1
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Zhang Q, Liu L. Novel insights into small open reading frame-encoded micropeptides in hepatocellular carcinoma: A potential breakthrough. Cancer Lett 2024; 587:216691. [PMID: 38360139 DOI: 10.1016/j.canlet.2024.216691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/13/2024] [Accepted: 01/27/2024] [Indexed: 02/17/2024]
Abstract
Traditionally, non-coding RNAs (ncRNAs) are regarded as a class of RNA transcripts that lack encoding capability; however, advancements in technology have revealed that some ncRNAs contain small open reading frames (sORFs) that are capable of encoding micropeptides of approximately 150 amino acids in length. sORF-encoded micropeptides (SEPs) have emerged as intriguing entities in hepatocellular carcinoma (HCC) research, shedding light on this previously unexplored realm. Recent studies have highlighted the regulatory functions of SEPs in the occurrence and progression of HCC. Some SEPs exhibit inhibitory effects on HCC, but others facilitate its development. This discovery has revolutionized the landscape of HCC research and clinical management. Here, we introduce the concept and characteristics of SEPs, summarize their associations with HCC, and elucidate their carcinogenic mechanisms in HCC metabolism, signaling pathways, cell proliferation, and metastasis. In addition, we propose a step-by-step workflow for the investigation of HCC-associated SEPs. Lastly, we discuss the challenges and prospects of applying SEPs in the diagnosis and treatment of HCC. This review aims to facilitate the discovery, optimization, and clinical application of HCC-related SEPs, inspiring the development of early diagnostic, individualized, and precision therapeutic strategies for HCC.
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Affiliation(s)
- Qiangnu Zhang
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
| | - Liping Liu
- Division of Hepatobiliary and Pancreas Surgery, Department of General Surgery, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China.
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2
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Chen H, Gong Z, Zhou H, Han Y. Deciphering chemoresistance in osteosarcoma: Unveiling regulatory mechanisms and function through the lens of noncoding RNA. Drug Dev Res 2024; 85:e22167. [PMID: 38444106 DOI: 10.1002/ddr.22167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/24/2024] [Accepted: 02/18/2024] [Indexed: 03/07/2024]
Abstract
Osteosarcoma (OS) is a primary malignant bone tumor and is prevalent in children, adolescents, and elderly individuals. It has the characteristics of high invasion and metastasis. Neoadjuvant chemotherapy combined with surgical resection is the most commonly used treatment for OS. However, the efficacy of OS is considerably diminished by chemotherapy resistance. In recent years, noncoding RNAs (ncRNAs), including microRNAs, long noncoding RNAs, and circular RNAs, are hot topics in the field of chemotherapy resistance research. Several studies have demonstrated that ncRNAs are substantially associated with chemoresistance in OS. Thus, the present study overviews the abnormally expressed ncRNAs in OS and the molecular mechanisms involved in chemoresistance, with an emphasis on their function in promoting or inhibiting chemoresistance. ncRNAs are expected to become potential therapeutic targets for overcoming drug resistance and predictive biomarkers in OS, which are of great significance for enhancing the therapeutic effect and improving the prognosis.
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Affiliation(s)
- Hefen Chen
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhujun Gong
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Hong Zhou
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Han
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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3
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Huang C, Aghaei-Zarch SM. From molecular pathogenesis to therapy: Unraveling non-coding RNAs/DNMT3A axis in human cancers. Biochem Pharmacol 2024; 222:116107. [PMID: 38438051 DOI: 10.1016/j.bcp.2024.116107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/03/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Cancer is a comprehensive classification encompassing more than 100 forms of malignancies that manifest in diverse tissues within the human body. Recent studies have provided evidence that aberrant epigenetic modifications are pivotal indicators of cancer. Epigenetics encapsulates DNA methyltransferases as a crucial class of modifiers. DNMTs, including DNMT3A, assume central roles in DNA methylation processes that orchestrate normal biological functions, such as gene transcription, predominantly in mammals. Typically, deviations in DNMT3A function engender distortions in factors that drive tumor growth and progression, thereby exacerbating the malignant phenotype of tumors. Consequently, such abnormalities pose significant challenges in cancer therapy because they impede treatment efficacy. Non-coding RNAs (ncRNAs) represent a group of RNA molecules that cannot encode functional proteins. Recent investigation attests to the crucial significance of regulatory ncRNAs in epigenetic regulation. Notably, recent reports have illuminated the complex interplay between ncRNA expression and epigenetic regulatory machinery, including DNMT3A, particularly in cancer. Recent findings have demonstrated that miRNAs, namely miR-770-5p, miR-101, and miR-145 exhibit the capability to target DNMT3A directly, and their aberration is implicated in diverse cellular abnormalities that predispose to cancer development. This review aims to articulate the interplay between DNMT3A and the ncRNAs, focusing on its impact on the development and progression of cancer, cancer therapy resistance, cancer stem cells, and prognosis. Importantly, the emergence of such reports that suggest a connection between DNMT3A and ncRNAs in several cancers indicates that this connecting axis offers a valuable target with significant therapeutic potential that might be exploited for cancer management.
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Affiliation(s)
- Chunjie Huang
- School of Medicine, Nantong University, Nantong 226001, China
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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4
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Ugalde AP, Roiz-Valle D, Moledo-Nodar L, Caravia XM, Freije JMP, López-Otín C. Noncoding RNA Contribution to Aging and Lifespan. J Gerontol A Biol Sci Med Sci 2024; 79:glae058. [PMID: 38394352 DOI: 10.1093/gerona/glae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Indexed: 02/25/2024] Open
Abstract
Aging is a multifactorial process characterized by an age-related decline in organismal fitness. This deterioration is the major risk factor for chronic diseases such as cardiovascular pathologies, neurodegeneration, or cancer, and it represents one of the main challenges of modern society. Therefore, understanding why and how we age would be a fundamental pillar to design strategies to promote a healthy aging. In the last decades, the study of the molecular bases of disease has been revolutionized by the discovery of different types of noncoding RNAs (ncRNAs) with regulatory potential. In this work, we will review the implication of ncRNAs in aging, with the aim to provide a first approach to the different aging-associated ncRNAs, their mechanism of action, and their potential relevance as therapeutic targets and disease biomarkers.
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Affiliation(s)
- Alejandro P Ugalde
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - David Roiz-Valle
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Lucas Moledo-Nodar
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - Xurde M Caravia
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - José M P Freije
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Facultad de Ciencias de la Vida y la Naturaleza, Universidad Nebrija, Madrid, Spain
- Centre de Recherche des Cordeliers, Université de Paris Cité, Sorbonne Université, INSERM, Paris, France
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5
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Liang D, Li G. Pulling the trigger: Noncoding RNAs in white adipose tissue browning. Rev Endocr Metab Disord 2024; 25:399-420. [PMID: 38157150 DOI: 10.1007/s11154-023-09866-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/03/2024]
Abstract
White adipose tissue (WAT) serves as the primary site for energy storage and endocrine regulation in mammals, while brown adipose tissue (BAT) is specialized for thermogenesis and energy expenditure. The conversion of white adipocytes to brown-like fat cells, known as browning, has emerged as a promising therapeutic strategy for reversing obesity and its associated co-morbidities. Noncoding RNAs (ncRNAs) are a class of transcripts that do not encode proteins but exert regulatory functions on gene expression at various levels. Recent studies have shed light on the involvement of ncRNAs in adipose tissue development, differentiation, and function. In this review, we aim to summarize the current understanding of ncRNAs in adipose biology, with a focus on their role and intricate mechanisms in WAT browning. Also, we discuss the potential applications and challenges of ncRNA-based therapies for overweight and its metabolic disorders, so as to combat the obesity epidemic in the future.
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Affiliation(s)
- Dehuan Liang
- The Key Laboratory of Geriatrics, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People's Republic of China
- Fifth School of Clinical Medicine (Beijing Hospital), Peking University, Beijing, 100730, People's Republic of China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Institute of Geriatric Medicine, Beijing Institute of Geriatrics, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730, People's Republic of China.
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6
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Khalafizadeh A, Hashemizadegan SD, Shokri F, Bakhshinejad B, Jabbari K, Motavaf M, Babashah S. Competitive endogenous RNA networks: Decoding the role of long non-coding RNAs and circular RNAs in colorectal cancer chemoresistance. J Cell Mol Med 2024; 28:e18197. [PMID: 38506091 PMCID: PMC10951891 DOI: 10.1111/jcmm.18197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 02/04/2024] [Indexed: 03/21/2024] Open
Abstract
Colorectal cancer (CRC) is recognized as one of the most common gastrointestinal malignancies across the globe. Despite significant progress in designing novel treatments for CRC, there is a pressing need for more effective therapeutic approaches. Unfortunately, many patients undergoing chemotherapy develop drug resistance, posing a significant challenge for cancer treatment. Non-coding RNAs (ncRNAs) have been found to play crucial roles in CRC development and its response to chemotherapy. However, there are still gaps in our understanding of interactions among various ncRNAs, such as long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs). These ncRNAs can act as either oncogenes or tumour suppressors, affecting numerous biological functions in different cancers including CRC. A class of ncRNA molecules known as competitive endogenous RNAs (ceRNAs) has emerged as a key player in various cellular processes. These molecules form networks through lncRNA/miRNA/mRNA and circRNA/miRNA/mRNA interactions. In CRC, dysregulation of ceRNA networks has been observed across various cellular processes, including proliferation, apoptosis and angiogenesis. These dysregulations are believed to play a significant role in the progression of CRC and, in certain instances, may contribute to the development of chemoresistance. Enriching our knowledge of these dysregulations holds promise for advancing the field of diagnostic and therapeutic modalities for CRC. In this review, we discuss lncRNA- and circRNA-associated ceRNA networks implicated in the emergence and advancement of drug resistance in colorectal carcinogenesis.
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Affiliation(s)
- Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | | | - Fatemeh Shokri
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Keyvan Jabbari
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Mahsa Motavaf
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
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7
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Zhong B, Dai Y, Chen L, Xu X, Lan Y, Deng L, Ren L, Luo N, Ning L. ncRS: A resource of non-coding RNAs in sepsis. Comput Biol Med 2024; 172:108256. [PMID: 38489989 DOI: 10.1016/j.compbiomed.2024.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/10/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Sepsis, a life-threatening condition triggered by the body's response to infection, presents a significant global healthcare challenge characterized by disarrayed host responses, widespread inflammation, organ impairment, and heightened mortality rates. This study introduces the ncRS database (http://www.ncrdb.cn), a meticulously curated repository housing 1144 experimentally validated non-coding RNAs (ncRNAs) intricately linked with sepsis. ncRS offers comprehensive RNA data, exhaustive experimental insights, and integrated annotations from diverse databases. This resource empowers researchers and clinicians to decipher ncRNAs' roles in sepsis pathogenesis, potentially identifying vital biomarkers for early diagnosis and prognosis, thus facilitating personalized treatments.
