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Yin F, Zhao W, Ding C, Hou C, Wang S, Sun C, Zhao Z, Zhang Z, Ren F, Liu Y, Li X. A Novel Cellular Senescence-related lncRNA Signature for Predicting the Prognosis of Breast Cancer Patients. J Cancer 2024; 15:4700-4716. [PMID: 39006073 PMCID: PMC11242350 DOI: 10.7150/jca.96107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/17/2024] [Indexed: 07/16/2024] Open
Abstract
Background: Long non-coding RNA (lncRNA), a crucial regulator in breast cancer (BC) development, is intricately linked with cellular senescence. However, there is a lack of cellular senescence-related lncRNAs (CSRLs) signature to evaluate the prognosis of BC patients. Methods: Correlation analysis was conducted to identify lncRNAs associated with cellular senescence. Subsequently, a CSRL signature was crafted in the training cohort. The model's accuracy was evaluated through survival analysis and receiver operating characteristic curves. Furthermore, prognostic nomograms amalgamating cellular senescence and clinical characteristics were devised. Tumor microenvironment and checkpoint disparities were compared between low-risk and high-risk groups. The correlation between these signatures and treatment response in BC patients was also investigated. Finally, functional experiments were conducted for validation. Results: A signature comprising nine CSRLs was devised, which demonstrated adept prognostic capability in BC patients. Functional enrichment analysis revealed that tumor and immune-related pathways were predominantly enriched. Compared to the low-risk group, the high-risk group could benefit more from immunotherapy and certain chemotherapeutic agents. The expression of the 9 CSRLs was validated through in vitro experiments in different subtypes of BC cell lines and tissues. AC098484.1 was specifically verified for its association with senescence-associated secretory phenotypes. Conclusion: The CSRLs signature emerges as a promising prognostic biomarker for BC, with implications for immunological studies and treatment strategies. AC098484.1 has potential relevance in the treatment of BC cell senescence, and these findings improve the clinical treatment levels for BC patients.
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Affiliation(s)
- Fangxu Yin
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Wenhao Zhao
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chen Ding
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chong Hou
- Department of Emergency medicine, Tianjin Medical University General Hospital, China
| | - Song Wang
- Department of Pediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chao Sun
- Department of Orthopedic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zexia Zhao
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhanrui Zhang
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Fan Ren
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuying Liu
- Department of Pathology, Nanjing Integrated Traditional Chinese and Western Medicine Hospital Affiliated with Nanjing University of Chinese Medicine, Nanjing, China
| | - Xuanguang Li
- Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin, China
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2
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Zhou X, Pan J, Chen L, Zhang S, Chen Y. DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data. Biomolecules 2024; 14:766. [PMID: 39062480 PMCID: PMC11274664 DOI: 10.3390/biom14070766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024] Open
Abstract
Understanding the dynamics of gene regulatory networks (GRNs) across diverse cell types poses a challenge yet holds immense value in unraveling the molecular mechanisms governing cellular processes. Current computational methods, which rely solely on expression changes from bulk RNA-seq and/or scRNA-seq data, often result in high rates of false positives and low precision. Here, we introduce an advanced computational tool, DeepIMAGER, for inferring cell-specific GRNs through deep learning and data integration. DeepIMAGER employs a supervised approach that transforms the co-expression patterns of gene pairs into image-like representations and leverages transcription factor (TF) binding information for model training. It is trained using comprehensive datasets that encompass scRNA-seq profiles and ChIP-seq data, capturing TF-gene pair information across various cell types. Comprehensive validations on six cell lines show DeepIMAGER exhibits superior performance in ten popular GRN inference tools and has remarkable robustness against dropout-zero events. DeepIMAGER was applied to scRNA-seq datasets of multiple myeloma (MM) and detected potential GRNs for TFs of RORC, MITF, and FOXD2 in MM dendritic cells. This technical innovation, combined with its capability to accurately decode GRNs from scRNA-seq, establishes DeepIMAGER as a valuable tool for unraveling complex regulatory networks in various cell types.
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Affiliation(s)
- Xiguo Zhou
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Jingyi Pan
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Liang Chen
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Shaoqiang Zhang
- College of Computer and Information Engineering, Tianjin Normal University, Tianjin 300387, China; (X.Z.); (J.P.); (L.C.)
| | - Yong Chen
- Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
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Kansara S, Sawant P, Kaur T, Garg M, Pandey AK. LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195017. [PMID: 38341138 DOI: 10.1016/j.bbagrm.2024.195017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024]
Abstract
Alternative splicing (AS) is a fundamental post-transcriptional process in eukaryotes, enabling a single gene to generate diverse mRNA transcripts, thereby enhancing protein variability. This process involves the excision of introns and the joining of exons in pre-mRNA(s) to form mature mRNA. The resulting mature mRNAs exhibit various combinations of exons, contributing to functional diversity. Dysregulation of AS can substantially modulate protein functions, impacting the onset and progression of numerous diseases, including cancer. Non-coding RNAs (ncRNAs) are distinct from protein-coding RNAs and consist of short and long types. Long non-coding RNAs (lncRNAs) play an important role in regulating several cellular processes, particularly alternative splicing, according to new research. This review provides insight into the latest discoveries concerning how lncRNAs influence alternative splicing within the realm of breast cancer. Additionally, it explores potential therapeutic strategies focused on targeting lncRNAs.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Prajwali Sawant
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Taranjeet Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Uttar Pradesh, Sector-125, Noida 201313, India
| | - Amit Kumar Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India.
