR-340-3p inhibition or FKBP5 overexpression could rescue the suppression of autophagy and radioresistance induced by CASC19 knockdown in CNE2R cells. In conclusion, the CASC19/miR-340-3p/FKBP5 network may be instrumental in regulating NPC radioresistance by enhancing autophagy, which provides potential new therapeutic targets for NPC.
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Affiliation(s)
- Hongxia Liu
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
- School of Stomatology, Henan University, Kaifeng 475001, China
| | - Qianping Chen
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Wang Zheng
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuchuan Zhou
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Bai
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yan Pan
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jianghong Zhang
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chunlin Shao
- Institute of Radiation Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Correspondence:
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Hoffmann M, Schwartz L, Ciora OA, Trummer N, Willruth LL, Jankowski J, Lee HK, Baumbach J, Furth P, Hennighausen L, List M. circRNA-sponging: a pipeline for extensive analysis of circRNA expression and their role in miRNA sponging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524495. [PMID: 36789427 PMCID: PMC9928029 DOI: 10.1101/2023.01.19.524495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Motivation Circular RNAs (circRNAs) are long non-coding RNAs (lncRNAs) often associated with diseases and considered potential biomarkers for diagnosis and treatment. Among other functions, circRNAs have been shown to act as microRNA (miRNA) sponges, preventing the role of miRNAs that repress their targets. However, there is no pipeline to systematically assess the sponging potential of circRNAs. Results We developed circRNA-sponging, a nextflow pipeline that (1) identifies circRNAs via back-splicing junctions detected in RNA-seq data, (2) quantifies their expression values in relation to their linear counterparts spliced from the same gene, (3) performs differential expression analysis, (4) identifies and quantifies miRNA expression from miRNA-sequencing (miRNA-seq) data, (5) predicts miRNA binding sites on circRNAs, (6) systematically investigates potential circRNA-miRNA sponging events, (7) creates a network of competing endogenous RNAs, and (8) identifies potential circRNA biomarkers. We showed the functionality of the circRNA-sponging pipeline using RNA sequencing data from brain tissues where we identified two distinct types of circRNAs characterized by a distinct ratio of the binding site length. The circRNA-sponging pipeline is the first end-to-end pipeline to identify circRNAs and their sponging systematically with raw total RNA-seq and miRNA-seq files, allowing us to better indicate the functional impact of circRNAs as a routine aspect in transcriptomic research. Availability https://github.com/biomedbigdata/circRNA-sponging. Contact markus.daniel.hoffmann@tum.de ; markus.list@tum.de. Supplementary Material Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Markus Hoffmann
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America,corresponding authors Contact:;
| | - Leon Schwartz
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Octavia-Andreea Ciora
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Nico Trummer
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Lina-Liv Willruth
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Jakub Jankowski
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Hye Kyung Lee
- National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Jan Baumbach
- Chair of Computational Systems Biology, University of Hamburg, Hamburg, Germany,Computational BioMedicine Lab, University of Southern Denmark, Odense, Denmark
| | - Priscilla Furth
- Departments of Oncology & Medicine, Georgetown University, Washington, DC, USA
| | - Lothar Hennighausen
- Institute for Advanced Study (Lichtenbergstrasse 2a, D-85748 Garching, Germany), Technical University of Munich, Germany,National Institute of Diabetes, Digestive, and Kidney Diseases, Bethesda, MD 20892, United States of America
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany,corresponding authors Contact:;
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Ciafrè SA, Russo M, Michienzi A, Galardi S. Long Noncoding RNAs and Cancer Stem Cells: Dangerous Liaisons Managing Cancer. Int J Mol Sci 2023; 24:ijms24031828. [PMID: 36768150 PMCID: PMC9915130 DOI: 10.3390/ijms24031828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Decades of research have investigated the mechanisms that lead to the origin of cancer, striving to identify tumor-initiating cells. These cells, also known as cancer stem cells, are characterized by the ability to self-renew, to give rise to differentiated tumor populations, and on a larger scale, are deemed responsible not only for tumor initiation but also for recurrent tumors, often resistant to chemotherapy and radiotherapy. Long noncoding RNAs are RNA molecules longer than 200 nt, lacking the ability to code for proteins, with recognized roles as fine regulators of gene expression. They can exert these functions through a variety of mechanisms, acting at almost all steps of gene expression, from modulation of the epigenetic state of chromatin to modulation of protein stability. In all cases, lncRNAs do not work alone, but they always interact with other RNA molecules, either coding or non-coding, or with protein factors. In this review, we summarize the latest results obtained about the involvement of lncRNAs in the initiating cells of several types of tumors, and highlight the different mechanisms through which they work, while discussing how the modulation of a lncRNA can affect several aspects of tumor onset and progression.
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Affiliation(s)
- Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
| | - Monia Russo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Silvia Galardi
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy
- Correspondence: (S.A.C.); (S.G.)