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Affiliation(s)
- Baocai Zhong
- School of Computer and Software, Chengdu Neusoft University, Chengdu, China
| | - Yongfang Dai
- School of Computer and Software, Chengdu Neusoft University, Chengdu, China
| | - Li Chen
- School of Computer and Software, Chengdu Neusoft University, Chengdu, China.
| | - Xinying Xu
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Yuxi Lan
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Leyao Deng
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Liping Ren
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China
| | - Nanchao Luo
- School of Computer Science and Technology, A Ba Teachers University, Wenchuan, China.
| | - Lin Ning
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, China; Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China.
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8
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Huang Q, Zhong X, Li J, Hu R, Yi J, Sun J, Xu Y, Zhou X. Exosomal ncRNAs: Multifunctional contributors to the immunosuppressive tumor microenvironment of hepatocellular carcinoma. Biomed Pharmacother 2024; 173:116409. [PMID: 38460375 DOI: 10.1016/j.biopha.2024.116409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/23/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignant liver cancer characterized by aggressive progression, unfavorable prognosis, and an increasing global health burden. Therapies that precisely target immunological checkpoints and immune cells have gained significant attention as possible therapeutics in recent years. In truth, the efficacy of immunotherapy is heavily contingent upon the tumor microenvironment (TME). Recent studies have indicated that exosomes serve as a sophisticated means of communication among biomolecules, executing an essential part in the TME of immune suppression. Exosomal non-coding RNAs (ncRNAs) can induce the activation of tumor cells and immunosuppressive immune cells that suppress the immune system, such as cancer-associated fibroblasts (CAFs), tumor-associated macrophages (TAMs), tumor-associated neutrophils (TANs), CD+8 T cells, regulatory T cells (Tregs), and regulatory B cells (Bregs). This cell-cell crosstalk triggered by exosomal ncRNAs promotes tumor proliferation and metastasis, angiogenesis, malignant phenotype transformation, and drug resistance. Hence, it is imperative to comprehend how exosomal ncRNAs regulate tumor cells or immune cells within the TME to devise more comprehensive and productive immunotherapy programs. This study discusses the features of exosomal ncRNAs in HCC and how the activation of the exosomes redefines the tumor's immunosuppressive microenvironment, hence facilitating the advancement of HCC. Furthermore, we also explored the potential of exosomal ncRNAs as a viable biological target or natural vehicle for HCC therapy.
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Affiliation(s)
- Qi Huang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Xin Zhong
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jing Li
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Rui Hu
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jinyu Yi
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China; Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Jialing Sun
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China
| | - Youhua Xu
- Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao PR China.
| | - Xiaozhou Zhou
- Department of Liver Disease, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, PR China; Department of Liver Disease, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, PR China.
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9
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Shi D, Huang H, Zhang Y, Qian Z, Du J, Huang L, Yan X, Lin S. The roles of non-coding RNAs in male reproductive development and abiotic stress responses during this unique process in flowering plants. Plant Sci 2024; 341:111995. [PMID: 38266717 DOI: 10.1016/j.plantsci.2024.111995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Successful male reproductive development is the guarantee for sexual reproduction of flowering plants. Male reproductive development is a complicated and multi-stage process that integrates physiological processes and adaptation and tolerance to a myriad of environmental stresses. This well-coordinated process is governed by genetic and epigenetic machineries. Non-coding RNAs (ncRNAs) play pleiotropic roles in the plant growth and development. The identification, characterization and functional analysis of ncRNAs and their target genes have opened a new avenue for comprehensively revealing the regulatory network of male reproductive development and its response to environmental stresses in plants. This review briefly addresses the types, origin, biogenesis and mechanisms of ncRNAs in plants, highlights important updates on the roles of ncRNAs in regulating male reproductive development and emphasizes the contribution of ncRNAs, especially miRNAs and lncRNAs, in responses to abiotic stresses during this unique process in flowering plants.
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Affiliation(s)
- Dexi Shi
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Huiting Huang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Yuting Zhang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Zhihao Qian
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Jiao Du
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Xiufeng Yan
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Sue Lin
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
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10
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Karthik S, Mohan S, Magesh I, Bharathy A, Kolipaka R, Ganesamoorthi S, Sathiya K, Shanmugavadivu A, Gurunathan R, Selvamurugan N. Chitosan nanocarriers for non-coding RNA therapeutics: A review. Int J Biol Macromol 2024; 263:130361. [PMID: 38395284 DOI: 10.1016/j.ijbiomac.2024.130361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/02/2024] [Accepted: 02/19/2024] [Indexed: 02/25/2024]
Abstract
Non-coding RNA (ncRNA)-based therapies entail delivering ncRNAs to cells to regulate gene expression and produce proteins that combat infections, cancer, neurological diseases, and bone abnormalities. Nevertheless, the therapeutic potential of these ncRNAs has been limited due to the difficulties in delivering them to specific cellular targets within the body. Chitosan (CS), a biocompatible cationic polymer, interacts with negatively charged RNA molecules to form stable complexes. It is a promising biomaterial to develop nanocarriers for ncRNA delivery, overcoming several disadvantages of traditional delivery systems. CS-based nanocarriers can protect ncRNAs from degradation and target-specific delivery by surface modifications and intracellular release profiles over an extended period. This review briefly summarizes the recent developments in CS nanocarriers' synthesis and design considerations and their applications in ncRNA therapeutics for treating various diseases. We also discuss the challenges and limitations of CS-based nanocarriers for ncRNA therapeutics and potential strategies for overcoming these challenges.
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Affiliation(s)
- S Karthik
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Sahithya Mohan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Induja Magesh
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Ashok Bharathy
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Rushil Kolipaka
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Srinidhi Ganesamoorthi
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - K Sathiya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Abinaya Shanmugavadivu
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - Raghav Gurunathan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603203, Tamil Nadu, India.
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11
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Sha G, Zhang W, Jiang Z, Zhao Q, Wang D, Tang D. Exosomal non-coding RNA: A new frontier in diagnosing and treating pancreatic cancer: A review. Int J Biol Macromol 2024; 263:130149. [PMID: 38365161 DOI: 10.1016/j.ijbiomac.2024.130149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/27/2024] [Accepted: 02/11/2024] [Indexed: 02/18/2024]
Abstract
Pancreatic cancer is the most fatal malignancy worldwide. Once diagnosed, most patients are already at an advanced stage because of their highly heterogeneous, drug-resistant, and metastatic nature and the lack of effective diagnostic markers. Recently, the study of proliferation, metastasis, and drug resistance mechanisms in pancreatic cancer and the search for useful diagnostic markers have posed significant challenges to the scientific community. Exosomes carry various biomolecules (DNA, non-coding RNAs (ncRNAs), proteins, and lipids) that mediate communication between tumors and other cells. ncRNAs can be transported through exosomes to numerous relevant receptor cells and regulate local epithelial-mesenchymal transition (EMT) in tumor tissue, proliferation, drug resistance, and the establishment of pre-metastatic ecological niches in distant organs. In summary, exosomal ncRNAs promote tumor cell proliferation, invasion, and metastasis through multiple EMT, immunosuppression, angiogenesis, and extracellular matrix remodeling pathways. Moreover, we discuss the significant therapeutic significance of exosomal ncRNAs as PC biomarkers.
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Affiliation(s)
- Gengyu Sha
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province 225000, China.
| | - Wenjie Zhang
- School of Medicine, Chongqing University, Chongqing 400030, China.
| | - Zhengting Jiang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province 225000, China.
| | - Qianqian Zhao
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province 225000, China.
| | - Daorong Wang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province 225000, China; Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225000, China.
| | - Dong Tang
- Clinical Medical College, Yangzhou University, Yangzhou, Jiangsu Province 225000, China; Department of General Surgery, Institute of General Surgery, Clinical Medical College, Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou 225000, China.
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12
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Zhu X, Liu K, Tang X, Chen G. A bibliometric analysis of non-coding RNA studies in acute pancreatitis. Medicine (Baltimore) 2024; 103:e37486. [PMID: 38518041 PMCID: PMC10956959 DOI: 10.1097/md.0000000000037486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/13/2024] [Indexed: 03/24/2024] Open
Abstract
BACKGROUND Non-coding RNA (ncRNA) is a type of RNA that does not code for proteins and plays a crucial role in the onset, progression, diagnosis, and therapy of acute pancreatitis. However, bibliometric, and visual analyses of studies on acute pancreatitis and ncRNA are lacking. This study seeks to provide a bibliometric overview of the knowledge structure and research hotspots of ncRNA in the field of acute pancreatitis research. MATERIALS AND METHODS Literature search and collection of information in the field of ncRNA-related research in acute pancreatitis from 2000-2023 through the Web of Science Core Collection. Use CiteSpace and VOSviewer to visually analyze countries, institutions, authors, and keywords. RESULTS A total of 563 articles have been published in the field of ncRNA-related research in acute pancreatitis, and the number of publications in this field is gradually increasing. The largest number of publications was from China. Four clusters were produced by the co-occurrence cluster analysis of the top 89 keywords: studies of ncRNA in inflammation, autophagy, and apoptosis in acute pancreatitis; studies related to microRNA expression in pancreatic cancer among ncRNA; studies related to microRNAs as diagnostic and therapeutic markers in acute pancreatitis; and studies related to ncRNA in acute pancreatitis; The key words "injury," "pathway" and "extracellular vesicles" are the key words of emerging research hotspots. CONCLUSION In conclusion, ncRNA research in acute pancreatitis is an established discipline. Researchers can use the research hotspots and frontiers in this field as a guide for choosing their research direction.
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Affiliation(s)
- Xiaodong Zhu
- Guangxi University of Chinese Medicine, Nanning, China
| | - Kunrong Liu
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
| | - Xiping Tang
- Guangxi Medical University Affiliated Cancer Hospital, Nanning, China
| | - Guozhong Chen
- The First Affiliated Hospital of Guangxi University of Chinese Medicine, Nanning, China
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13
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Li Z, Ma Z, Wang S, Yan Q, Zhuang H, Zhou Z, Liu C, Chen Y, Han M, Wu Z, Huang S, Zhou Q, Hou B, Zhang C. LINC00909 up-regulates pluripotency factors and promotes cancer stemness and metastasis in pancreatic ductal adenocarcinoma by targeting SMAD4. Biol Direct 2024; 19:24. [PMID: 38504385 PMCID: PMC10949730 DOI: 10.1186/s13062-024-00463-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Pancreatic cancer stem cells are crucial for tumorigenesis and cancer metastasis. Presently, long non-coding RNAs were found to be associated with Pancreatic Ductal Adenocarcinoma stemness characteristics but the underlying mechanism is largely known. Here, we aim to explore the function of LINC00909 in regulating pancreatic cancer stemness and cancer metastasis. METHODS The expression level and clinical characteristics of LINC00909 were verified in 80-paired normal pancreas and Pancreatic Ductal Adenocarcinoma tissues from Guangdong Provincial People's Hospital cohort by in situ hybridization. RNA sequencing of PANC-1 cells with empty vector or vector encoding LINC00909 was experimented for subsequent bioinformatics analysis. The effect of LINC00909 in cancer stemness and metastasis was examined by in vitro and in vivo experiments. The interaction between LINC00909 with SMAD4 and the pluripotency factors were studied. RESULTS LINC00909 was generally upregulated in pancreatic cancer tissues and was associated with inferior clinicopathologic features and outcome. Over-expression of LINC00909 enhanced the expression of pluripotency factors and cancer stem cells phenotype, while knock-down of LINC00909 decreased the expression of pluripotency factors and cancer stem cells phenotype. Moreover, LINC00909 inversely regulated SMAD4 expression, knock-down of SMAD4 rescued the effect of LINC00909-deletion inhibition on pluripotency factors and cancer stem cells phenotype. These indicated the effect of LINC00909 on pluripotency factors and CSC phenotype was dependent on SMAD4 and MAPK/JNK signaling pathway, another downstream pathway of SMAD4 was also activated by LINC00909. Specifically, LINC00909 was localized in the cytoplasm in pancreatic cancer cells and decreased the stability the SMAD4 mRNA. Finally, we found over-expression of LINC00909 not only accelerated tumor growth in subcutaneous mice models, but also facilitated tumorigenicity and spleen metastasis in orthotopic mice models. CONCLUSION We demonstrate LINC00909 inhibits SMAD4 expression at the post-transcriptional level, which up-regulates the expression of pluripotency factors and activates the MAPK/JNK signaling pathway, leading to enrichment of cancer stem cells and cancer metastasis in pancreatic cancer.