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4
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Shalaby R, Ibrahim S, Kotb AAW, Baz S, Hafed L, Shaker O, Afifi S. MALAT1 as a potential salivary biomarker in oral squamous cell carcinoma through targeting miRNA-124. Oral Dis 2024; 30:2075-2083. [PMID: 37703315 DOI: 10.1111/odi.14730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/15/2023]
Abstract
OBJECTIVES To determine the diagnostic accuracy of the long non-coding RNA "MALAT1" measured in the saliva of patients with oral squamous cell carcinoma (OSCC) and assess the salivary expression of microRNA-124, which MALAT1 targets. SUBJECTS AND METHODS Forty subjects were collected in a consecutive pattern and allocated into two groups. Group A included 20 patients with OSCC, while Group B included 20 healthy subjects. Salivary expression of MALAT1 and microRNA (miRNA)-124 was evaluated in the two study groups using quantitative real-time polymerase chain reaction and correlated with histopathological examination of OSCC subjects. RESULTS OSCC yielded a statistically significant higher expression of MALAT1 than healthy controls and a lower expression of miRNA-124 in OSCC than controls. There is a statistically significant inverse relationship between salivary MALAT1 and miRNA-124. Moreover, there is a statistically significant difference in the MALAT1 expression in saliva samples from metastatic cases compared with non-metastatic cases, as well as in patients with lymph node involvement compared with those without involvement. At a cut-off value of 2.24, salivary MALAT1 exhibited 95% sensitivity and 90% specificity in differentiating OSCC from healthy subjects. CONCLUSION Salivary MALAT1 acts as a sponge for miRNA-124 and could be a potential salivary biomarker for OSCC.
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Affiliation(s)
- Rania Shalaby
- Oral Medicine, Oral Diagnosis and Periodontology, Faculty of Dentistry, Fayoum University, Fayoum, Egypt
| | - Sally Ibrahim
- Oral and Maxillofacial Pathology, Faculty of Dentistry, Fayoum University, Fayoum, Egypt
| | - Ali A W Kotb
- Oral and Maxillofacial Pathology, Faculty of Dentistry, Cairo University, Giza, Egypt
| | - Safaa Baz
- Oral Pathology, Faculty of Dentistry, The British University in Egypt, El Shorouk City, Egypt
| | - Layla Hafed
- Oral and Maxillofacial Pathology, Al-Mamoon Diagnostic Medical Center, Sana'a, Yemen
| | - Olfat Shaker
- Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Salsabeel Afifi
- Oral Medicine, Oral Diagnosis and Periodontology, Faculty of Dentistry, Fayoum University, Fayoum, Egypt
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Li X, Ding Z, Tong Y. Correlations of m 6A Methylation-Related lncRNAs with the Prognosis of Papillary Thyroid Carcinoma. Int J Gen Med 2024; 17:775-790. [PMID: 38476625 PMCID: PMC10929225 DOI: 10.2147/ijgm.s449827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Purpose Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid cancer. Recurrence makes the prognosis for some patients with PTC worse. Increasing evidence have suggested that N6-methyladenosine (m6A) RNA methylation plays an important role in tumorigenesis. However, the significance of m6A-related lncRNAs in the malignant progression of PTC remains unknown. In this study, we explored the significance of M6A-related lncrnas in the malignant progression of PTC. Patients and Methods Transcriptome and clinical data of PTC were achieved and integrated from The Cancer Genome Atlas (TCGA). Firstly, a Spearman correlation analysis was performed to obtain m6A RNA methylation-associated lncRNAs. Next, We constructed a prognostic signature and assessed the accuracy of the signature by receiver operating characteristic (ROC) curve and Kaplan Meier survival analyses. Furthermore, functional enrichment analysis was performed on the high- and low-risk groups. Finally, we determined prognostic gene expression in clinical samples using quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results We identified 56 differentially expressed lncRNAs associated with m6A RNA methylation. Univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses showed that the survival-related lncRNAs associated with m6A RNA methylation were detected, which showed superior calibration and discrimination. Moreover, the biological processes related to energy metabolism were significantly activated in the high-risk group. Finally, the co-expressed genes of lncRNAs in the risk model were significantly enriched in biological processes related to copper ion response. Finally, we validated the expression levels of three prognostic genes in clinical samples using RT-qPCR. Conclusion Our study revealed m6A RNA methylation-associated lncRNAs were significantly associated with disease-free survival in patients with papillary thyroid cancer, which would improve our understanding of the relationship between m6A RNA methylation-associated lncRNAs and PTC.
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Affiliation(s)
- Xiang Li
- Department of General Surgery, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
| | - Zigang Ding
- Department of General Surgery, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
| | - Yun Tong
- Department of Pain, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
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Deb P, Chini A, Guha P, Rishi A, Bhan A, Brady B, Perrotti LI, Mandal SS. Dynamic regulation of BDNF gene expression by estradiol and lncRNA HOTAIR. Gene 2024; 897:148055. [PMID: 38043834 DOI: 10.1016/j.gene.2023.148055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/05/2023]
Abstract
Brain derived neurotrophic factor (BDNF) is a major neurotransmitter that controls growth and maintenance of neurons and its misregulation is linked to neurodegeneration and human diseases. Estradiol (E2) is well-known to regulate the process of differentiation and plasticity of hippocampal neurons. Here we examined the mechanisms of BDNF gene regulation under basal conditions and under stimuli such as E2. Our results demonstrated that BDNF expression is induced by E2 in vitro in HT22 cells (hippocampal neuronal cells) and in vivo (in ovariectomized mouse brain under E2-treatment). Using chromatin immunoprecipitation assay, we demonstrated that estrogen receptors (ERα, ERβ) were enriched at the BDNF promoter in presence of E2. Additionally, ER-coregulators (e.g., CBP/p300, MLL3), histone acetylation, H3K4-trimethylation, and RNA polymerase II levels were also elevated at the BDNF promoter in an E2-dependent manner. Additionally, under the basal conditions (in the absence of E2), the long noncoding RNA HOTAIR and its interacting partners PRC2 and LSD1 complexes binds to the promoter of BDNF and represses its expression. HOTAIR knockdown -relieves the repression resulting in elevation of BDNF expression. Further, levels of HOTAIR-interacting partners, EZH2 and LSD1 were reduced at the BDNF promoter upon HOTAIR-knockdown revealing that HOTAIR plays a regulatory role in BDNF gene expression by modulating promoter histone modifications. Additionally, we showed that E2 induced-BDNF expression is mediated by the displacement of silencing factors, EZH2 and LSD1 at BDNF promoter and subsequent recruitment of active transcription machinery. These results reveal the mechanisms of BDNF gene regulation under the basal condition and in presence of a positive regulator such as E2 in neuronal cells.
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Affiliation(s)
- Paromita Deb
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Avisankar Chini
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Prarthana Guha
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Ashcharya Rishi
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Arunoday Bhan
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Blake Brady
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Linda I Perrotti
- Department of Psychology, The University of Texas at Arlington, Arlington, TX 76019, United States
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Lab, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, United States.