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Ma J, Wang F, Chen C, Ji J, Huang P, Wei D, Zhang Y, Ren L. Identification of prognostic genes signature and construction of ceRNA network in pirarubicin treatment of triple-negative breast cancer. Breast Cancer 2023; 30:379-392. [PMID: 36622564 DOI: 10.1007/s12282-023-01433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/30/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND The altered long non-coding RNA (lncRNA), circular RNA (circRNA) and mRNA expression in triple-negative breast cancer (TNBC) after pirarubicin (THP) treatment can be a critical factor in the development of tumor. Here, we identify a set of lncRNA, circRNA, and mRNA that can reveal the molecular target and molecular mechanism of THP, and can be used to predict the prognostic characteristics of TNBC. METHODS Affymetrix GeneChip sequencing was performed to determine whether lncRNA, circRNA, and mRNA were changed in MDA-MB-231 cells after THP treatment, and qRT-PCR was used to verify the accuracy of GeneChip results. Bioinformatics methods were used to analyze the differentially expressed (DE) lncRNA, circRNA and mRNA, and the co-expression network and ceRNA network were constructed. The STRING database, Kaplan-meier Mapper database, GEPIA database, and Tumor Immunity Estimation Resource were used to screen hub genes with clinical value and important significance. RESULTS THP 5 μM could significantly inhibit proliferation, migration and invasion of MDA-MB-231 cells for 24 h. 1547 DE lncRNAs, 4992 DE circRNAs, and 5777 DE mRNAs were identified. The reliability of the GeneChip was verified by qRT-PCR. An mRNA-lncRNA/circRNA co-expression network was constructed based on the Pearson correlation coefficient. Finally, we established a new ceRNA network, including three circRNAs, five miRNAs, and three mRNAs. The mRNAs are associated with immune infiltration. The mRNAs and miRNAs are significantly associated with survival outcomes in TNBC. CONCLUSION The results reveal the molecular target and mechanism of THP treatment of TNBC. These ceRNA network can be used as molecular targets for the treatment of TNBC patients and as molecular biomarkers to predict patient prognosis.
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Affiliation(s)
- Jiulong Ma
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Fengjun Wang
- Department of Hepatobiliary Surgery, Songyuan Central Hospital, Songyuan, China
| | - Chen Chen
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Jiahua Ji
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Peng Huang
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Dexian Wei
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Yang Zhang
- Department of Vascular Surgery, The First Hospital of Jilin University, Changchun, China.
| | - Liqun Ren
- Department of Experimental Pharmacology and Toxicology, School of Pharmaceutical Sciences, Jilin University, Changchun, China.
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Zhang B, Liu T, Gu Y, Ren L, Wang J, Feng C, Song Z. Long Non-Coding RNA LPP-AS2 Plays an Anti-Tumor Role in Thyroid Carcinoma by Regulating the miR-132-3p/OLFM1 Axis. Crit Rev Eukaryot Gene Expr 2023; 33:73-86. [PMID: 37199315 DOI: 10.1615/critreveukaryotgeneexpr.v33.i5.70] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The cancer-promoting function of the long non-coding RNA (lncRNA) LPP-AS2 has been documented in different cancers. Nonetheless, its role in thyroid carcinoma (THCA) remains unestablished. Reverse transcription quantitative polymerase chain reaction and Western blotting were conducted to estimate the expressions of lncRNA LPP-AS2, miR-132-3p, and OLFM1. The THCA cells' functions were assessed through CCK8 assays, Transwell invasion assays, scratch wound-healing migration assays, and quantification of caspase-3 activity. The in vivo assays were also implemented to assess tumor growth. Luciferase reporter and RNA immuno-precipitation assay (RIPA) experiments were executed to elucidate the interactions of miR-132-3p with lncRNA LPP-AS2 and OLFM1. THCA tissues and cells exhibited poor lncRNA LPP-AS2 and OLFM1 expressions and a robust expression of miR-132-3p. Overexpressing lncRNA LPP-AS2 constrained THCA cell proliferation, migration, and invasion and improved caspase-3 activity. The anti-tumor function of lncRNA LPP-AS2 was also validated in vivo. miR-132-3p had an interplay with lncRNA LPP-AS2 and OLFM1. Functionally, overexpressing miR-132-3p promoted the malignant THCA cell phenotypes. However, that tumor promotion was abolished by the additional overexpression of lncRNA LPP-AS2. The in vitro experiments also demonstrated that the repressive effect of OLFM1 overexpression on THCA cell malignant action could be offset by the miR-132-3p mimic. lncRNA LPP-AS2 impedes THCA progression via the miR-132-3p/OLFM1 axis. Our findings contribute a potential strategy in interfering with THCA progression.