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Affiliation(s)
- Zhenchong Li
- Department of General Surgery, Heyuan people's Hospital, Heyuan, 517000, China
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- Junior Clinical Cooperation Unit Translational Gastrointestinal Oncology and Preclinical Models, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Zuyi Ma
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 100730, China
| | - Shujie Wang
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Qian Yan
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Hongkai Zhuang
- Department of Hepatobiliary Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Zixuan Zhou
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Chunsheng Liu
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Yubin Chen
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Mingqian Han
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Zelong Wu
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
| | - Shanzhou Huang
- Department of General Surgery, Heyuan people's Hospital, Heyuan, 517000, China
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China
| | - Qi Zhou
- Department of General Surgery, Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-sen University, Huizhou, Guangdong, 516081, China.
- Department of Liver Surgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510080, China.
| | - Baohua Hou
- Department of General Surgery, Heyuan people's Hospital, Heyuan, 517000, China.
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China.
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China.
| | - Chuanzhao Zhang
- Department of General Surgery, Heyuan people's Hospital, Heyuan, 517000, China.
- Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong Province, 510515, China.
- South China University of Technology School of Medicine, Guangzhou, Guangdong Province, 510006, China.
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14
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Liu S, Huang J, Zhou J, Chen S, Zheng W, Liu C, Lin Q, Zhang P, Wu D, He S, Ye J, Liu S, Zhou K, Li B, Qu L, Yang J. NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions. Nat Commun 2024; 15:2425. [PMID: 38499544 PMCID: PMC10948791 DOI: 10.1038/s41467-024-46596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
Up to 80% of the human genome produces "dark matter" RNAs, most of which are noncapped RNAs (napRNAs) that frequently act as noncoding RNAs (ncRNAs) to modulate gene expression. Here, by developing a method, NAP-seq, to globally profile the full-length sequences of napRNAs with various terminal modifications at single-nucleotide resolution, we reveal diverse classes of structured ncRNAs. We discover stably expressed linear intron RNAs (sliRNAs), a class of snoRNA-intron RNAs (snotrons), a class of RNAs embedded in miRNA spacers (misRNAs) and thousands of previously uncharacterized structured napRNAs in humans and mice. These napRNAs undergo dynamic changes in response to various stimuli and differentiation stages. Importantly, we show that a structured napRNA regulates myoblast differentiation and a napRNA DINAP interacts with dyskerin pseudouridine synthase 1 (DKC1) to promote cell proliferation by maintaining DKC1 protein stability. Our approach establishes a paradigm for discovering various classes of ncRNAs with regulatory functions.
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Affiliation(s)
- Shurong Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Junhong Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Siyan Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Wujian Zheng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Qiao Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Ping Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Di Wu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Simeng He
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China
| | - Jiayi Ye
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, 91016, USA
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, Guangdong, China.
- The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519082, Guangdong, China.
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15
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Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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16
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You JR, Wen ZJ, Tian JW, Lv XB, Li R, Li SP, Xin H, Li PF, Zhang YF, Zhang R. Crosstalk between ubiquitin ligases and ncRNAs drives cardiovascular disease progression. Front Immunol 2024; 15:1335519. [PMID: 38515760 PMCID: PMC10954775 DOI: 10.3389/fimmu.2024.1335519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
Cardiovascular diseases (CVDs) are multifactorial chronic diseases and have the highest rates of morbidity and mortality worldwide. The ubiquitin-proteasome system (UPS) plays a crucial role in posttranslational modification and quality control of proteins, maintaining intracellular homeostasis via degradation of misfolded, short-lived, or nonfunctional regulatory proteins. Noncoding RNAs (ncRNAs, such as microRNAs, long noncoding RNAs, circular RNAs and small interfering RNAs) serve as epigenetic factors and directly or indirectly participate in various physiological and pathological processes. NcRNAs that regulate ubiquitination or are regulated by the UPS are involved in the execution of target protein stability. The cross-linked relationship between the UPS, ncRNAs and CVDs has drawn researchers' attention. Herein, we provide an update on recent developments and perspectives on how the crosstalk of the UPS and ncRNAs affects the pathological mechanisms of CVDs, particularly myocardial ischemia/reperfusion injury, myocardial infarction, cardiomyopathy, heart failure, atherosclerosis, hypertension, and ischemic stroke. In addition, we further envision that RNA interference or ncRNA mimics or inhibitors targeting the UPS can potentially be used as therapeutic tools and strategies.
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Affiliation(s)
- Jia-Rui You
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Zeng-Jin Wen
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Jia-Wei Tian
- Department of Emergency Internal Medicine, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xiao-Bing Lv
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Rong Li
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Shu-Ping Li
- Department of Cardiology, The Affiliated Qingdao Third People's Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Hui Xin
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin-Feng Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Rui Zhang
- Department of Cardiology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, Shandong, China
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17
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Sadeghian I, Akbarpour M, Chafjiri FMA, Chafjiri PMA, Heidari R, Morowvat MH, Sadeghian R, Raee MJ, Negahdaripour M. Potential of oligonucleotide- and protein/peptide-based therapeutics in the management of toxicant/stressor-induced diseases. Naunyn Schmiedebergs Arch Pharmacol 2024; 397:1275-1310. [PMID: 37688622 DOI: 10.1007/s00210-023-02683-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
Exposure to toxicants/stressors has been linked to the development of many human diseases. They could affect various cellular components, such as DNA, proteins, lipids, and non-coding RNAs (ncRNA), thereby triggering various cellular pathways, particularly oxidative stress, inflammatory responses, and apoptosis, which can contribute to pathophysiological states. Accordingly, modulation of these pathways has been the focus of numerous investigations for managing related diseases. The involvement of various ncRNAs, such as small interfering RNA (siRNA), microRNAs (miRNA), and long non-coding RNAs (lncRNA), as well as various proteins and peptides in mediating these pathways, provides many target sites for pharmaceutical intervention. In this regard, various oligonucleotide- and protein/peptide-based therapies have been developed to treat toxicity-induced diseases, which have shown promising results in vitro and in vivo. This comprehensive review provides information about various aspects of toxicity-related diseases including their causing factors, main underlying mechanisms and intermediates, and their roles in pathophysiological states. Particularly, it highlights the principles and mechanisms of oligonucleotide- and protein/peptide-based therapies in the treatment of toxicity-related diseases. Furthermore, various issues of oligonucleotides and proteins/peptides for clinical usage and potential solutions are discussed.
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Affiliation(s)
- Issa Sadeghian
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Biotechnology Incubator, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mina Akbarpour
- Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | | | - Reza Heidari
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Hossein Morowvat
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Mohammad Javad Raee
- Center for Nanotechnology in Drug Delivery, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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18
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Alharbi KS. Noncoding RNAs in hepatitis: Unraveling the apoptotic pathways. Pathol Res Pract 2024; 255:155170. [PMID: 38324964 DOI: 10.1016/j.prp.2024.155170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/09/2024]
Abstract
Hepatitis is a worldwide health issue that causes inflammation of the liver and is frequently brought on by viral infections, specifically those caused by the hepatitis B and C viruses. Although the pathophysiological causes of hepatitis are complex, recent research indicates that noncoding RNAs (ncRNAs) play a crucial role in regulating apoptosis, an essential process for maintaining liver homeostasis and advancing the illness. Noncoding RNAs have been linked to several biological processes, including apoptosis. These RNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). Distinct expression patterns characterising different stages of the disease have been discovered, indicating dysregulation of these non-coding RNAs in liver tissues infected with hepatitis. The complex interplay that exists between these noncoding RNAs and apoptotic effectors, including caspases and members of the Bcl-2 family, plays a role in the precarious equilibrium that regulates cell survival and death during hepatitis. The purpose of this review is to provide an overview of ncRNA-mediated apoptosis in hepatitis, as well as insights into possible therapeutic targets and diagnostic indicators.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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19
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Li J, Fang J, Jiang X, Zhang Y, Vidal-Puig A, Zhang CY. RNAkines are secreted messengers shaping health and disease. Trends Endocrinol Metab 2024; 35:201-218. [PMID: 38160178 DOI: 10.1016/j.tem.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/03/2024]
Abstract
Extracellular noncoding RNAs (ncRNAs) have crucial roles in intercellular communications. The process of ncRNA secretion is highly regulated, with specific ncRNA profiles produced under different physiological and pathological circumstances. These ncRNAs are transported primarily via extracellular vesicles (EVs) from their origin cells to target cells, utilising both endocrine and paracrine pathways. The intercellular impacts of extracellular ncRNAs are essential for maintaining homeostasis and the pathogenesis of various diseases. Given the unique aspects of extracellular ncRNAs, here we propose the term 'RNAkine' to describe these recently identified secreted factors. We explore their roles as intercellular modulators, particularly in their ability to regulate metabolism and influence tumorigenesis, highlighting their definition and importance as a distinct class of secreted factors.
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Affiliation(s)
- Jing Li
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China.
| | - Jingwen Fang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Xiaohong Jiang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Yujing Zhang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China
| | - Antonio Vidal-Puig
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, University of Cambridge Metabolic Research Laboratories, Cambridge, UK; Cambridge University Nanjing Centre of Technology and Innovation, Nanjing, China.
| | - Chen-Yu Zhang
- Nanjing Drum Tower Hospital Centre of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Centre for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), Institute of Artificial Intelligence Biomedicine, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, PR China; Research Unit of Extracellular RNA, Chinese Academy of Medical Sciences, Nanjing, Jiangsu 210023, PR China; Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100144, PR China.