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Chen YN, Fu XR, Guo H, Fu XY, Shi KS, Gao T, Yu HQ. YY1-induced lncRNA00511 promotes melanoma progression via the miR-150-5p/ADAM19 axis. Am J Cancer Res 2024; 14:809-831. [PMID: 38455406 PMCID: PMC10915319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/07/2024] [Indexed: 03/09/2024] Open
Abstract
Increasing evidence indicates that long noncoding RNAs (lncRNAs) are therapeutic targets and key regulators of tumors development and progression, including melanoma. Long intergenic non-protein-coding RNA 511 (LINC00511) has been demonstrated as an oncogenic molecule in breast, stomach, colorectal, and lung cancers. However, the precise role and functional mechanisms of LINC00511 in melanoma remain unknown. This study confirmed that LINC00511 was highly expressed in melanoma cells (A375 and SK-Mel-28 cells) and tissues, knockdown of LINC00511 could inhibit melanoma cell migration and invasion, as well as the growth of subcutaneous tumor xenografts in vivo. By using Chromatin immunoprecipitation (ChIP) assay, it was demonstrated that the transcription factor Yin Yang 1 (YY1) is capable of binding to the LINC00511 promoter and enhancing its expression in cis. Further mechanistic investigation showed that LINC00511 was mainly enriched in the cytoplasm of melanoma cells and interacted directly with microRNA-150-5p (miR-150-5p). Consistently, the knockdown of miR-150-5p could recover the effects of LINC00511 knockdown on melanoma cells. Furthermore, ADAM metallopeptidase domain expression 19 (ADAM19) was identified as a downstream target of miR-150-5p, and overexpression of ADAM19 could promote melanoma cell proliferation. Rescue assays indicated that LINC00511 acted as a competing endogenous RNA (ceRNA) to sponge miR-150-5p and increase the expression of ADAM19, thereby activating the PI3K/AKT pathway. In summary, we identified LINC00511 as an oncogenic lncRNA in melanoma and defined the LINC00511/miR-150-5p/ADAM19 axis, which might be considered a potential therapeutic target and novel molecular mechanism the treatment of patients with melanoma.
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Affiliation(s)
- Ya-Ni Chen
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Xin-Rui Fu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Hua Guo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Xin-Yao Fu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Ke-Song Shi
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Tian Gao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
| | - Hai-Quan Yu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University Hohhot 010020, Inner Mongolia, China
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Zhu Y, Zhang C, Zhang C, Chen S, Jin Z. Silencing Lnc-HES1-10 Inhibits Osteosarcoma Cells Proliferation, Invasive Ability, and Metastasis. J Pediatr Hematol Oncol 2024; 46:15-20. [PMID: 37882055 PMCID: PMC10756700 DOI: 10.1097/mph.0000000000002770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 08/16/2023] [Indexed: 10/27/2023]
Abstract
BACKGROUND Long noncoding RNA (LncRNA) play a vital role in the development and pathophysiology of osteosarcoma (OS). However, the LncRNA activated by HES1-10 in OS has not been furthered investigated. This present study aims to show the possible function of Lnc-HES1-10 in OS. METHODS Cell proliferation in vitro were assessed by the MTT assay, whereas the migration and invasion abilities of OS cell lines were measured by wound-healing migration assay and transwell invasion assay, respectively. Quantitative reverse transcriptase polymerase chain reaction and western blot analysis was used to detected the expression level of HES1-10. RESULTS The present study demonstrated that the Lnc-HES1-10 is overexpressed in OS and associated with poor prognosis of patients. In addition, the results revealed that Lnc-HES1-10 is overexpressed in MG63 and 143B OS cell lines and promote proliferation on both cell lines in vitro. Furthermore, migration and invasion abilities of MG63 and 143B cells are suppressed after silencing Lnc-HES1-10. CONCLUSION Our finding demonstrates that HES1-10 plays a crucial role in regulating OS growth and metastasis.
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Li F, Wang Y, Wen M, Aizezi G, Yuan J, Zhou T, Shen G. NPHS2-6 drives cervical squamous cell carcinoma (CSCC) progression via hsa-miR-1323/SMC1B axis to activate PI3K-Akt pathway. Clin Transl Oncol 2024; 26:245-259. [PMID: 37322227 DOI: 10.1007/s12094-023-03248-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
PURPOSE A substantial amount of evidence demonstrates suggests that long non-coding RNAs (lncRNAs) play a key role in the progression of various malignancies, cervical squamous cell carcinoma (CSCC) included. In our study, we deeply investigated the role and molecular mechanism of lncRNA NPHS2-6 in CSCC. METHODS The expression level of gene and protein expression were measured by qRT-PCR and western blot. To test the cell proliferation and cell metastasis ability, we carried out the CCK-8 experiment, clone formation assay, transwell assay and wound healing, respectively. The interactivity among NPHS2-6, miR-1323 and SMC1B were co demonstrated using the bioinformatics tool, dual-luciferase reporter system, and RNA pulldown assay. The subcutaneous tumor model of nude mice was established to verify the results of previous studies at the in vivo. NPHS2-6 was upregulated in CSCC tissues and cells. RESULTS NPHS2-6 deficiency significantly inhibited CSCC cell growth and EMT in vitro. In addition, NPHS2-6 deficiency also inhibited the growth of CSCC xenograft tumors in mice in vivo. Importantly, NPHS2-6 was a competing endogenous RNA (ceRNA) to increases SMC1B levels by binding to miR-1323, leading to activate the PI3K/Akt pathway, thereby exacerbating tumorigenesis of CSCC. CONCLUSIONS In conclusion, NPHS2-6/miR-1323/SMC1B/PI3K/Akt signaling accelerates the progression of CSCC, providing a new direction for the treatment strategy of CSCC.
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Affiliation(s)
- Fen Li
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Yan Wang
- Key Laboratory of Oncology of Xinjiang Uyghur Autonomous Region, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, 830011, China
| | - Mengke Wen
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Gulibiya Aizezi
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Jinrui Yuan
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Tongjunnan Zhou
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China
| | - Guqun Shen
- The Second Department of Gynecology, Affiliated Tumor Hospital of Xinjiang Medical University, 789 Suzhou East Street, Urumqi, 830011, Xinjiang Province, China.