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Affiliation(s)
- Bowei Zhang
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Tong Liu
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Yi Gu
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Li Ren
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Jinju Wang
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Chao Feng
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
| | - Zhe Song
- Department of Vascular and Thyroid Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, Sichuan, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, Sichuan, China
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Circ_0044411 silencing protects infantile pneumonia from lipopolysaccharide-induced cell injury by sponging miR-141-3p to inhibit CCL16 expression. Int Immunopharmacol 2023; 114:109425. [PMID: 36700761 DOI: 10.1016/j.intimp.2022.109425] [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: 04/05/2022] [Revised: 10/21/2022] [Accepted: 10/31/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Circular RNA (circRNA) has been found to play an important role in the progression of many diseases, including infantile pneumonia. However, the role of circ_0044411 in infantile pneumonia progression is still unclear. METHODS MRC-5 cells were incubated with lipopolysaccharide (LPS) for 12 h to establish the in vitro cellular model for infantile pneumonia. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to detect the levels of circ_0044411, miR-141-3p (micoRNA-141-3p) and CCL16 (CC motif chemokine ligand 16). Cell viability and proliferation was assessed by 3-(4, 5-dimethylthiazol-2-y1)-2, 5-diphenyl tetrazolium bromide (MTT) assay and 5-ethynyl-2'-deoxyuridine (EdU) assay. The levels of inflammatory factors IL-1β, IL-6 and TNF-α were determined by enzyme-linked immunosorbent assay kits. Cell apoptosis and caspase-3 activity were detected by flow cytometry analysis and caspase-3 activity assay kit. The target interaction was confirmed by dual-luciferase reporter assay, RNA immunoprecipitation assay and RNA pull-down assay. RESULTS Circ_0044411 was highly repressed in the serum of infantile pneumonia patients and LPS-induced MRC-5 cells. Circ_0044411 could promote the cell viability and proliferation, inhibit inflammatory response and apoptosis in LPS-induced MRC-5 cells. Circ_0044411 could serve as a sponge of miR-141-3p, and miR-141-3p could reverse the function of circ_0044411 on LPS-induced MRC-5 cell injury. In addition, miR-141-3p could target CCL16, and miR-141-3p could protect MRC-5 cells from LPS-induced cell injury by targeting CCL16. Furthermore, circ_0044411 sponged miR-141-3p to positively regulate CCL16 expression. CONCLUSION Circ_0044411 knockdown promoted cell viability and proliferation, inhibited inflammatory response and apoptosis by regulating miR-141-3p/CCL16 axis, indicating that circ_0044411 might be a potential therapeutic target for IP.
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Qi Y, Huang C, Zhao M, Wu X, Li G, Zhang Y, Zhang L. milR20 negatively regulates the development of fruit bodies in Pleurotus cornucopiae. Front Microbiol 2023; 14:1177820. [PMID: 37213518 PMCID: PMC10192896 DOI: 10.3389/fmicb.2023.1177820] [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: 03/02/2023] [Accepted: 04/10/2023] [Indexed: 05/23/2023] Open
Abstract
The mechanism underlying the development of fruit bodies in edible mushroom is a widely studied topic. In this study, the role of milRNAs in the development of fruit bodies of Pleurotus cornucopiae was studied by comparative analyses of the mRNAs and milRNAs at different stages of development. The genes that play a crucial role in the expression and function of milRNAs were identified and subsequently expressed and silenced at different stages of development. The total number of differentially expressed genes (DEGs) and differentially expressed milRNAs (DEMs) at different stages of development was determined to be 7,934 and 20, respectively. Comparison of the DEGs and DEMs across the different development stages revealed that DEMs and its target DEGs involved in the mitogen-activated protein kinase (MAPK) signaling pathway, protein processing in endoplasmic reticulum, endocytosis, aminoacyl-tRNA biosynthesis, RNA transport, and other metabolism pathways, which may play important roles in the development of the fruit bodies of P. cornucopiae. The function of milR20, which targeted pheromone A receptor g8971 and was involved in the MAPK signaling pathway, was further verified by overexpression and silencing in P. cornucopiae. The results demonstrated that the overexpression of milR20 reduced the growth rate of mycelia and prolonged the development of the fruit bodies, while milR20 silencing had an opposite effect. These findings indicated that milR20 plays a negative role in the development of P. cornucopiae. This study provides novel insights into the molecular mechanism underlying the development of fruit bodies in P. cornucopiae.
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Affiliation(s)
- Yuhui Qi
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
| | - Xiangli Wu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
| | - Guangyu Li
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
| | - Yingjie Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
- College of Life Sciences, Shanxi Normal University, Taiyuan, China
| | - Lijiao Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture and Rural Affairs, Beijing, China
- State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China, Beijing, China
- *Correspondence: Lijiao Zhang,
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Taheri F, Ebrahimi SO, Heidari R, Pour SN, Reiisi S. Mechanism and function of miR-140 in human cancers: A review and in silico study. Pathol Res Pract 2023; 241:154265. [PMID: 36509008 DOI: 10.1016/j.prp.2022.154265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA-140 (miR-140) acts as a tumor suppressor and plays a vital role in cell biological functions such as cell proliferation, apoptosis, and DNA repair. The expression of this miRNA has been shown to be considerably decreased in cancer tissues and cell lines compared with normal adjacent tissues. Consequently, aberrant expression of some miR-140 target genes can lead to the initiation and progression of various human cancers, such as breast cancer, gastrointestinal cancers, lung cancer, and prostate cancer. The dysregulation of the miR-140 network also affects cell proliferation, invasion, metastasis, and apoptosis of cancer cells by affecting various signaling pathways. Besides, up-regulation of miR-140 could enhance the efficacy of chemotherapeutic agents in different cancer. We aimed to cover most aspects of miR-140 function in cancer development and address its importance in different stages of cancer progression.