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20
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Zhan Y, Yang Z, Zeng H, Yu J, Chen X, Wu Y. Extracellular vesicle-derived non-coding RNAs in remodeling melanoma. Biomed Pharmacother 2024; 172:116213. [PMID: 38306847 DOI: 10.1016/j.biopha.2024.116213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024] Open
Abstract
Melanoma is one of the most lethal cutaneous malignancies. Despite great advances in radiotherapy, chemotherapy, and immunotherapy, the survival rate and prognosis of patients with melanoma remain poor. The abundant and sophisticated reciprocal communication network between melanoma cells and non-tumor cells contributes to the high heterogeneity of the melanoma microenvironment and is intimately related to varying treatment responses and clinical courses. Extracellular vesicles (EVs) are membrane structures generated by nearly all cell types. EVs contain biologically active molecules, mainly comprising proteins, lipids, and RNAs, and undoubtedly play multifaceted roles in numerous diseases, represented by melanoma. Non-coding RNAs (ncRNAs) mainly encompass long non-coding RNAs, microRNAs, and circular RNAs and constitute the majority of the human transcriptome. Multiple ncRNAs encapsulated in EVs coordinate various pathophysiological processes in melanoma. This review summarizes the mechanisms by which EV-ncRNAs modulate biological behaviors and immunity, and their potential diagnostic and therapeutic applications in melanoma. Undoubtedly, further insight into EV-ncRNAs and their functions in melanoma will contribute to the clinical treatment of melanoma and the implementation of precision medicine.
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Affiliation(s)
- Yuanyuan Zhan
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zihui Yang
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hong Zeng
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xue Chen
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yiping Wu
- Department of Plastic and Cosmetic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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21
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Tosar JP, Castellano M, Costa B, Cayota A. Small RNA structural biochemistry in a post-sequencing era. Nat Protoc 2024; 19:595-602. [PMID: 38057624 DOI: 10.1038/s41596-023-00936-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/25/2023] [Indexed: 12/08/2023]
Abstract
High-throughput sequencing has had an enormous impact on small RNA research during the past decade. However, sequencing only offers a one-dimensional view of the transcriptome and is often highly biased. Additionally, the 'sequence, map and annotate' approach, used widely in small RNA research, can lead to flawed interpretations of the data, lacking biological plausibility, due in part to database issues. Even in the absence of technical biases, the loss of three-dimensional information is a major limitation to understanding RNA stability, turnover and function. For example, noncoding RNA-derived fragments seem to exist mainly as dimers, tetramers or as nicked forms of their parental RNAs, contrary to widespread assumptions. In this perspective, we will discuss main sources of bias during small RNA-sequencing, present several useful bias-reducing strategies and provide guidance on the interpretation of small RNA-sequencing results, with emphasis on RNA fragmentomics. As sequencing offers a one-dimensional projection of a four-dimensional reality, prior structure-level knowledge is often needed to make sense of the data. Consequently, while less-biased sequencing methods are welcomed, integration of orthologous experimental techniques is also strongly recommended.
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Affiliation(s)
- Juan Pablo Tosar
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay.
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay.
| | - Mauricio Castellano
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Biochemistry Department, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Bruno Costa
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Analytical Biochemistry Unit, Center for Nuclear Research, School of Science, Universidad de la República, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Hospital de Clínicas, Universidad de la República, Montevideo, Uruguay
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22
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Khojali WMA, Khalifa NE, Alshammari F, Afsar S, Aboshouk NAM, Khalifa AAS, Enrera JA, Elafandy NM, Abdalla RAH, Ali OHH, Syed RU, Nagaraju P. Pyroptosis-related non-coding RNAs emerging players in atherosclerosis pathology. Pathol Res Pract 2024; 255:155219. [PMID: 38401375 DOI: 10.1016/j.prp.2024.155219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Globally, atherosclerosis a persistent inflammatory condition of the artery walls continues to be the primary cause of cardiovascular illness and death. The ncRNAs are important regulators of important signalling pathways that affect pyroptosis and the inflammatory environment in atherosclerotic plaques. Comprehending the complex interaction between pyroptosis and non-coding RNAs (ncRNAs) offers fresh perspectives on putative therapeutic targets for ameliorating cardiovascular problems linked to atherosclerosis. The discovery of particular non-coding RNA signatures linked to the advancement of atherosclerosis could lead to the creation of novel biomarkers for risk assessment and customised treatment approaches. A thorough investigation of the regulatory networks regulated by these non-coding RNAs has been made possible by the combination of cutting-edge molecular methods and bioinformatics tools. Studying pyroptosis-related ncRNAs in detail appears to be a promising way to advance our understanding of disease pathophysiology and develop focused therapeutic methods as we work to unravel the complex molecular tapestry of atherosclerosis. This review explores the emerging significance of non-coding RNAs (ncRNAs) in the regulation of pyroptosis and their consequential impact on atherosclerosis pathology.
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Affiliation(s)
- Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman 14415, Republic of the Sudan
| | - Nasrin E Khalifa
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia; Department of Pharmaceutics, Faculty of Pharmacy, University of Khartoum, Khartoum 11115, Republic of the Sudan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
| | - S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh 517502, India.
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Amna Abakar Suleiman Khalifa
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Jerlyn Apatan Enrera
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Nancy Mohammad Elafandy
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Randa Abdeen Husien Abdalla
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Omar Hafiz Haj Ali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, Hail 81442, Saudi Arabia
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia.
| | - Potnuri Nagaraju
- Department of Pharmaceutics, Mandesh Institute of Pharmaceutical Science and Research Center, Maharashtra, India
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23
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Kang J, Rhee J, Wang C, Yang Y, Li G, Li H. Unlocking the dark matter: noncoding RNAs and RNA modifications in cardiac aging. Am J Physiol Heart Circ Physiol 2024; 326:H832-H844. [PMID: 38305752 DOI: 10.1152/ajpheart.00532.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
Cardiac aging is a multifaceted process that encompasses structural and functional alterations culminating in heart failure. As the elderly population continues to expand, there is a growing urgent need for interventions to combat age-related cardiac functional decline. Noncoding RNAs have emerged as critical regulators of cellular and biochemical processes underlying cardiac disease. This review summarizes our current understanding of how noncoding RNAs function in the heart during aging, with particular emphasis on mechanisms of RNA modification that control their activity. Targeting noncoding RNAs as potential novel therapeutics in cardiac aging is also discussed.
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Affiliation(s)
- Jiayi Kang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - James Rhee
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
| | - Chunyan Wang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Yolander Yang
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Guoping Li
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
- Cardiovascular Research Center, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
| | - Haobo Li
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Anaesthesia, Harvard Medical School, Boston, Massachusetts, United States
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24
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Abu-Alghayth MH, Khan FR, Belali TM, Abalkhail A, Alshaghdali K, Nassar SA, Almoammar NE, Almasoudi HH, Hessien KBG, Aldossari MS, Binshaya AS. The emerging role of noncoding RNAs in the PI3K/AKT/mTOR signalling pathway in breast cancer. Pathol Res Pract 2024; 255:155180. [PMID: 38330621 DOI: 10.1016/j.prp.2024.155180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/10/2024]
Abstract
Breast cancer persists as a major problem for the world's healthcare, thus it is essential to fully understand the complex molecular processes that cause its growth and development. ncRNAs had been discovered to serve critical roles in a variety of cellular functions, including the regulation of signalling pathways. Within different pathways, the AKT/PI3K/mTOR signalling cascade has received a lot of interest because of its role in cancer. A complex interaction between ncRNAs, notably miRNAs, lncRNAs, and circRNAs, and the AKT/PI3K/mTOR signalling pathway exerts both oncogenic and tumor-suppressive activities by targeting critical components of the pathway directly or indirectly. Through miRNA-mediated post-transcriptional regulation, lncRNA-guided chromatin remodelling, and circRNA sequestration, ncRNAs modulate the activity of PI3K, AKT, and mTOR, influencing cell proliferation, survival, and metastasis. Furthermore, ncRNAs can serve as promising biomarkers for breast cancer prognosis, diagnosis, and treatment response, as their dysregulation is commonly observed in breast cancer patients. Harnessing the potential of ncRNAs as therapeutic targets or tools for restoring pathway homeostasis holds promise for innovative treatment strategies in breast cancer. Understanding the intricate regulatory networks orchestrated by ncRNAs in this context may pave the way for novel diagnostic approaches, therapeutic interventions, and a deeper comprehension of breast cancer's molecular landscape, ultimately improving patient outcomes. This abstract underscores the emerging significance of ncRNAs in the AKT/PI3K/mTOR signaling pathway in breast cancer.
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Affiliation(s)
- Mohammed H Abu-Alghayth
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Farhan R Khan
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | - Tareg M Belali
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha, P.O. Box 255, 67714, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Khalid Alshaghdali
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, P.O Box 2440, Saudi Arabia
| | - Somia A Nassar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia; Department of Parasitology & Animal Diseases, National Research Centre, 33 Bohouth St., Dokki, Giza 12622, Egypt
| | - Nasser Eissa Almoammar
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Hassan H Almasoudi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia
| | - Khater Balatone G Hessien
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Al- Quwayiyah, Shaqra University, Riyadh, Saudi Arabia
| | | | - Abdulkarim S Binshaya
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia.
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25
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Zhang Y, Xie J. Unveiling the role of ferroptosis-associated exosomal non-coding RNAs in cancer pathogenesis. Biomed Pharmacother 2024; 172:116235. [PMID: 38308967 DOI: 10.1016/j.biopha.2024.116235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
The pivotal regulatory role of non-coding RNAs (ncRNAs), especially exosomal ncRNAs, in ferroptosis significantly influences cancer cell fate. This review explores their involvement across various human cancers, focusing on microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA). These ncRNAs either stimulate or inhibit ferroptosis by targeting key components, impacting cancer susceptibility to this form of cell death. Specific studies in lung, gastric, liver, cervical, bladder, pancreatic, and osteosarcoma cancers underscore the crucial role of exosomal ncRNAs in modulating ferroptosis, influencing cancer progression, and therapeutic responses. Emphasizing the therapeutic potential of exosomal ncRNAs, we discuss their ability to deliver circRNA, miRNA, and lncRNA to target cells. Despite being in early stages with challenges in bioengineering for drug delivery, these studies hold promise for future clinical applications. Noteworthy findings include inhibiting exosome production to overcome ferroptosis resistance in lung adenocarcinoma and the potential of exosomal DACT3-AS1 to sensitize gastric cancer cells to ferroptosis. The review concludes by highlighting exosomal ncRNAs like miR-4443 and miR-660-5p as promising therapeutic targets, offering avenues for precise cancer interventions by modulating signaling pathways and sensitizing cells to ferroptosis. Overall, this review enhances our understanding of cancer pathogenesis and presents new horizons for targeted therapeutic interventions, revealing the intricate interplay between exosomal ncRNAs and ferroptosis.
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Affiliation(s)
- Yiping Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China; Wanchuanhui (Shanghai) Medical Technology Co., Ltd, Shanghai 201501, China.
| | - Jun Xie
- School of Life Sciences, Fudan University, Shanghai 200438, China; Wanchuanhui (Shanghai) Medical Technology Co., Ltd, Shanghai 201501, China.