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Xiao L, Zhang Y, Luo Q, Guo C, Chen Z, Lai C. DHRS4-AS1 regulate gastric cancer apoptosis and cell proliferation by destabilizing DHX9 and inhibited the association between DHX9 and ILF3. Cancer Cell Int 2023; 23:304. [PMID: 38041141 PMCID: PMC10693172 DOI: 10.1186/s12935-023-03151-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 11/18/2023] [Indexed: 12/03/2023] Open
Abstract
Gastric cancer (GC) causes millions of cancer-related deaths due to anti-apoptosis and rapid proliferation. However, the molecular mechanisms underlying GC cell proliferation and anti-apoptosis remain unclear. The expression levels of DHRS4-AS1 in GC were analyzed based on GEO database and recruited GC patients in our institution. We found that DHRS4-AS1 was significantly downregulated in GC. The expression of DHRS4-AS1 in GC tissues showed a significant correlation with tumor size, advanced pathological stage, and vascular invasion. Moreover, DHRS4-AS1 levels in GC tissues were significantly associated with prognosis. DHRS4-AS1 markedly inhibited GC cell proliferation and promotes apoptosis in vitro and in vivo assays. Mechanically, We found that DHRS4-AS1 bound to pro-oncogenic DHX9 (DExH-box helicase 9) and recruit the E3 ligase MDM2 that contributed to DHX9 degradation. We also confirmed that DHRS4-AS1 inhibited DHX9-mediated cell proliferation and promotes apoptosis. Furthermore, we found DHX9 interact with ILF3 (Interleukin enhancer Binding Factor 3) and activate NF-kB Signaling in a ILF3-dependent Manner. Moreover, DHRS4-AS1 can also inhibit the association between DHX9 and ILF3 thereby interfered the activation of the signaling pathway. Our results reveal new insights into mechanisms underlying GC progression and indicate that LncRNA DHRS4-AS1 could be a future therapeutic target and a biomarker for GC diagnosis.
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Affiliation(s)
- Lei Xiao
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yang Zhang
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Qingqing Luo
- Department of Oncology, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, 410000, Hunan Province, China
| | - Cao Guo
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zihua Chen
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Chen Lai
- Department of General Surgery, Xiangya Hospital of Central South University, Xiangya Road No. 87, Kaifu District, Changsha, 410000, Hunan Province, China.
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumors, Xiangya Hospital of Central South University, Changsha, 410000, Hunan Province, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Zhao J, Li G, Ren Y, Zhang Z, Chen H, Zhang H, Zhao X, Li W, Jia Y, Guan X, Liu M. Ellagic acid inhibits human colon cancer HCT-116 cells by regulating long noncoding RNAs. Anticancer Drugs 2023; 34:1112-1121. [PMID: 36847079 PMCID: PMC10569677 DOI: 10.1097/cad.0000000000001513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 03/01/2023]
Abstract
The natural phenolic compound ellagic acid exerts anti-cancer effects, including activity against colorectal cancer (CRC). Previously, we reported that ellagic acid can inhibit the proliferation of CRC, and can induce cell cycle arrest and apoptosis. This study investigated ellagic acid-mediated anticancer effects using the human colon cancer HCT-116 cell line. After 72 h of ellagic acid treatment, a total of 206 long noncoding RNAs (lncRNAs) with differential expression greater than 1.5-fold were identified (115 down-regulated and 91 up-regulated). Furthermore, the co-expression network analysis of differentially expressed lncRNA and mRNA showed that differential expressed lncRNA might be the target of ellagic acid activity in inhibiting CRC.
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Affiliation(s)
- Jinlu Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Guodong Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Yi Ren
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Zhicheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Hongsheng Chen
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Haopeng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Xingyu Zhao
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Wang Li
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Yucheng Jia
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Xue Guan
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
| | - Ming Liu
- Department of General Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, PR China
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12
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Li H, Jiang H, Huang Z, Chen Z, Chen N. Construction and validation of cuproptosis-related lncRNA prediction signature for bladder cancer and immune infiltration analysis. Aging (Albany NY) 2023; 15:8325-8344. [PMID: 37616061 PMCID: PMC10496989 DOI: 10.18632/aging.204972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023]
Abstract
Bladder cancer (BC) is a common urologic tumor with a high recurrence rate. Cuproptosis and long noncoding RNAs (lncRNAs) have demonstrated essential roles in the tumorigenesis of many malignancies. Nevertheless, the prognostic value of cuproptosis-related lncRNA (CRLs) in BC is still unclear. The public data used for this study were acquired from the Cancer Genome Atlas database. A comprehensive exploration of the expression profile, mutation, co-expression, and enrichment analyses of cuproptosis-related genes was performed. A total of 466 CRLs were identified using Pearson's correlation analysis. 16 prognostic CRLs were then retained by univariate Cox regression. Unsupervised clustering divided the patients into two clusters with diverse survival outcomes. The signature consists of 7 CRLs was constructed using the least absolute shrinkage and selection operator (LASSO) Cox regression analyses. Survival curves and receiver operating characteristics showed the prognostic signature possessed good predictive value, which was validated in the testing and entire sets. The reliability and stability of our signature were further confirmed by stratified analysis. Additionally, the signature-based risk score was confirmed as an independent prognostic factor. Gene set enrichment analysis showed molecular alteration in the high-risk group was closely associated with cancer. We then developed the clinical nomogram using independent prognostic indicators. Notably, the infiltration of immune cells and expression of immune checkpoints were higher in the high-risk group, suggesting that they may benefit more from immunotherapy. In summary, the prognostic signature might effectively predict the prognosis and provide new insight into the clinical treatment of BC patients.