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Affiliation(s)
- Forough Taheri
- Department of Genetics, Sharekord Branch, Islamic Azad University, Sharekord, Iran
| | - Seyed Omar Ebrahimi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Razieh Heidari
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Somaye Nezamabadi Pour
- Department of Obstetrics and Gynecology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Somayeh Reiisi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
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Li N, Amatjan M, He P, Wu M, Yan H, Shao X. Whole transcriptome expression profiles in kidney samples from rats with hyperuricaemic nephropathy. PLoS One 2022; 17:e0276591. [PMID: 36534664 PMCID: PMC9762607 DOI: 10.1371/journal.pone.0276591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/10/2022] [Indexed: 12/24/2022] Open
Abstract
Hyperuricaemic nephropathy (HN) is a common clinical complication of hyperuricaemia (HUA) and poses a huge threat to human health. Hence, we aimed to prospectively investigate the dysregulated genes, pathways and networks involved in HN by performing whole transcriptome sequencing using RNA sequencing. Six kidney samples from HN group (n = 3) and a control group (n = 3) were obtained to conduct RNA sequencing. To disclose the relevant signalling pathways, we conducted the analysis of differentially expressed genes (DEGs), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. A competitive endogenous RNA (ceRNA) network was established to reveal the interactions between lncRNAs, circRNAs, mRNAs and miRNAs and investigate the potential mechanisms of HN. Ultimately, 2250 mRNAs, 306 lncRNAs, 5 circRNAs, and 70 miRNAs were determined to be significantly differentially expressed in the HN group relative to the control group. We further authenticated 8 differentially expressed (DE)-ncRNAs by quantitative real-time polymerase chain reaction, and these findings were in accordance with the sequencing results. The analysis results evidently showed that these DE-ncRNAs were significantly enriched in pathways related to inflammatory reaction. In conclusion, HUA may generate abnormal gene expression changes and regulate signalling pathways in kidney samples. Potentially related genes and pathways involved in HN were identified.
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Affiliation(s)
- Na Li
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Mukaram Amatjan
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Pengke He
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Meiwei Wu
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Hengxiu Yan
- College of Pharmacy, Southwest Minzu University, Chengdu, China
| | - Xiaoni Shao
- College of Pharmacy, Southwest Minzu University, Chengdu, China
- * E-mail:
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Plasil SL, Collins VJ, Baratta AM, Farris SP, Homanics GE. Hippocampal ceRNA networks from chronic intermittent ethanol vapor-exposed male mice and functional analysis of top-ranked lncRNA genes for ethanol drinking phenotypes. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10831. [PMID: 36908580 PMCID: PMC10004261 DOI: 10.3389/adar.2022.10831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular mechanisms regulating the development and progression of alcohol use disorder (AUD) are largely unknown. While noncoding RNAs have previously been implicated as playing key roles in AUD, long-noncoding RNA (lncRNA) remains understudied in relation to AUD. In this study, we first identified ethanol-responsive lncRNAs in the mouse hippocampus that are transcriptional network hub genes. Microarray analysis of lncRNA, miRNA, circular RNA, and protein coding gene expression in the hippocampus from chronic intermittent ethanol vapor- or air- (control) exposed mice was used to identify ethanol-responsive competing endogenous RNA (ceRNA) networks. Highly interconnected lncRNAs (genes that had the strongest overall correlation to all other dysregulated genes identified) were ranked. The top four lncRNAs were novel, previously uncharacterized genes named Gm42575, 4930413E15Rik, Gm15767, and Gm33447, hereafter referred to as Pitt1, Pitt2, Pitt3, and Pitt4, respectively. We subsequently tested the hypothesis that CRISPR/Cas9 mutagenesis of the putative promoter and first exon of these lncRNAs in C57BL/6J mice would alter ethanol drinking behavior. The Drinking in the Dark (DID) assay was used to examine binge-like drinking behavior, and the Every-Other-Day Two-Bottle Choice (EOD-2BC) assay was used to examine intermittent ethanol consumption and preference. No significant differences between control and mutant mice were observed in the DID assay. Female-specific reductions in ethanol consumption were observed in the EOD-2BC assay for Pitt1, Pitt3, and Pitt4 mutant mice compared to controls. Male-specific alterations in ethanol preference were observed for Pitt1 and Pitt2. Female-specific increases in ethanol preference were observed for Pitt3 and Pitt4. Total fluid consumption was reduced in Pitt1 and Pitt2 mutants at 15% v/v ethanol and in Pitt3 and Pitt4 at 20% v/v ethanol in females only. We conclude that all lncRNAs targeted altered ethanol drinking behavior, and that lncRNAs Pitt1, Pitt3, and Pitt4 influenced ethanol consumption in a sex-specific manner. Further research is necessary to elucidate the biological mechanisms for these effects. These findings add to the literature implicating noncoding RNAs in AUD and suggest lncRNAs also play an important regulatory role in the disease.