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26
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Saadh MJ, Allela OQB, Sattay ZJ, Al Zuhairi RAH, Ahmad H, Eldesoky GE, Adil M, Ali MS. Deciphering the functional landscape and therapeutic implications of noncoding RNAs in the TGF-β signaling pathway in colorectal cancer: A comprehensive review. Pathol Res Pract 2024; 255:155158. [PMID: 38320438 DOI: 10.1016/j.prp.2024.155158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
Abstract
Colorectal cancer (CRC) remains a major global health concern, necessitating an in-depth exploration of the intricate molecular mechanisms underlying its progression and potential therapeutic interventions. Transforming Growth Factor-β (TGF-β) signaling, a pivotal pathway implicated in CRC plays a dual role as a tumor suppressor in the early stages and a promoter of tumor progression in later stages. Recent research has shed light on the critical involvement of noncoding RNAs (ncRNAs) in modulating the TGF-β signaling pathway, introducing a new layer of complexity to our understanding of CRC pathogenesis. This comprehensive review synthesizes the current state of knowledge regarding the function and therapeutic potential of various classes of ncRNAs, including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), in the context of TGF-β signaling in CRC. The intricate interplay between these ncRNAs and key components of the TGF-β pathway is dissected, revealing regulatory networks that contribute to the dynamic balance between tumor suppression and promotion. Emphasis is placed on how dysregulation of specific ncRNAs can disrupt this delicate equilibrium, fostering CRC initiation, progression, and metastasis. Moreover, the review provides a critical appraisal of the emerging therapeutic strategies targeting ncRNAs associated with TGF-β signaling in CRC. The potential of these ncRNAs as diagnostic and prognostic biomarkers is discussed, highlighting their clinical relevance. Additionally, the challenges and prospects of developing RNA-based therapeutics, such as RNA interference and CRISPR/Cas-based approaches, are explored in the context of modulating TGF-β signaling for CRC treatment. In conclusion, this review offers a comprehensive overview of the intricate interplay between ncRNAs and the TGF-β signaling pathway in CRC. By unraveling the functional significance of these regulatory elements, we gain valuable insights into the molecular landscape of CRC, paving the way for the development of novel and targeted therapeutic interventions aimed at modulating the TGF-β signaling cascade through the manipulation of ncRNAs.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman 11831, Jordan
| | | | - Zahraa Jasim Sattay
- Department of Medical Laboratory Technology l, University of imam Jaafar Al-Sadiq, Iraq
| | | | - Hijaz Ahmad
- Section of Mathematics, International Telematic University Uninettuno, Corso Vittorio Emanuele II, 39, Rome 00186, Italy; Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Kuwait; Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Gaber E Eldesoky
- Chemistry Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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27
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Talepoor AG, Doroudchi M. Regulatory RNAs in immunosenescence. Immun Inflamm Dis 2024; 12:e1209. [PMID: 38456619 PMCID: PMC10921898 DOI: 10.1002/iid3.1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Immunosenescence is a multifactorial stress response to different intrinsic and extrinsic insults that cause immune deterioration and is accompanied by genomic or epigenomic perturbations. It is now widely recognized that genes and proteins contributing in the process of immunosenescence are regulated by various noncoding (nc) RNAs, including microRNAs (miRNAs), long ncRNAs, and circular RNAs. AIMS This review article aimed to evaluate the regulatore RNAs roles in the process of immunosenescence. METHODS We analyzed publications that were focusing on the different roles of regulatory RNAs on the several aspects of immunosenescence. RESULTS In the immunosenescence setting, ncRNAs have been found to play regulatory roles at both transcriptional and post-transcriptional levels. These factors cooperate to regulate the initiation of gene expression programs and sustaining the senescence phenotype and proinflammatory responses. CONCLUSION Immunosenescence is a complex process with pivotal alterations in immune function occurring with age. The extensive network that drive immunosenescence-related features are are mainly directed by a variety of regulatory RNAs such as miRNAs, lncRNAs, and circRNAs. Latest findings about regulation of senescence by ncRNAs in the innate and adaptive immune cells as well as their role in the immunosenescence pathways, provide a better understanding of regulatory RNAs function in the process of immunosenescence.
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Affiliation(s)
- Atefe Ghamar Talepoor
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
- Autoimmune Diseases Research CenterUniversity of Medical SciencesShirazIran
| | - Mehrnoosh Doroudchi
- Department of Immunology, School of MedicineShiraz University of Medical SciencesShirazIran
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28
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Xie G, Du X, Hu H, Du J. Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation. Trends Biochem Sci 2024; 49:247-256. [PMID: 38072749 DOI: 10.1016/j.tibs.2023.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 03/10/2024]
Abstract
In plants, two atypical DNA-dependent RNA polymerases, RNA polymerase IV (Pol IV) and Pol V, and an RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) together produce noncoding RNAs (ncRNAs) to guide the plant-specific RNA-directed DNA methylation (RdDM). Although both Pol IV and Pol V have evolved from the canonical Pol II, they have adapted to different roles in RdDM. The mechanisms of their adaptation are key to understanding plant DNA methylation and the divergent evolution of polymerases. In this review, we summarize insights that have emerged from recent structural studies of Pol IV, Pol V, and RDR2 and discuss their structural features critical for efficient ncRNA production in RdDM.
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Affiliation(s)
- Guohui Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen 518060, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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29
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Sarfraz M, Abida, Eltaib L, Asdaq SMB, Guetat A, Alzahrani AK, Alanazi SS, Aaghaz S, Singla N, Imran M. Overcoming chemoresistance and radio resistance in prostate cancer: The emergent role of non-coding RNAs. Pathol Res Pract 2024; 255:155179. [PMID: 38320439 DOI: 10.1016/j.prp.2024.155179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/08/2024]
Abstract
Prostate cancer (PCa) continues to be a major health concern worldwide, with its resistance to chemotherapy and radiation therapy presenting major hurdles in successful treatment. While patients with localized prostate cancer generally have a good survival rate, those with metastatic prostate cancer often face a grim prognosis, even with aggressive treatments using various methods. The high mortality rate in severe cases is largely due to the lack of treatment options that can offer lasting results, especially considering the significant genetic diversity found in tumors at the genomic level. This comprehensive review examines the intricate molecular mechanisms governing resistance in PCa, emphasising the pivotal contributions of non-coding RNAs (ncRNAs). We delve into the diverse roles of microRNAs, long ncRNAs, and other non-coding elements as critical regulators of key cellular processes involved in CR & RR. The review emphasizes the diagnostic potential of ncRNAs as predictive biomarkers for treatment response, offering insights into patient stratification and personalized therapeutic approaches. Additionally, we explore the therapeutic implications of targeting ncRNAs to overcome CR & RR, highlighting innovative strategies to restore treatment sensitivity. By synthesizing current knowledge, this review not only provides a comprehension of the chemical basis of resistance in PCa but also identifies gaps in knowledge, paving the way for future research directions. Ultimately, this exploration of ncRNA perspectives offers a roadmap for advancing precision medicine in PCa, potentially transforming therapeutic paradigms and improving outcomes for patients facing the challenges of treatment resistance.
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Affiliation(s)
- Muhammad Sarfraz
- College of Pharmacy, Al Ain University, Al Ain Campus, Al Ain 64141, United Arab Emirates
| | - Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | | | - Arbi Guetat
- Department of Biological Sciences, College of Sciences, Northern Border University, Arar 73213, Saudi Arabia
| | - A Khuzaim Alzahrani
- Department of Medical Laboratory Technology, Faculty of Medical Applied Science, Northern Border University, Arar 91431, Saudi Arabia
| | | | - Shams Aaghaz
- Department of Pharmacy, School of Medical & Allied Sciences, Galgotias University, Greater Noida 203201, India
| | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur 302017, India
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia.
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30
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Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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31
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Mattoo S, Gupta A, Chauhan M, Agrawal A, Pore SK. Prospects and challenges of noncoding-RNA-mediated inhibition of heat shock protein 90 for cancer therapy. Biochim Biophys Acta Gene Regul Mech 2024; 1867:195006. [PMID: 38218528 DOI: 10.1016/j.bbagrm.2024.195006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Heat Shock Protein 90 (HSP90) is a potential drug target for cancer therapy as it is often dysregulated in several cancers, including lung, breast, pancreatic, and prostate cancers. In cancer, HSP90 fails to maintain the structural and functional integrity of its several client proteins which are involved in the hallmarks of cancer such as cell proliferation, invasion, migration, angiogenesis, and apoptosis. Several small molecule inhibitors of HSP90 have been shown to exhibit anticancer effects in vitro and in vivo animal models. However, a few of them are currently under clinical studies. The status and potential limitations of these inhibitors are discussed here. Studies demonstrate that several noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) regulate HSP90 and its client proteins to modulate cellular processes to exhibit oncogenic or tumor suppressing properties. Over the last decade, miRNAs and lncRNAs have drawn significant interest from the scientific community as therapeutic agents or targets for clinical applications. Here, we discuss the detailed mechanistic regulation of HSP90 and its client proteins by ncRNAs. Moreover, we highlight the significance of these ncRNAs as potential therapeutic agents/targets, and the challenges associated with ncRNA-based therapies. This article aims to provide a holistic view on HSP90-regulating ncRNAs for the development of novel therapeutic strategies to combat cancer.
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Affiliation(s)
- Shria Mattoo
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Noida 201311, India
| | - Abha Gupta
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Noida 201311, India
| | - Manvee Chauhan
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Noida 201311, India
| | - Akshi Agrawal
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida 201311, India
| | - Subrata Kumar Pore
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University Uttar Pradesh, Noida 201311, India.
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Feng X, Yang X, Zhong Y, Cheng X. The role of ncRNAs-mediated pyroptosis in diabetes and its vascular complications. Cell Biochem Funct 2024; 42:e3968. [PMID: 38439590 DOI: 10.1002/cbf.3968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
Over the past decade, the prevalence of diabetes has increased significantly worldwide, leading to an increase in vascular complications of diabetes (VCD), such as diabetic cardiomyopathy (DCM), diabetic nephropathy (DN), and diabetic retinopathy (DR). Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), long Noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), play a key role in cellular processes, including the pathophysiology of diabetes and VCD via pyroptosis. ncRNAs (e.g., miR-17, lnc-MEG3, and lnc-KCNQ1OT1) can regulate pyroptosis in pancreatic β cells. Some ncRNAs are involved in VCD progression. For example, miR-21, lnc-KCNQ1OT1, lnc-GAS5, and lnc-MALAT1 were reported in DN and DCM, and lnc-MIAT was identified in DCM and DR. Herein, this review aimed to summarize recent research findings related to ncRNAs-mediated pyroptosis at the onset and progression of diabetes and VCD.