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Affiliation(s)
- Hanrong Li
- Department of Extracorporeal Shock Wave Lithotripsy, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Huiming Jiang
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Zhicheng Huang
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Zhilin Chen
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
| | - Nanhui Chen
- Department of Urology, Meizhou People’s Hospital (Huangtang Hospital), Meizhou 514031, China
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13
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Jin J, Cong J, Lei S, Zhang Q, Zhong X, Su Y, Lu M, Ma Y, Li Z, Wang L, Zhu N, Yang J. Cracking the code: Deciphering the role of the tumor microenvironment in osteosarcoma metastasis. Int Immunopharmacol 2023; 121:110422. [PMID: 37302370 DOI: 10.1016/j.intimp.2023.110422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/13/2023]
Abstract
Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. It is characterized by a rapid progression, poor prognosis, and early pulmonary metastasis. Over the past 30 years, approximately 85% of patients with osteosarcoma have experienced metastasis. The five-year survival of patients with lung metastasis during the early stages of treatment is less than 20%. The tumor microenvironment (TME) not only provides conditions for tumor cell growth but also releases a variety of substances that can promote the metastasis of tumor cells to other tissues and organs. Currently, there is limited research on the role of the TME in osteosarcoma metastasis. Therefore, to explore methods for regulating osteosarcoma metastasis, further investigations must be conducted from the perspective of the TME. This will help to identify new potential biomarkers for predicting osteosarcoma metastasis and assist in the discovery of new drugs that target regulatory mechanisms for clinical diagnosis and treatment. This paper reviews the research progress on the mechanism of osteosarcoma metastasis based on TME theory, which will provide guidance for the clinical treatment of osteosarcoma.
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Affiliation(s)
- Jiamin Jin
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guangxi, Guilin 541001, China; Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Jiacheng Cong
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Shangbo Lei
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Qiujin Zhang
- Department of Immunology, Guilin Medical University, Guilin 541199, China
| | - Xinyi Zhong
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Yingying Su
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Mingchuan Lu
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Yifen Ma
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Zihe Li
- Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China
| | - Liyan Wang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guangxi, Guilin 541001, China
| | - Ningxia Zhu
- Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China.
| | - Jinfeng Yang
- Department of Gastroenterology, Affiliated Hospital of Guilin Medical University, Guangxi, Guilin 541001, China; Department of Immunology, Guilin Medical University, Guilin 541199, China; Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin 541199, China.
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14
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Hosseini SA, Haddadi MH, Fathizadeh H, Nemati F, Aznaveh HM, Taraj F, Aghabozorgizadeh A, Gandomkar G, Bazazzadeh E. Long non-coding RNAs and gastric cancer: An update of potential biomarkers and therapeutic applications. Biomed Pharmacother 2023; 163:114407. [PMID: 37100014 DOI: 10.1016/j.biopha.2023.114407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/12/2023] [Accepted: 02/15/2023] [Indexed: 04/28/2023] Open
Abstract
The frequent metastasis of gastric cancer (GC) complicates the cure and therefore the development of effective diagnostic and therapeutic approaches is urgently necessary. In recent years, lncRNA has emerged as a drug target in the treatment of GC, particularly in the areas of cancer immunity, cancer metabolism, and cancer metastasis. This has led to the demonstration of the importance of these RNAs as prognostic, diagnostic and therapeutic agents. In this review, we provide an overview of the biological activities of lncRNAs in GC development and update the latest pathological activities, prognostic and diagnostic strategies, and therapeutic options for GC-related lncRNAs.
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Affiliation(s)
- Sayedeh Azimeh Hosseini
- Department of Medical Biotechnology, School of Advanced Technology, Shahrekord University of Medical Sciences, Shahrekord, Iran; Student Research Committee, Shahrekord University of Medical Sciences, Shahrekord, Iran; USERN office, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | | | - Hadis Fathizadeh
- Student Research Committee, Sirjan School of Medical Sciences, Sirjan, Iran; Department of Laboratory sciences, Sirjan School of Medical Sciences, Sirjan, Iran
| | - Foroogh Nemati
- Department of Microbiology, Kashan University of Medical Sciences, Kashan, Iran
| | - Hooman Mahmoudi Aznaveh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
| | - Farima Taraj
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - AmirArsalan Aghabozorgizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Golmaryam Gandomkar
- Department of Animal Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Elaheh Bazazzadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, P.O. Box: 14115-154, Tehran, Iran
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15
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Zhang Y, Hu X, Liu S, Zhou M, Wang C, Cao H. Identification and analysis of long non-coding RNAs that are involved in response to GCRV infection in grass carp (Ctenopharyngodon idella). FISH & SHELLFISH IMMUNOLOGY 2023; 134:108623. [PMID: 36809843 DOI: 10.1016/j.fsi.2023.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in many biological processes including the immune response against virus infection. However, their roles in grass carp reovirus (GCRV) pathogenicity are largely unknown. In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in GCRV-infected and mock-infected grass carp kidney (CIK) cells. Our results showed that 37 lncRNAs and 1039 mRNA transcripts exhibited differential expression in CIK cells after GCRV infection compared with the mock infection. Functional analysis through the gene ontology and Kyoto Encyclopedia of Genes and Genomes databases (KEGG) indicated that target genes of the differentially expressed lncRNAs were mainly enriched in the biological processes - biological regulation, cellular process, metabolic process and regulation of the biological process, such as MAPK signaling pathway and Notch signaling. Furthermore, we observed that the lncRNA3076 (ON693852) was markedly upregulated after the GCRV infection. In addition, silencing lncRNA3076 decreased the GCRV replication, which indicates that it might play an important role in the replication of GCRV.
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Affiliation(s)
- Yexuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xudong Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuai Liu
- College of Fishery and Life Sciences, Dalian Ocean University, Dalian, 116023, China
| | - Man Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunling Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong Cao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Chen W, Qian W, Nie J, Dai M. A study of the prognostic value of long non-coding RNA CASC15 in human solid tumors utilizing The Cancer Genome Atlas (TCGA) datasets and a meta-analysis. Clin Exp Med 2023; 23:65-78. [PMID: 35103883 DOI: 10.1007/s10238-021-00789-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/17/2021] [Indexed: 12/01/2022]
Abstract
BACKGROUND AND AIMS Several malignant solid tumors have been reported to have an abnormal expression of the long non-coding RNA CASC15 (lncRNA CASC15). However, the clinicopathologic and prognostic importance of CASC15 in solid tumors are unknown. As a result, we examined the interrelationship between CASC15, overall survival length, and clinicopathological attributes of cancers affecting humans by analyzing various studies and The Cancer Genome Atlas (TCGA) data related to CASC15 expression. METHODS Web of Science, PubMed, Cochrane Library, Embase, Chinese WanFang, and Chinese CNKI databases were used to conduct a literature search. Hazard ratios (HRs) and Pooled odds ratios (ORs) were calculated taking 95% confidence intervals (CIs). The results of the current meta-analysis were further validated using TCGA datasets. RESULTS A total of 12 eligible studies enrolling 767 patients were included in this meta-analysis. Findings of the analysis showed that CASC15 expression had a significant relation to the metastasis of lymph node (OR = 3.30, 95%CI = 1.88-5.81, p < 0.001), distant metastasis (OR = 2.64, 95%CI = 1.24-5.63, p = 0.012), and high TNM/clinical stage (OR = 2.67, 95%CI = 1.34-5.32, p = 0.005). Additionally, we found that a poor outcome for overall survival (OS) was predicted by an elevation in CASC15 expression (HR = 2.01, 95%CI = 1.71-2.36, p < 0.001). Further investigation of the TCGA dataset revealed that CASC15 had abnormal expression in many cancers, which at least partially validated the findings of the current meta-analysis. CONCLUSIONS According to the latest meta-analysis and systematic review, high expression levels of CASC15 are associated with poor survival outcomes for solid tumor patients, and the use of CASC15 as a solid tumor prognostic predictor has a solid theoretical foundation.