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Affiliation(s)
- SL Plasil
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - VJ Collins
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - AM Baratta
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - SP Farris
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - GE Homanics
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Anesthesiology and Perioperative Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
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Liu G, Yang ZF, Sun J, Sun BY, Zhou PY, Zhou C, Guan RY, Wang ZT, Yi Y, Qiu SJ. The LINC00152/miR-205-5p/CXCL11 axis in hepatocellular carcinoma cancer-associated fibroblasts affects cancer cell phenotypes and tumor growth. Cell Oncol 2022; 45:1435-1449. [PMID: 36435866 DOI: 10.1007/s13402-022-00730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND CXCL11 has been reported to be up-regulated in hepatocellular carcinoma (HCC) tissues and cancer-associated fibroblasts (CAFs), and CAF-secreted CXCL11 has been found to promote HCC cell proliferation and migration. Knowledge on how CAFs promote HCC progression is imperative for the future design of anti-tumor drugs addressing the high rates of disease recurrence. Herein, we propose a mechanism by which LINC00152 positively regulates CXCL11 expression and, subsequently, HCC cell phenotypes and growth characteristics via miR-205-5p in CAFs. METHODS The expression of LINC00152, miR-205-5p in HCC/non-cancerous tissues, CAFs/NFs and HCC cell lines was determined by RT-qPCR. The CXCL11 expression and secretion were determined by westernblot and ELISA. Different expressions of LINC00152, CXCL11 and miR-205-5p in CAFs were achieved by transfection with corresponding overexpression/knockdown vectors or mimics/inhibitor. The interactions among LINC00152, miR-205-5p and CXCL11 were confirmed by FISH, luciferase, AGO2 and RNA-pulldown assays. Transwell, colony formation and MTT assays were performed to assess the role of CAFs conditioned medium (CM) in HCC cell phenotype. BALB/c nude mice xenografts were used to determine the role of CAFs on HCC growth in vivo. RESULTS We found that in vitro, CM from CAFs transfected with sh-LINC00152 dramatically suppressed HCC cell viability, colony formation and migration, and that CM from CAFs transfected with miR-205-5p inhibitor (CAF-CM (miR-205-5p inhibitor)) exerted opposite effects on HCC cell phenotypes. Exogenous overexpression of CXCL11 in CAFs or CAF-CM (miR-205-5p inhibitor) could partially attenuate the effects of LINC00152 knockdown. In contrast, CM from CAFs transfected with LINC00152 dramatically increased HCC cell viability, colony formation and migration, and CM from CAFs transfected with miR-205-5p mimics (CAF-CM (miR-205-5p mimics)) exerted opposite effects on HCC cell phenotypes. Knockdown of CXCL11 in CAFs or CAF-CM (miR-205-5p mimics) could partially attenuate the effects of LINC00152 overexpression. In vivo, LINC00152 knockdown in CAFs inhibited tumor growth in a mouse model, which could be reversed by CXCL11 overexpression in CAFs. Mechanistically, we found that LINC00152 could act as a ceRNA to counteract miR-205-5p-mediated suppression on CXCL11 by directly binding to miR-205-5p and the 3'UTR of CXCL11. CONCLUSION Our data indicate that a LINC00152/miR-205-5p/CXCL11 axis in HCC CAFs can affect the proliferative and migrative abilities of HCC cells in vitro and HCC tumor growth in vivo.
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Affiliation(s)
- Gao Liu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Zhang-Fu Yang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Jian Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Bao-Ye Sun
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Pei-Yun Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Cheng Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Ruo-Yu Guan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Zhu-Tao Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China
| | - Yong Yi
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China.
| | - Shuang-Jian Qiu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute and Biomedical Research Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, People's Republic of China.