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Affiliation(s)
- Xinyao Feng
- Hunan Key laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaoxu Yang
- Hunan Key laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Yancheng Zhong
- Hunan Key laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha, China
| | - Xihua Cheng
- Hunan Key laboratory of Vascular Biology and Translational Medicine, Medical School, Hunan University of Chinese Medicine, Changsha, China
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33
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Shbeer AM. Mystery of COVID 19: Focusing on important ncRNAs and effective signaling pathways. Pathol Res Pract 2024; 255:155155. [PMID: 38354486 DOI: 10.1016/j.prp.2024.155155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 02/16/2024]
Abstract
This article provides a thorough investigation of the essential role of non-coding RNAs (ncRNAs) in the context of COVID-19, emphasizing their impact on the complex molecular dynamics of the viral infection. By conducting a systematic review of existing literature, we identify key ncRNAs involved in different stages of the viral life cycle, modulation of host immune response, and disease progression. The importance of microRNAs, long non-coding RNAs, and other ncRNA types emerges as influential factors in shaping the interaction between the host and the virus. Additionally, the study delves into the effective signaling pathways linked to COVID-19 pathogenesis, uncovering intricate molecular cascades that govern viral entry, replication, and host cell response. This exploration encompasses established pathways such as IL-6/JAK/STAT signaling, highlighting their interplay within the context of COVID-19. By synthesizing this knowledge, our aim is not only to enhance our understanding of the molecular complexities of COVID-19 but also to reveal potential therapeutic targets. Through elucidating the interaction between ncRNAs and signaling pathways, our article seeks to contribute to ongoing efforts in developing targeted interventions against COVID-19, ultimately advancing our ability to address this global health crisis.
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Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
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Hussain MS, Shaikh NK, Agrawal M, Tufail M, Bisht AS, Khurana N, Kumar R. Osteomyelitis and non-coding RNAS: A new dimension in disease understanding. Pathol Res Pract 2024; 255:155186. [PMID: 38350169 DOI: 10.1016/j.prp.2024.155186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/15/2024]
Abstract
Osteomyelitis, a debilitating bone infection, presents considerable clinical challenges due to its intricate etiology and limited treatment options. Despite strides in surgical and chemotherapeutic interventions, the treatment landscape for osteomyelitis remains unsatisfactory. Recent attention has focused on the role of non-coding RNAs (ncRNAs) in the pathogenesis and progression of osteomyelitis. This review consolidates current knowledge on the involvement of distinct classes of ncRNAs, including microRNAs, long ncRNAs, and circular RNAs, in the context of osteomyelitis. Emerging evidence from various studies underscores the potential of ncRNAs in orchestrating gene expression and influencing the differentiation of osteoblasts and osteoclasts, pivotal processes in bone formation. The review initiates by elucidating the regulatory functions of ncRNAs in fundamental cellular processes such as inflammation, immune response, and bone remodeling, pivotal in osteomyelitis pathology. It delves into the intricate network of interactions between ncRNAs and their target genes, illuminating how dysregulation contributes to the establishment and persistence of osteomyelitic infections. Understanding their regulatory roles may pave the way for targeted diagnostic tools and innovative therapeutic interventions, promising a paradigm shift in the clinical approach to this challenging condition. Additionally, we delve into the promising therapeutic applications of these molecules, envisioning novel diagnostic and treatment approaches to enhance the management of this challenging bone infection.
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Affiliation(s)
- Md Sadique Hussain
- Department of Pharmacology, School of Pharmaceutical Sciences, Jaipur National University, Jaipur, Rajasthan 302017, India
| | - Nusrat K Shaikh
- Department of Quality Assurance, Smt. N. M. Padalia Pharmacy College, Ahmedabad, 382210 Gujarat, India
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K.R. Mangalam University, Gurugram 122103, India
| | - Muhammad Tufail
- Department of Oral and Maxillofacial Surgery, Center of Stomatology, Xiangya Hospital, Central South University, Changsha, China.
| | - Ajay Singh Bisht
- School of Pharmaceutical Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand 248001, India
| | - Navneet Khurana
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Rajesh Kumar
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, India
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35
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Feng W, Liang H, Liu D, Ruan S. The SNHG12/microRNA-15b-5p/MYLK axis regulates vascular smooth muscle cell phenotype to affect intracranial aneurysm formation. Microvasc Res 2024; 152:104643. [PMID: 38081409 DOI: 10.1016/j.mvr.2023.104643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/13/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVE This research was dedicated to investigating the impact of the SNHG12/microRNA (miR)-15b-5p/MYLK axis on the modulation of vascular smooth muscle cell (VSMC) phenotype and the formation of intracranial aneurysm (IA). METHODS SNHG12, miR-15b-5p and MYLK expression in IA tissue samples from IA patients were tested by RT-qPCR and western blot. Human aortic vascular smooth muscle cells (VSMCs) were cultivated with H2O2 to mimic IA-like conditions in vitro, and the cell proliferation and apoptosis were measured by MTT assay and Annexin V/PI staining. IA mouse models were established by induction with systemic hypertension combined with elastase injection. The blood pressure in the tail artery of mice in each group was assessed and the pathological changes in arterial tissues were observed by HE staining and TUNEL staining. The expression of TNF-α and IL-1β, MCP-1, iNOS, caspase-3, and caspase-9 in the arterial tissues were tested by RT-qPCR and ELISA. The relationship among SNHG12, miR-15b-5p and MYLK was verified by bioinformatics, RIP, RNA pull-down, and luciferase reporter assays. RESULTS The expression levels of MYLK and SNHG12 were down-regulated and that of miR-15b-5p was up-regulated in IA tissues and H2O2-treated human aortic VSMCs. Overexpressed MYLK or SNHG12 mitigated the decrease in proliferation and increase in apoptosis of VSMCs caused by H2O2 induction, and overexpression of miR-15b-5p exacerbated the decrease in proliferation and increase in apoptosis of VSMCs caused by H2O2 induction. Overexpression of miR-15b-5p reversed the H2O2-treated VSMC phenotypic changes caused by SNHG12 up-regulation, and overexpression of MYLK reversed the H2O2-treated VSMC phenotypic changes caused by up-regulation of miR-15b-5p. Overexpression of SNHG12 reduced blood pressure and ameliorated arterial histopathological damage and VSMC apoptosis in IA mice. The mechanical analysis uncovered that SNHG12 acted as an endogenous RNA that competed with miR-15b-5p, thus modulating the suppression of its endogenous target, MYLK. CONCLUSION Decreased expression of SNHG12 in IA may contribute to the increasing VSMC apoptosis via increasing miR-15b-5p expression and subsequently decreasing MYLK expression. These findings provide potential new strategies for the clinical treatment of IA.
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Affiliation(s)
- Wenxian Feng
- Stroke Center Neurointervention Ward, Zhumadian Central Hospital, Zhumadian 463000, Henan, China.
| | - Hao Liang
- Stroke Center Neurointervention Ward, Zhumadian Central Hospital, Zhumadian 463000, Henan, China
| | - Dan Liu
- Stroke Center Neurointervention Ward, Zhumadian Central Hospital, Zhumadian 463000, Henan, China
| | - Shiwang Ruan
- Neurology Department 2, Zhumadian Central Hospital, Zhumadian 463000, Henan, China
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36
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Alpuche-Lazcano SP, Scarborough RJ, Gatignol A. MicroRNAs and long non-coding RNAs during transcriptional regulation and latency of HIV and HTLV. Retrovirology 2024; 21:5. [PMID: 38424561 PMCID: PMC10905857 DOI: 10.1186/s12977-024-00637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
Human immunodeficiency virus (HIV) and human T cell leukemia virus (HTLV) have replicative and latent stages of infection. The status of the viruses is dependent on the cells that harbour them and on different events that change the transcriptional and post-transcriptional events. Non-coding (nc)RNAs are key factors in the regulation of retrovirus replication cycles. Notably, micro (mi)RNAs and long non-coding (lnc)RNAs are important regulators that can induce switches between active transcription-replication and latency of retroviruses and have important impacts on their pathogenesis. Here, we review the functions of miRNAs and lncRNAs in the context of HIV and HTLV. We describe how specific miRNAs and lncRNAs are involved in the regulation of the viruses' transcription, post-transcriptional regulation and latency. We further discuss treatment strategies using ncRNAs for HIV and HTLV long remission, reactivation or possible cure.
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Affiliation(s)
- Sergio P Alpuche-Lazcano
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- National Research Council Canada, Montréal, QC, H4P 2R2, Canada
| | - Robert J Scarborough
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada
| | - Anne Gatignol
- Virus-Cell Interactions Laboratory, Lady Davis Institute for Medical Research, 3999, Côte Ste Catherine St., Montréal, QC, H3T 1E2, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Medicine, Division of Infectious Diseases, McGill University, Montréal, QC, H4A 3J1, Canada.
- Department of Microbiology and Immunology, McGill University, Montréal, QC, H3A 2B4, Canada.
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37
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Xia Q, Shen J, Wang Q, Chen R, Zheng X, Yan Q, Du L, Li H, Duan S. Cuproptosis-associated ncRNAs predict breast cancer subtypes. PLoS One 2024; 19:e0299138. [PMID: 38408075 PMCID: PMC10896520 DOI: 10.1371/journal.pone.0299138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 02/05/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND Cuproptosis is a novel copper-dependent mode of cell death that has recently been discovered. The relationship between Cuproptosis-related ncRNAs and breast cancer subtypes, however, remains to be studied. METHODS The aim of this study was to construct a breast cancer subtype prediction model associated with Cuproptosis. This model could be used to determine the subtype of breast cancer patients. To achieve this aim, 21 Cuproptosis-related genes were obtained from published articles and correlation analysis was performed with ncRNAs differentially expressed in breast cancer. Random forest algorithms were subsequently utilized to select important ncRNAs and build breast cancer subtype prediction models. RESULTS A total of 94 ncRNAs significantly associated with Cuproptosis were obtained and the top five essential features were chosen to build a predictive model. These five biomarkers were differentially expressed in the five breast cancer subtypes and were closely associated with immune infiltration, RNA modification, and angiogenesis. CONCLUSION The random forest model constructed based on Cuproptosis-related ncRNAs was able to accurately predict breast cancer subtypes, providing a new direction for the study of clinical therapeutic targets.
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Affiliation(s)
- Qing Xia
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Jinze Shen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qurui Wang
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Ruixiu Chen
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Xinying Zheng
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Qibin Yan
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Lihua Du
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
| | - Hanbing Li
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, China
| | - Shiwei Duan
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of Medicine, Hangzhou City University, Hangzhou, Zhejiang, China
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38
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Xu S, Wang L, Zhao Y, Mo T, Wang B, Lin J, Yang H. Metabolism-regulating non-coding RNAs in breast cancer: roles, mechanisms and clinical applications. J Biomed Sci 2024; 31:25. [PMID: 38408962 PMCID: PMC10895768 DOI: 10.1186/s12929-024-01013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/17/2024] [Indexed: 02/28/2024] Open
Abstract
Breast cancer is one of the most common malignancies that pose a serious threat to women's health. Reprogramming of energy metabolism is a major feature of the malignant transformation of breast cancer. Compared to normal cells, tumor cells reprogram metabolic processes more efficiently, converting nutrient supplies into glucose, amino acid and lipid required for malignant proliferation and progression. Non-coding RNAs(ncRNAs) are a class of functional RNA molecules that are not translated into proteins but regulate the expression of target genes. NcRNAs have been demonstrated to be involved in various aspects of energy metabolism, including glycolysis, glutaminolysis, and fatty acid synthesis. This review focuses on the metabolic regulatory mechanisms and clinical applications of metabolism-regulating ncRNAs involved in breast cancer. We summarize the vital roles played by metabolism-regulating ncRNAs for endocrine therapy, targeted therapy, chemotherapy, immunotherapy, and radiotherapy resistance in breast cancer, as well as their potential as therapeutic targets and biomarkers. Difficulties and perspectives of current targeted metabolism and non-coding RNA therapeutic strategies are discussed.