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Affiliation(s)
- Weiwei Chen
- Department of Gastroenterology, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, People's Republic of China.
| | - Wenqi Qian
- Department of Pharmacy, People's Hospital of Qiandongnan and Dong Autonomous Prefecture, Kaili, People's Republic of China
| | - Jun Nie
- Department of Gastroenterology, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, People's Republic of China
| | - Mintao Dai
- Department of Gastroenterology, The First People's Hospital of Zunyi (The Third Affiliated Hospital of Zunyi Medical University), Zunyi, People's Republic of China
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17
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Patiyal S, Dhall A, Bajaj K, Sahu H, Raghava GPS. Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile. Brief Bioinform 2023; 24:6901899. [PMID: 36516298 DOI: 10.1093/bib/bbac538] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/28/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022] Open
Abstract
This paper describes a method Pprint2, which is an improved version of Pprint developed for predicting RNA-interacting residues in a protein. Training and independent/validation datasets used in this study comprises of 545 and 161 non-redundant RNA-binding proteins, respectively. All models were trained on training dataset and evaluated on the validation dataset. The preliminary analysis reveals that positively charged amino acids such as H, R and K, are more prominent in the RNA-interacting residues. Initially, machine learning based models have been developed using binary profile and obtain maximum area under curve (AUC) 0.68 on validation dataset. The performance of this model improved significantly from AUC 0.68 to 0.76, when evolutionary profile is used instead of binary profile. The performance of our evolutionary profile-based model improved further from AUC 0.76 to 0.82, when convolutional neural network has been used for developing model. Our final model based on convolutional neural network using evolutionary information achieved AUC 0.82 with Matthews correlation coefficient of 0.49 on the validation dataset. Our best model outperforms existing methods when evaluated on the independent/validation dataset. A user-friendly standalone software and web-based server named 'Pprint2' has been developed for predicting RNA-interacting residues (https://webs.iiitd.edu.in/raghava/pprint2 and https://github.com/raghavagps/pprint2).
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Affiliation(s)
- Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Khushboo Bajaj
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Harshita Sahu
- Department of Computer Science and Engineering, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
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Yan X, Jia H, Zhao J. LncRNA MEG3 attenuates the malignancy of retinoblastoma cells through inactivating PI3K /Akt/mTOR signaling pathway. Exp Eye Res 2023; 226:109340. [PMID: 36476400 DOI: 10.1016/j.exer.2022.109340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/19/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Retinoblastoma (RB) is the most common neoplasm found in the eye of children. There are increasing interests to develop targeted gene therapy for this disease. This study was performed to investigate the impact of long non-coding RNA (lncRNA) MEG3 on the biological features of RB cells. Vector overexpressing MEG3 was constructed and introduced into two RB cell lines. Transfected RB cells were assessed for proliferation, apoptosis, migration ability, expression levels of important genes in the PI3K/Akt/mTOR signaling pathway using qRT-PCR and Western blot analysis. Xenograft mouse models were constructed to determine the tumorigenicity of RB cells overexpressing MEG3. MEG3 mRNA level was significantly lower in RB cells than in non-cancer cells (p < 0.01). Overexpressing MEG3 resulted in significant reduction in cell proliferation (p < 0.05), migration (p < 0.01) and significant increase in apoptosis (p < 0.01). After overexpressing MEG3, p-PI3K, p-Akt and p-mTOR levels were significantly downregulated (p < 0.01). Furthermore, in the xenograft model, RB cells overexpressing MEG3 generated significantly smaller tumors as compared to RB cells that did not overexpress MEG3 (p < 0.05). Our data suggest that MEG3 increases apoptosis and reduces tumorigenicity of RB cells through inactivating the PI3K/Akt/mTOR pathway. Therefore, MEG3 could be further investigated as a potential new therapeutic agent and target for RB therapy.
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Affiliation(s)
- Xiaoxiao Yan
- Department of Ophthalmology, Handan Central Hospital, Handan, China
| | - Haibo Jia
- Department of Neurosurgery, Handan Central Hospital, Handan, China.
| | - Junbo Zhao
- Department of Ophthalmology, Handan Central Hospital, Handan, China
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Deng M, Yuan H, Peng H, Liu S, Xiao X, Wang Z, Zhang G, Xiao H. LINC00461 Knockdown Enhances the Effect of Ixazomib in Multiple Myeloma Cells. Curr Cancer Drug Targets 2023; 23:643-652. [PMID: 36927430 DOI: 10.2174/1568009623666230316152713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/23/2022] [Accepted: 01/11/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND LINC00461 has been implicated to be involved in several types of cancer while its roles in multiple myeloma remain unclear. Our study aims to investigate the roles of LINC00461 in multiple myeloma and explore its effects on ixazomib therapy. METHODS LINC00461 and small nuclear ribonucleoprotein polypeptide (SNRP) B2 knockdown stable cell lines were constructed. Cell viability assays including MTT, cell number counting, and colony formation were performed. RNA-pull down and immunoblotting assays were conducted to determine the intramolecular interactions. qRT-PCR and western blotting were conducted to determine the levels of target genes. Kaplan-Meier analysis was used to evaluate overall survival rates. RESULTS Knockdown of LINC00461 or SNRPB2 enhanced ixazomib's cytotoxicity, as well as affected its regulatory effects on cell apoptosis and cell cycle distribution. Further results showed that LINC00461 knockdown reduced the expression levels of SNRPB2 by their interactions. Additionally, a positive correlation between LINC00461 and SNRPB2 was found in patients with multiple myeloma. Low expression of SNRPB2 was associated with a high survival rate in patients with multiple myeloma. CONCLUSION Knockdown of LINC00461 enhanced the therapeutic effects of ixazomib against multiple myeloma in part by the regulation of SNRPB2.