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Li F, Tan B, Chen Z, Zhao Q, Li S, Ding P, Liu C, Wang X, Li X, Li Y. Long non-coding RNA CNALPTC1 promotes gastric cancer progression by regulating the miR-6788-5p/PAK1 pathway. J Gastrointest Oncol 2022; 13:2809-2822. [PMID: 36636079 PMCID: PMC9830357 DOI: 10.21037/jgo-22-1069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Background Gastric cancer (GC) is a globally prevalent gastrointestinal tumor. Long non-coding RNAs (lncRNAs) are a new type of transcript which has become a hotspot of current research; however, the function of most lncRNAs in the advancement of GC is still not clear. The focus of this research was to elucidate the role and expression of lncRNA CNALPTC1 in GC. Methods In GC cells and tissues, the detection of CNALPTC1 expression was carried out using quantitative real-time polymerase chain reaction (qRT-PCR), and the link between its expression and clinicopathological features was investigated. The impacts of inhibition and upregulation of CNALPTC1 on the physiological behavior of GC cells were observed. Furthermore, through bioinformatics analysis and prediction of microRNA (miRNA) targeted to CNALPTC1 and target genes interacting with miRNA, the effects on invasion, proliferation, and migration of GC cells were investigated. Results The elevated expression level of CNALPTC1 was observed in GC tissues and cell lines. The in vitro analysis indicated that gene silencing of CNALPTC1 resulted in inhibition, whereas upregulation of CNALPTC1 resulted in the promotion of invasion, proliferation, and migration of GC cells, respectively. In addition, we observed that CNALPTC1 functions as a molecular sponge for miR-6788-5p, and the level of expression of CNALPTC1 exhibited a negative correlation with miR-6788-5p. Moreover, it was revealed that the miR-6788-5p's direct target was PAK1, which could reverse the inhibitory function of miR-6788-5p. Conclusions Our research revealed that the CNALPTC1 promotes GC development by negatively regulating the miR-6788-5p/PAK1 pathway. GC therapy may be improved by conducting targeted studies of the CNALPTC1/miR-6788-5p/PAK1 axis.
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Affiliation(s)
- Fang Li
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Bibo Tan
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zihao Chen
- Department of Surgery, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qun Zhao
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shi Li
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Pingan Ding
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chang Liu
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoxiao Wang
- Department of Pathology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaoya Li
- Department of Scientific Research Center, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yong Li
- The Third Department of Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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Sun Q, Wang L, Zhang C, Hong Z, Han Z. Cervical cancer heterogeneity: a constant battle against viruses and drugs. Biomark Res 2022; 10:85. [PMCID: PMC9670454 DOI: 10.1186/s40364-022-00428-7] [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: 08/16/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Cervical cancer is the first identified human papillomavirus (HPV) associated cancer and the most promising malignancy to be eliminated. However, the ever-changing virus subtypes and acquired multiple drug resistance continue to induce failure of tumor prevention and treatment. The exploration of cervical cancer heterogeneity is the crucial way to achieve effective prevention and precise treatment. Tumor heterogeneity exists in various aspects including the immune clearance of viruses, tumorigenesis, neoplasm recurrence, metastasis and drug resistance. Tumor development and drug resistance are often driven by potential gene amplification and deletion, not only somatic genomic alterations, but also copy number amplifications, histone modification and DNA methylation. Genomic rearrangements may occur by selection effects from chemotherapy or radiotherapy which exhibits genetic intra-tumor heterogeneity in advanced cervical cancers. The combined application of cervical cancer therapeutic vaccine and immune checkpoint inhibitors has become an effective strategy to address the heterogeneity of treatment. In this review, we will integrate classic and recently updated epidemiological data on vaccination rates, screening rates, incidence and mortality of cervical cancer patients worldwide aiming to understand the current situation of disease prevention and control and identify the direction of urgent efforts. Additionally, we will focus on the tumor environment to summarize the conditions of immune clearance and gene integration after different HPV infections and to explore the genomic factors of tumor heterogeneity. Finally, we will make a thorough inquiry into completed and ongoing phase III clinical trials in cervical cancer and summarize molecular mechanisms of drug resistance among chemotherapy, radiotherapy, biotherapy, and immunotherapy.
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Affiliation(s)
- Qian Sun
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Liangliang Wang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Cong Zhang
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhenya Hong
- grid.33199.310000 0004 0368 7223Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
| | - Zhiqiang Han
- grid.33199.310000 0004 0368 7223Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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Yuan P, Zhao Y, Li H, Li S, Fan S, Zhai B, Li Y, Han R, Liu X, Tian Y, Kang X, Zhang Y, Li G. CircRNAs Related to Breast Muscle Development and Their Interaction Regulatory Network in Gushi Chicken. Genes (Basel) 2022; 13:1974. [PMID: 36360215 PMCID: PMC9689937 DOI: 10.3390/genes13111974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 08/26/2023] Open
Abstract
Circular RNAs (circRNAs) play a significant regulatory role during skeletal muscle development. To identify circRNAs during postnatal skeletal muscle development in chickens, we constructed 12 cDNA libraries from breast muscle tissues of Chinese Gushi chickens at 6, 14, 22, and 30 weeks and performed RNA sequencing. In total, 2112 circRNAs were identified, and among them 79.92% were derived from exons. CircRNAs are distributed on all chromosomes of chickens, especially chromosomes 1-9 and Z. Bioinformatics analysis showed that each circRNA had an average of 38 miRNA binding sites, 61.32% of which have internal ribosomal entry site (IRES) elements. Furthermore, in total 543 differentially expressed circRNAs (DE-circRNAs) were identified. Functional enrichment analysis revealed that DE-circRNAs source genes are engaged in biological processes and muscle development-related pathways; for example, cell differentiation, sarcomere, and myofibril formation, mTOR signaling pathway, and TGF-β signaling pathway, etc. We also established a competitive endogenous RNA (ceRNA) regulatory network associated with skeletal muscle development. The results in this report indicate that circRNAs can mediate the development of chicken skeletal muscle by means of a complex ceRNA network among circRNAs, miRNAs, genes, and pathways. The findings of this study might help increase the number of known circRNAs in skeletal muscle tissue and offer a worthwhile resource to further investigate the function of circRNAs in chicken skeletal muscle development.