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Affiliation(s)
- Shiliang Xu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Lingxia Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Yuexin Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Tong Mo
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Bo Wang
- Department of Oncology, The Second Affiliated Hospital of Soochow University, 1055 Sanxiang Road, Suzhou, Jiangsu, 215004, People's Republic of China
| | - Jun Lin
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China.
| | - Huan Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215004, People's Republic of China.
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Sharma H, Valentine MNZ, Toki N, Sueki HN, Gustincich S, Takahashi H, Carninci P. Decryption of sequence, structure, and functional features of SINE repeat elements in SINEUP non-coding RNA-mediated post-transcriptional gene regulation. Nat Commun 2024; 15:1400. [PMID: 38383605 PMCID: PMC10881587 DOI: 10.1038/s41467-024-45517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
RNA structure folding largely influences RNA regulation by providing flexibility and functional diversity. In silico and in vitro analyses are limited in their ability to capture the intricate relationships between dynamic RNA structure and RNA functional diversity present in the cell. Here, we investigate sequence, structure and functional features of mouse and human SINE-transcribed retrotransposons embedded in SINEUPs long non-coding RNAs, which positively regulate target gene expression post-transcriptionally. In-cell secondary structure probing reveals that functional SINEs-derived RNAs contain conserved short structure motifs essential for SINEUP-induced translation enhancement. We show that SINE RNA structure dynamically changes between the nucleus and cytoplasm and is associated with compartment-specific binding to RBP and related functions. Moreover, RNA-RNA interaction analysis shows that the SINE-derived RNAs interact directly with ribosomal RNAs, suggesting a mechanism of translation regulation. We further predict the architecture of 18 SINE RNAs in three dimensions guided by experimental secondary structure data. Overall, we demonstrate that the conservation of short key features involved in interactions with RBPs and ribosomal RNA drives the convergent function of evolutionarily distant SINE-transcribed RNAs.
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Affiliation(s)
- Harshita Sharma
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Matthew N Z Valentine
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Naoko Toki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Hiromi Nishiyori Sueki
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | | | - Hazuki Takahashi
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan.
- Human Technopole, Milan, 20157, Italy.
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40
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Xie M, Zhang Y, Yan L, Jin M, Lu X, Yu Q. Peripheral Blood Non-Coding RNA as Biomarker for Schizophrenia: A Review. J Integr Neurosci 2024; 23:42. [PMID: 38419436 DOI: 10.31083/j.jin2302042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/23/2023] [Accepted: 06/09/2023] [Indexed: 03/02/2024] Open
Abstract
Schizophrenia (SCZ) is a complex and heterogeneous neuropsychiatric disorder that lacks objective diagnostic indicators and the pathogenesis remain unclear. Genetic factors may exert a significant impact on the development of the condition. While obtaining brain tissue for biopsy in the course of adjuvant diagnosis of SCZ patients may not be possible, the collection of peripheral blood is more accessible and easier to implement. In recent years, the development and application of RNA sequencing technology has made seeking biomarkers of SCZ becomes more feasible. There is emerging evidence suggesting that certain non-coding RNAs (ncRNA) are distinctly different in the peripheral blood of SCZ patients and healthy controls. Although the mechanisms remain unclear, these aberrantly expressed ncRNAs may be intimately associated with the onset and development of SCZ and may be of great significance for the diagnosis and treatment of SCZ. Therefore, we reviewed the expression of distinct types of ncRNAs that have been found in the peripheral blood of SCZ patients and explored their potential application as diagnostic biomarkers of SCZ. Differentially expressed ncRNAs in the peripheral blood of SCZ patients could not only serve as potential diagnostic biomarkers and therapeutic targets for SCZ but may also have implications for advancing understanding of the molecular mechanisms underlying the development of SCZ and elucidating the complex etiology of SCZ. Early diagnostic biomarkers obtained directly from peripheral blood are of great significance for the timely diagnosis and treatment of SCZ. Our review will enhance the comprehension of molecular mechanisms of SCZ and contribute to the identification of promising ncRNAs in peripheral blood for both diagnosis and therapy of SCZ.
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Affiliation(s)
- Mengtong Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
| | - Yanchi Zhang
- Department of Psychology, Changchun Sixth Hospital, 130052 Changchun, Jilin, China
| | - Lijuan Yan
- Department of Psychology, Changchun Sixth Hospital, 130052 Changchun, Jilin, China
| | - Mengdi Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
| | - Xiaoyu Lu
- Innovative Biotechnology Laboratory, Jilin Biological Research Institute, 130012 Changchun, Jilin, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, 130021 Changchun, Jilin, China
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Leone S, Srivastava A, Herrero-Ruiz A, Hummel B, Tittel L, Campalastri R, Aprile-Garcia F, Tan JH, Rawat P, Andersson P, Willis AE, Sawarkar R. HSP70 binds to specific non-coding RNA and regulates human RNA polymerase III. Mol Cell 2024; 84:687-701.e7. [PMID: 38266641 DOI: 10.1016/j.molcel.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 10/20/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024]
Abstract
Molecular chaperones are critical for protein homeostasis and are implicated in several human pathologies such as neurodegeneration and cancer. While the binding of chaperones to nascent and misfolded proteins has been studied in great detail, the direct interaction between chaperones and RNA has not been systematically investigated. Here, we provide the evidence for widespread interaction between chaperones and RNA in human cells. We show that the major chaperone heat shock protein 70 (HSP70) binds to non-coding RNA transcribed by RNA polymerase III (RNA Pol III) such as tRNA and 5S rRNA. Global chromatin profiling revealed that HSP70 binds genomic sites of transcription by RNA Pol III. Detailed biochemical analyses showed that HSP70 alleviates the inhibitory effect of cognate tRNA transcript on tRNA gene transcription. Thus, our study uncovers an unexpected role of HSP70-RNA interaction in the biogenesis of a specific class of non-coding RNA with wider implications in cancer therapeutics.
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Affiliation(s)
- Sergio Leone
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK.
| | | | | | - Barbara Hummel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Lena Tittel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | | | | | - Jun Hao Tan
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK
| | - Prashant Rawat
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany
| | - Patrik Andersson
- Safety Innovation, Clinical Pharmacology and Safety Sciences, AstraZeneca R&D, Gothenburg 43183, Sweden
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK
| | - Ritwick Sawarkar
- MRC Toxicology Unit, University of Cambridge, Cambridge CB21QR, UK; Max Planck Institute of Immunobiology and Epigenetics, Freiburg 79108, Germany.
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42
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Liu J, Zhong X. Epiallelic variation of non-coding RNA genes and their phenotypic consequences. Nat Commun 2024; 15:1375. [PMID: 38355746 PMCID: PMC10867003 DOI: 10.1038/s41467-024-45771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Epigenetic variations contribute greatly to the phenotypic plasticity and diversity. Current functional studies on epialleles have predominantly focused on protein-coding genes, leaving the epialleles of non-coding RNA (ncRNA) genes largely understudied. Here, we uncover abundant DNA methylation variations of ncRNA genes and their significant correlations with plant adaptation among 1001 natural Arabidopsis accessions. Through genome-wide association study (GWAS), we identify large numbers of methylation QTL (methylQTL) that are independent of known DNA methyltransferases and enriched in specific chromatin states. Proximal methylQTL closely located to ncRNA genes have a larger effect on DNA methylation than distal methylQTL. We ectopically tether a DNA methyltransferase MQ1v to miR157a by CRISPR-dCas9 and show de novo establishment of DNA methylation accompanied with decreased miR157a abundance and early flowering. These findings provide important insights into the genetic basis of epigenetic variations and highlight the contribution of epigenetic variations of ncRNA genes to plant phenotypes and diversity.
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Affiliation(s)
- Jie Liu
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Xuehua Zhong
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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43
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Cipriano GL, Schepici G, Mazzon E, Anchesi I. Multiple Sclerosis: Roles of miRNA, lcnRNA, and circRNA and Their Implications in Cellular Pathways. Int J Mol Sci 2024; 25:2255. [PMID: 38396932 PMCID: PMC10889752 DOI: 10.3390/ijms25042255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Multiple sclerosis (MS) is a degenerative condition characterized by axonal damage and demyelination induced by autoreactive immune cells that occur in the Central Nervous System (CNS). The interaction between epigenetic changes and genetic factors can be widely involved in the onset, development, and progression of the disease. Although numerous efforts were made to discover new therapies able to prevent and improve the course of MS, definitive curative treatments have not been found yet. However, in recent years, it has been reported that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs), acting as gene expression regulators, could be used as potential therapeutic targets or biomarkers to diagnose and fight MS. In this review, we discussed the role of miRNAs, lncRNAs, and circRNAs, as well as their expression level changes and signaling pathways that are related to preclinical and human MS studies. Hence, the investigation of ncRNAs could be important to provide additional information regarding MS pathogenesis as well as promote the discovery of new therapeutic strategies or biomarkers.
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Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Strada Statale 113, Contrada Casazza, 98124 Messina, Italy; (G.L.C.); (G.S.); (I.A.)
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44
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Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024; 20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute 98-99% of the human genome. Non-coding RNAs encompass diverse functional classes, including microRNAs, small interfering RNAs, PIWI-interacting RNAs, small nuclear RNAs, small nucleolar RNAs, and long non-coding RNAs. With critical involvement in gene expression and regulation across various biological and physiopathological contexts, such as neuronal disorders, immune responses, cardiovascular diseases, and cancer, non-coding RNAs are emerging as disease biomarkers and therapeutic targets. In this review, after providing an overview of non-coding RNAs' role in cell homeostasis, we illustrate the potential and the challenges of state-of-the-art computational methods exploited to study non-coding RNAs biogenesis, function, and modulation. This can be done by directly targeting them with small molecules or by altering their expression by targeting the cellular engines underlying their biosynthesis. Drawing from applications, also taken from our work, we showcase the significance and role of computer simulations in uncovering fundamental facets of ncRNA mechanisms and modulation. This information may set the basis to advance gene modulation tools and therapeutic strategies to address unmet medical needs.