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Affiliation(s)
- Mingyang Deng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Huan Yuan
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Hongling Peng
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Sufang Liu
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Xiang Xiao
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zhihua Wang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Guangsen Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Han Xiao
- Department of Neurology, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
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Siri G, Yazdani O, Esbati R, Akhavanfar R, Asadi F, Adili A, Ebrahimzadeh F, Hosseini SME. A comprehensive review of the role of lncRNAs in gastric cancer (GC) pathogenesis, immune regulation, and their clinical applications. Pathol Res Pract 2023; 241:154221. [PMID: 36563559 DOI: 10.1016/j.prp.2022.154221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Gastric cancer (GC) is the fifth most common malignant tumor and the third leading cause of cancer-related deaths worldwide. Although numerous studies have been conducted on advanced GC, the molecular mechanisms behind it remain obscure. Long non-coding RNAs (lncRNAs) are a family of RNA transcripts capable of regulating target genes at transcriptional, post-transcriptional, and translational stages. They do this by modifying mRNAs, miRNAs, and proteins. These RNAs are critical regulators of many biological processes, including gene epigenetics, transcription, and post-transcriptional levels. This article highlights recent results on lncRNAs involved in drug resistance, proliferation, migration, angiogenesis, apoptosis, autophagy, and immune response in GC. The potential clinical implications of lncRNAs as biomarkers and therapeutic targets in GC are also discussed.
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Affiliation(s)
- Goli Siri
- Department of Internal Medicine, Amir Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Omid Yazdani
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Romina Esbati
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roozbeh Akhavanfar
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Asadi
- Department of Genetics, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Ali Adili
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South Florida, Tampa, FL, USA; Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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21
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Xu G, Liu J, He J, He H, Su X, Gui Q. LOC554202 contributes to chordoma progression by sponging miR-377-3p and up-regulating SMAD3. Anticancer Drugs 2023; 34:15-28. [PMID: 36206143 PMCID: PMC9760475 DOI: 10.1097/cad.0000000000001327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 12/31/2022]
Abstract
Chordoma is a rare malignant bone tumor originating from the remnants of the notochord. Here, the role of long noncoding LOC554202 in chordoma progression and its associated mechanism were explored. Cell proliferation was analyzed by 3-(4, 5-dimethylthiazol-2-yl)-2, 5 diphenyltetrazolium bromide and colony formation assays. Flow cytometry was conducted to analyze cell apoptosis rate. The migration and invasion of chordoma cells were analyzed by transwell migration and invasion assays and wound healing assays. A xenograft tumor model was established in nude mice to explore the role of LOC554202 in regulating tumor growth in vivo . The interaction between microRNA-377-3p (miR-377-3p) and LOC554202 or sekelsky mothers against d PP (SMAD) family member 3 (SMAD3) was verified by dual-luciferase reporter and RNA immunoprecipitation assays. The glycolytic rate of chordoma cells was analyzed using glucose assay kit, lactic acid kit and ApoSENSOR ADP/ATP ratio assay kit. LOC554202 expression was upregulated in chordoma tissues and cell lines. LOC554202 silencing suppressed the proliferation, migration and invasion and induced the apoptosis of chordoma cells. LOC554202 knockdown restrained xenograft tumor growth in vivo . miR-377-3p was confirmed as a target of LOC554202, and miR-377-3p silencing largely overturned LOC554202 knockdown-mediated anti-tumor effects in chordoma cells. miR-377-3p interacted with the 3' untranslated region (3'UTR) of SMAD3 and miR-377-3p overexpression-mediated antitumor effects in chordoma cells were largely attenuated by SMAD3 overexpression. LOC554202 could positively regulate SMAD3 expression by sponging miR-377-3p in chordoma cells. LOC554202 contributed to the glycolysis of chordoma cells by targeting binding to miR-377-3p/SMAD3 axis. LOC554202 facilitated the proliferation, migration, invasion and glycolysis and inhibited the apoptosis of chordoma cells by mediating miR-377-3p/SMAD3 axis.
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Affiliation(s)
- Guang Xu
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jingnan Liu
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jun He
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Haibo He
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Xiaotao Su
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Qianhuan Gui
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
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Lv Y, Wang Y, Zhang Z. Potentials of lncRNA-miRNA-mRNA networks as biomarkers for laryngeal squamous cell carcinoma. Hum Cell 2023; 36:76-97. [PMID: 36181662 DOI: 10.1007/s13577-022-00799-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/26/2022] [Indexed: 01/11/2023]
Abstract
Chemoresistance, radioresistance, and facile spreading of laryngeal squamous cell carcinoma (LSCC) make the practically clinical treatment invalid. Such dismal outcome mainly originates from the lack of effective biomarkers which are highly desirable to understand the pathogenesis of LSCC, and strives to find promising novel biomarkers to improve early screening, effective treatment, and prognosis evaluation in LSCC. Recently, long non-coding RNAs (lncRNAs), a kind of non-coding RNAs longer than 200 nucleotides, can participate in the process of tumorigenesis and progression through many regulatory modalities, such as epigenetic transcriptional regulation and post-transcriptional regulation. Meanwhile, microRNAs (miRNAs, miRs), essentially involved in the post-transcriptional regulation of gene expression, are aberrantly expressed in cancer-related genomic regions or susceptible sites. An increasing number of studies have shown that lncRNAs are important regulators of miRNAs expression in LSCC, and that miRNAs can also target to regulate the expression of lncRNAs, and they can target to regulate downstream messenger RNAs (mRNAs) transcriptionally or post-transcriptionally, thereby affecting various physiopathological processes of LSCC. Complex cross-regulatory networks existing among lncRNAs, miRNAs, and mRNAs can regulate the tumorigenesis and development of LSCC. Such networks may become promising biomarkers and potential therapeutic targets in the research field of LSCC. In this review, we mainly summarize the latest research progress on the regulatory relationships among lncRNAs, miRNAs, and downstream mRNAs, and highlight the potential applications of lncRNA-miRNA-mRNA regulatory networks as biomarkers for the early diagnosis, epithelial-mesenchymal transition (EMT) process, chemoresistance, radioresistance, and prognosis of LSCC, aiming to provide important clues for understanding the pathogenesis of LSCC and developing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Yan Lv
- The Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
| | - Yanhua Wang
- The Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China. .,Department of Morphology, Medical College of China Three Gorges University, Life Science Building, No.8 Daxue Road, Yichang, 443002, China.