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Affiliation(s)
- Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Yanhua Zhang
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, Zhengzhou 450001, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450001, China
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Zhang X, Han Y, Hu X, Wang H, Tian Z, Zhang Y, Wang X. Competing endogenous RNA networks related to prognosis in chronic lymphocytic leukemia: comprehensive analyses and construction of a novel risk score model. Biomark Res 2022; 10:75. [PMID: 36271413 PMCID: PMC9585723 DOI: 10.1186/s40364-022-00423-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell malignancy that lacks specific biomarkers and drug targets. Competing endogenous RNAs (ceRNAs) play vital roles in oncogenesis and tumor progression by sponging microRNAs (miRNAs). Nevertheless, the regulatory mechanisms of survival-related ceRNA networks in CLL remain to be uncovered. METHODS We included 865 de novo CLL patients to investigate RNA expression profiles and Illumina sequencing was performed on four CLL patients, two CLL cell lines and six healthy donors in our center. According to univariate Cox regression, LASSO regression as well as multivariate Cox regression analyses, we established a novel risk score model in CLL patients. Immune signatures were compared between the low- and high-risk groups with CIBERSORT and ESTIMATE program. Afterwards, we analyzed the relationship between differentially expressed miRNAs (DEmiRNAs) and IGHV mutational status, p53 mutation status and del17p. Based on the survival analyses and differentially expressed RNAs with targeting relationships, the lncRNA/circRNA-miRNA-mRNA ceRNA networks were constructed. In addition, the circRNA circ_0002078/miR-185-3p/TCF7L1 axis was verified and their interrelations were delineated by dual-luciferase reporter gene assay. RESULTS Totally, 57 differentially expressed mRNAs (DEmRNAs) and 335 DEmiRNAs were identified between CLL patient specimens and normal B cells. A novel risk score model consisting of HTN3, IL3RA and NCK1 was established and validated. The concordance indexes of the model were 0.825, 0.719 and 0.773 in the training, test and total sets, respectively. The high-risk group was related to del(13q14) as well as shorter overall survival (OS). Moreover, we identified DEmiRNAs that related to cytogenetic abnormality of CLL patients, which revealed that miR-324-3p was associated with IGHV mutation, p53 mutation and del17p. The survival-related lncRNA/circRNA-miRNA-mRNA ceRNA networks were constructed to further facilitate the development of potential predictive biomarkers. Besides, the expression of circ_0002078 and TCF7L1 were significantly elevated and miR-185-3p was obviously decreased in CLL patients. Circ_0002078 regulated TCF7L1 expression by competing with TCF7L1 for miR-185-3p. CONCLUSIONS The comprehensive analyses of RNA expression profiles provide pioneering insights into the molecular mechanisms of CLL. The novel risk score model and survival-related ceRNA networks promote the development of prognostic biomarkers and potential therapeutic vulnerabilities for CLL.
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Affiliation(s)
- Xin Zhang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China.,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Yang Han
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China.,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Xinting Hu
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China.,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Hua Wang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China.,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Zheng Tian
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China.,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China.,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China.,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China
| | - Ya Zhang
- Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China. .,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
| | - Xin Wang
- Department of Hematology, Shandong Provincial Hospital, Shandong University, No.324, Jingwu Road, Jinan, 250021, Shandong, China. .,Department of Hematology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, No.324, Jingwu Road, Jinan, 250021, Shandong, China. .,Shandong Provincial Engineering Research Center of Lymphoma, Jinan, 250021, Shandong, China. .,Branch of National Clinical Research Center for Hematologic Diseases, Jinan, 250021, Shandong, China. .,National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, 251006, China.
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Santos F, Capela AM, Mateus F, Nóbrega-Pereira S, Bernardes de Jesus B. Non-coding antisense transcripts: fine regulation of gene expression in cancer. Comput Struct Biotechnol J 2022; 20:5652-5660. [PMID: 36284703 PMCID: PMC9579725 DOI: 10.1016/j.csbj.2022.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/14/2022] Open
Abstract
Natural antisense transcripts (NATs) are coding or non-coding RNA sequences transcribed on the opposite direction from the same genomic locus. NATs are widely distributed throughout the human genome and seem to play crucial roles in physiological and pathological processes, through newly described and targeted mechanisms. NATs represent the intricate complexity of the genome organization and constitute another layer of potential targets in disease. Here, we focus on the interesting and unique role of non-coding NATs in cancer, paying particular attention to those acting as miRNA sponges.