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Affiliation(s)
- Silvia Rinaldi
- National Research Council of Italy (CNR) - Institute of Chemistry of OrganoMetallic Compounds (ICCOM), c/o Area di Ricerca CNR di Firenze Via Madonna del Piano 10, 50019 Sesto Fiorentino, Florence, Italy
| | - Elisabetta Moroni
- National Research Council of Italy (CNR) - Institute of Chemical Sciences and Technologies (SCITEC), via Mario Bianco 9, 20131 Milano, Italy
| | - Riccardo Rozza
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
| | - Alessandra Magistrato
- National Research Council of Italy (CNR) - Institute of Material Foundry (IOM) c/o International School for Advanced Studies (SISSA), Via Bonomea, 265, 34136 Trieste, Italy
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45
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Tang C, Hu W. Non-coding RNA regulates the immune microenvironment in recurrent spontaneous abortion (RSA): new insights into immune mechanisms†. Biol Reprod 2024; 110:220-229. [PMID: 37956412 PMCID: PMC10873270 DOI: 10.1093/biolre/ioad157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 11/15/2023] Open
Abstract
Recurrent spontaneous abortion (RSA) has various causes, including chromosomal abnormalities, prethrombotic state, and abnormal uterine anatomical factors. However, the pathogenesis of RSA is still unclear. Surprisingly, non-coding RNA can stably express at the maternal-fetal interface and regulate immune cells' proliferation, apoptosis, invasion, metastasis, and angiogenesis. Accumulating evidence suggests that the competing endogenous RNA (ceRNA) regulatory network between non-coding RNAs complicates RSA's pathological process and maybe a new starting point for exploring RSA. In this review, we mainly discuss the regulatory network and potential significance of non-coding RNA in the immune microenvironment of RSA patients. In addition, the cellular interactions of non-coding RNA transported through vesicles were introduced from aspects of trophoblast function and immune regulation. Finally, we analyze previous studies and further discuss that the stable expression of non-coding RNA may be used as a biomarker of some disease states and a prediction target of RSA.
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Affiliation(s)
- Cen Tang
- Obstetrics Department, Kunming Medical University Second Affiliated Hospital, Kunming, Yunnan, China
| | - Wanqin Hu
- Obstetrics Department, Kunming Medical University Second Affiliated Hospital, Kunming, Yunnan, China
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46
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Sabet Sarvestani F, Afshari A, Azarpira N. The role of non-protein-coding RNAs in ischemic acute kidney injury. Front Immunol 2024; 15:1230742. [PMID: 38390339 PMCID: PMC10881863 DOI: 10.3389/fimmu.2024.1230742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/26/2024] [Indexed: 02/24/2024] Open
Abstract
Acute kidney injury (AKI) is a condition characterized by a rapid decline in kidney function within a span of 48 hours. It is influenced by various factors including inflammation, oxidative stress, excessive calcium levels within cells, activation of the renin-angiotensin system, and dysfunction in microcirculation. Ischemia-reperfusion injury (IRI) is recognized as a major cause of AKI; however, the precise mechanisms behind this process are not yet fully understood and effective treatments are still needed. To enhance the accuracy of diagnosing AKI during its early stages, the utilization of innovative markers is crucial. Numerous studies suggest that certain noncoding RNAs (ncRNAs), such as long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), play a central role in regulating gene expression and protein synthesis. These ncRNAs are closely associated with the development and recovery of AKI and have been detected in both kidney tissue and bodily fluids. Furthermore, specific ncRNAs may serve as diagnostic markers and potential targets for therapeutic interventions in AKI. This review aims to summarize the functional roles and changes observed in noncoding RNAs during ischemic AKI, as well as explore their therapeutic potential.
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Affiliation(s)
| | - Afsoon Afshari
- Shiraz Nephro-Urology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Azarpira
- Shiraz Transplant Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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47
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Gu YY, Liu XS, Lan HY. Therapeutic potential for renal fibrosis by targeting Smad3-dependent noncoding RNAs. Mol Ther 2024; 32:313-324. [PMID: 38093516 PMCID: PMC10861968 DOI: 10.1016/j.ymthe.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/13/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024] Open
Abstract
Renal fibrosis is a characteristic hallmark of chronic kidney disease (CKD) that ultimately results in renal failure, leaving patients with few therapeutic options. TGF-β is a master regulator of renal fibrosis and mediates progressive renal fibrosis via both canonical and noncanonical signaling pathways. In the canonical Smad signaling, Smad3 is a key mediator in tissue fibrosis and mediates renal fibrosis via a number of noncoding RNAs (ncRNAs). In this regard, targeting Smad3-dependent ncRNAs may offer a specific therapy for renal fibrosis. This review highlights the significance and innovation of TGF-β/Smad3-associated ncRNAs as biomarkers and therapeutic targets in renal fibrogenesis. In addition, the underlying mechanisms of these ncRNAs and their future perspectives in the treatment of renal fibrosis are discussed.
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Affiliation(s)
- Yue-Yu Gu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China; Departments of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong; Department of Pharmacology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China; Departments of Nephrology and Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xu-Sheng Liu
- State Key Laboratory of Traditional Chinese Medicine Syndrome, Department of Nephrology, Guangdong Provincial Hospital of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.
| | - Hui-Yao Lan
- Departments of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, and Lui Che Woo Institute of Innovative Medicine, The Chinese University of Hong Kong, Hong Kong; Departments of Nephrology and Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China.
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48
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Soares LW, King CG, Fernando CM, Roth A, Breaker RR. Genetic disruption of the bacterial raiA motif noncoding RNA causes defects in sporulation and aggregation. Proc Natl Acad Sci U S A 2024; 121:e2318008121. [PMID: 38306478 PMCID: PMC10861870 DOI: 10.1073/pnas.2318008121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/02/2023] [Indexed: 02/04/2024] Open
Abstract
Several structured noncoding RNAs in bacteria are essential contributors to fundamental cellular processes. Thus, discoveries of additional ncRNA classes provide opportunities to uncover and explore biochemical mechanisms relevant to other major and potentially ancient processes. A candidate structured ncRNA named the "raiA motif" has been found via bioinformatic analyses in over 2,500 bacterial species. The gene coding for the RNA typically resides between the raiA and comFC genes of many species of Bacillota and Actinomycetota. Structural probing of the raiA motif RNA from the Gram-positive anaerobe Clostridium acetobutylicum confirms key features of its sophisticated secondary structure model. Expression analysis of raiA motif RNA reveals that the RNA is constitutively produced but reaches peak abundance during the transition from exponential growth to stationary phase. The raiA motif RNA becomes the fourth most abundant RNA in C. acetobutylicum, excluding ribosomal RNAs and transfer RNAs. Genetic disruption of the raiA motif RNA causes cells to exhibit substantially decreased spore formation and diminished ability to aggregate. Restoration of normal cellular function in this knock-out strain is achieved by expression of a raiA motif gene from a plasmid. These results demonstrate that raiA motif RNAs normally participate in major cell differentiation processes by operating as a trans-acting factor.
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Affiliation(s)
- Lucas W. Soares
- Department of Microbial Pathogenesis, Yale University, New Haven, CT06536
| | - Christopher G. King
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Chrishan M. Fernando
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
| | - Adam Roth
- HHMI, Yale University, New Haven, CT06511-8103
| | - Ronald R. Breaker
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06511-8103
- HHMI, Yale University, New Haven, CT06511-8103
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT06511-8103
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Zhang X, Li Y, Cao Y, Wu Y, Cheng G. The Role of Noncoding RNA in the Transmission and Pathogenicity of Flaviviruses. Viruses 2024; 16:242. [PMID: 38400018 PMCID: PMC10892091 DOI: 10.3390/v16020242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/25/2024] Open
Abstract
Noncoding RNAs (ncRNAs) constitute a class of RNA molecules that lack protein-coding capacity. ncRNAs frequently modulate gene expression through specific interactions with target proteins or messenger RNAs, thereby playing integral roles in a wide array of cellular processes. The Flavivirus genus comprises several significant members, such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV), which have caused global outbreaks, resulting in high morbidity and mortality in human populations. The life cycle of arthropod-borne flaviviruses encompasses their transmission between hematophagous insect vectors and mammalian hosts. During this process, a complex three-way interplay occurs among the pathogen, vector, and host, with ncRNAs exerting a critical regulatory influence. ncRNAs not only constitute a crucial regulatory mechanism that has emerged from the coevolution of viruses and their hosts but also hold potential as antiviral targets for controlling flavivirus epidemics. This review introduces the biogenesis of flavivirus-derived ncRNAs and summarizes the regulatory roles of ncRNAs in viral replication, vector-mediated viral transmission, antiviral innate immunity, and viral pathogenicity. A profound comprehension of the interplay between ncRNAs and flaviviruses will help formulate efficacious prophylactic and therapeutic strategies against flavivirus-related diseases.
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Affiliation(s)
- Xianwen Zhang
- Shenzhen Bay Laboratory, Institute of Infectious Diseases, Shenzhen 518000, China
| | - Yuhan Li
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Yingyi Cao
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
| | - Ying Wu
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan 430072, China;
| | - Gong Cheng
- New Cornerstone Science Laboratory, Tsinghua University-Peking University Joint Center for Life Sciences, School of Basic Medical Sciences, Tsinghua University, Beijing 100084, China; (Y.L.); (Y.C.)
- Institute of Pathogenic Organisms, Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China
- Southwest United Graduate School, Kunming 650092, China
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50
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Alharbi KS. The ncRNA-TGF-β axis: Unveiling new frontiers in colorectal cancer research. Pathol Res Pract 2024; 254:155138. [PMID: 38266458 DOI: 10.1016/j.prp.2024.155138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/07/2024] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
Colorectal cancer (CRC) poses a substantial global challenge, necessitating a deeper understanding of the molecular underpinnings governing its onset and progression. The transforming growth factor beta (TGF-β) network has been a well-recognized cornerstone in advancing CRC. Nevertheless, a recent study has highlighted the growing importance of non-coding RNAs (ncRNAs) in this context. This comprehensive review aims to present an extensive examination of the interaction between ncRNAs and TGF-signaling. Noncoding RNAs (ncRNAs), encompassing circular RNAs (circRNAs), long-ncRNAs (lncRNAs), and microRNAs (miRNAs), have surfaced as pivotal modulators governing various aspects of TGF-β signaling. MiRNAs have been discovered to target elements within the TGF-β signaling, either enhancing or inhibiting signaling, depending on the context. LncRNAs have been associated with CRC progression, functioning as miRNA sponges or directly influencing TGF-β pathway elements. Even circRNAs, a relatively recent addition to the ncRNA family, have impacted CRC, affecting TGF-β signaling through diverse mechanisms. This review encompasses recent progress in comprehending specific ncRNAs involved in TGF-β signaling, their functional roles, and their clinical relevance in CRC. We investigate the possibility of ncRNAs as targets for detection, prognosis, and therapy. Additionally, we explore the interaction of TGF-β and other pathways in CRC and the role of ncRNAs within this intricate network. As we unveil the intricate regulatory function of ncRNAs in the TGF-β signaling in CRC, we gain valuable insights into the disease's pathogenesis. Incorporating these discoveries into clinical settings holds promise for more precise diagnosis, prognosis, and targeted therapeutic approaches, ultimately enhancing the care of CRC patients. This comprehensive review underscores the ever-evolving landscape of ncRNA research in CRC and the potential for novel interventions in the battle against this formidable disease.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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