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Affiliation(s)
| | | | | | | | - Bruno Bernardes de Jesus
- Corresponding author at: Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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You X, Liu M, Liu Q, Li H, Qu Y, Gao X, Huang C, Luo G, Cao G, Xu D. miRNA let-7 family regulated by NEAT1 and ARID3A/NF-κB inhibits PRRSV-2 replication in vitro and in vivo. PLoS Pathog 2022; 18:e1010820. [PMID: 36215225 PMCID: PMC9550049 DOI: 10.1371/journal.ppat.1010820] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/21/2022] [Indexed: 11/05/2022] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is one of the most economically devastating diseases affecting the swine industry worldwide. To investigate the role of miRNAs in the infection and susceptibility of PRRS virus (PRRSV), twenty-four miRNA libraries were constructed and sequenced from PRRSV-infected and mock-infected Porcine alveolar macrophages (PAMs) of Meishan, Landrace, Pietrain and Qingping pigs at 9 hours post infection (hpi), 36 hpi, and 60 hpi. The let-7 family miRNAs were significantly differentially expressed between PRRSV-infected and mock-infected PAMs from 4 pig breeds. The let-7 family miRNAs could significantly inhibit PRRSV-2 replication by directly targeting the 3’UTR of the PRRSV-2 genome and porcine IL6, which plays an important role in PRRSV replication and lung injury. NEAT1 acts as a competing endogenous lncRNA (ceRNA) to upregulate IL6 by attaching let-7 in PAMs. EMSA and ChIP results confirmed that ARID3A could bind to the promoter region of pri-let-7a/let-7f/let-7d gene cluster and inhibit the expression of the let-7 family. Moreover, the NF-κB signaling pathway inhibits the expression of the let-7 family by affecting the nuclear import of ARID3A. The pEGFP-N1-let-7 significantly reduced viral infections and pathological changes in PRRSV-infected piglets. Taken together, NEAT1/ARID3A/let-7/IL6 play significant roles in PRRSV-2 infection and may be promising therapeutic targets for PRRS. There are significant differences in susceptibility/resistance to PRRSV among different pig breeds. Especially the local pig breeds in China had strong resistance to PRRSV. However, due to the complexity of the interaction mechanism between pigs and PRRSV, the genetic mechanism leading to PRRSV susceptibility/resistance in different pig breeds is still unclear. MiRNAs play a vital regulatory role in immune response and development of PRRS. In this study, we found that the expression of miRNA let-7 family members were significantly different in PRRSV-infected/mock-infected PAMs from Pietrain, Qingping, Meishan, and Landrace pigs. Our findings illustrated that NEAT1/ARID3A/let-7/IL6 had a significant role in PRRSV-2 infection. What’s more, let-7 family could significantly reduce PRRSV infection and pathological changes in vitro and in vivo. This discovery provided a new idea for breeding PRRSV resistant pigs by revealing the molecular mechanism of PRRSV susceptibility in different pig breeds. Altogether, let-7 family have significant roles in PRRSV infection and may be promising therapeutic targets for PRRS.
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Affiliation(s)
- Xiangbin You
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Henan University of Science and Technology, Luoyang, China
| | - Min Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qian Liu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Henan University of Science and Technology, Luoyang, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Huijuan Li
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yilin Qu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaoxiao Gao
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengyu Huang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gan Luo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Dequan Xu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- College of Animal Science & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Hsa_circ_0000877 facilitates the progression of diffuse large B-cell lymphoma by miR-370-3p/mitogen-activated protein kinase kinase kinase kinase 4/Hippo pathway. Anticancer Drugs 2022; 33:1091-1102. [PMID: 36066383 DOI: 10.1097/cad.0000000000001366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Diffuse large B-cell lymphoma (DLBCL) originates from B lymphocytes and is a fatal hematological malignancy. Circular RNAs have been increasingly reported as a promising biological target for cancer therapy, but their role in DLBCL remains poorly studied. Relative expression levels of has_circ_0000877 (circ_0000877), microRNA-370-3p (miR-370-3p), and mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) were assessed by quantitative real-time PCR. Western blot analysis was employed to measure protein levels. Cell Counting Kit-8 assay and 5-ethynyl-2'-deoxyuridine (EdU) assay were used to detect the proliferation of TMD8 and U2932 cells. Cell cycle and apoptosis were investigated by flow cytometry. Transwell assay was used to analyze cell migration and invasion. Molecular interaction was determined by dual-luciferase reporter assay and RNA immunoprecipitation assay. The protein expression of Ki67 in tumor tissues of mice was detected by immunohistochemistry assay. The expression of circ_0000877 was markedly elevated in DLBCL tissues and cell lines. The decreased expression of circ_0000877 significantly inhibited proliferation, migration, and invasion of DLBCL cell lines. In addition, silencing circ_0000877 promoted cell apoptosis and induced cell cycle arrest in G0/G1 phase. Then, miR-370-3p directly interacted with circ_0000877 and MAP4K4. Circ_0000877 promoted MAP4K4 level by sponging miR-370-3p. MAP4K4 depletion inhibited the activation of Hippo pathway. Finally, circ_0000877 silencing significantly prevented the growth of DLBCL cells in vivo . Our findings revealed that circ_0000877 could regulate the malignant evolution of DLBCL by miR-370-3p/MAP4K4/Hippo pathway.
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