| | - Zhikai Zhang
- The Third-Grade Pharmacological Laboratory on Chinese Medicine Approved by State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
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Lv Y, Yin W, Zhang Z. Non-coding RNAs as potential biomarkers of gallbladder cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2022; 25:1489-1511. [PMID: 36576705 DOI: 10.1007/s12094-022-03056-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
Gallbladder cancer (GBC) performs strongly invasive and poor prognosis, and adenocarcinoma is the most common histological type in it. Statistically, the 5-year survival rate of patients with advanced GBC is less than 5%. Such dismal outcome might be caused by chemotherapy resistance and native biology of tumor cells, regardless of emerging therapeutic strategies. Early diagnosis, depending on biomarkers, receptors and secretive proteins, is more important than clinical therapy, guiding the pathologic stage of cancer and the choice of medication. Therefore, it is in urgent need to understand the specific pathogenesis of GBC and strive to find promising novel biomarkers for early screening in GBC. Non-coding RNAs (ncRNAs), especially microRNAs (miRNAs, miRs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are confirmed to participate in and regulate the occurrence and development of GBC. Exceptionally, lncRNAs and circRNAs could act as competing endogenous RNAs (ceRNAs) containing binding sites for miRNAs and crosstalk with miRNAs to target regulatory downstream protein-coding messenger RNAs (mRNAs), thus affecting the expression levels of specific proteins to participate in and regulate the development and progression of GBC. It follows that ncRNAs may become promising biomarkers and potential therapeutic targets for GBC. In this review, we mainly summarize the recent research progress of miRNAs and lncRNAs in regulating the development and progression of GBC, chemoresistance, and predicting the prognosis of patients, and highlight the potential applications of the lncRNA/circRNA-miRNA-mRNA cross-regulatory networks in early diagnosis, chemoresistance, and prognostic evaluation, aiming to better understand the pathogenesis of GBC and develop new diagnostic and therapeutic strategies.
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Affiliation(s)
- Yan Lv
- The Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China.
- College of Basic Medical Science, China Three Gorges University, Life Science Building, No.8 Daxue Road, Yichang, 443002, China.
| | - Wanyue Yin
- College of Basic Medical Science, China Three Gorges University, Life Science Building, No.8 Daxue Road, Yichang, 443002, China
| | - Zhikai Zhang
- The Third-Grade Pharmacological Laboratory On Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
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Ahangar Davoodi N, Najafi S, Naderi Ghale-Noie Z, Piranviseh A, Mollazadeh S, Ahmadi Asouri S, Asemi Z, Morshedi M, Tamehri Zadeh SS, Hamblin MR, Sheida A, Mirzaei H. Role of non-coding RNAs and exosomal non-coding RNAs in retinoblastoma progression. Front Cell Dev Biol 2022; 10:1065837. [PMID: 36619866 PMCID: PMC9816416 DOI: 10.3389/fcell.2022.1065837] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Retinoblastoma (RB) is a rare aggressive intraocular malignancy of childhood that has the potential to affect vision, and can even be fatal in some children. While the tumor can be controlled efficiently at early stages, metastatic tumors lead to high mortality. Non-coding RNAs (ncRNAs) are implicated in a number of physiological cellular process, including differentiation, proliferation, migration, and invasion, The deregulation of ncRNAs is correlated with several diseases, particularly cancer. ncRNAs are categorized into two main groups based on their length, i.e. short and long ncRNAs. Moreover, ncRNA deregulation has been demonstrated to play a role in the pathogenesis and development of RB. Several ncRNAs, such as miR-491-3p, miR-613,and SUSD2 have been found to act as tumor suppressor genes in RB, but other ncRNAs, such as circ-E2F3, NEAT1, and TUG1 act as tumor promoter genes. Understanding the regulatory mechanisms of ncRNAs can provide new opportunities for RB therapy. In the present review, we discuss the functional roles of the most important ncRNAs in RB, their interaction with the genes responsible for RB initiation and progression, and possible future clinical applications as diagnostic and prognostic tools or as therapeutic targets.
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Affiliation(s)
- Nasrin Ahangar Davoodi
- Eye Research Center, Rassoul Akram Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zari Naderi Ghale-Noie
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ashkan Piranviseh
- Brain and Spinal Cord Injury Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Mollazadeh
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Sahar Ahmadi Asouri
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammadamin Morshedi
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | | | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Amirhossein Sheida
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran,School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Amirhossein Sheida, ; Hamed Mirzaei, ,
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Abushouk AI, Kattan SW, Ahmedah HT, Baothman E, Shaheen S, Toraih EA, Fawzy MS. Expression of oncolong noncoding RNA taurine-upregulated gene-1 in colon cancer: A clinical study supported by in silico analysis. J Cancer Res Ther 2022; 18:S374-S382. [PMID: 36510991 DOI: 10.4103/jcrt.jcrt_484_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Context Recent studies confirmed that dysregulation of long noncoding RNAs (lncRNAs) is a potential contributor to the development and progression of colon cancer. However, the prognostic value of these RNA molecules remains controversial. Aims This study aimed to investigate the expression of taurine-upregulated gene-1 (TUG1) lncRNA in colon cancer and its clinical implications. Subjects and Methods A retrospective study on 47 formalin-fixed, paraffin-embedded samples of surgically resected primary colon cancer specimens was done. Total RNA purified from the colon cancer samples and noncancer adjacent tissue sections was quantified by real-time reverse transcription-polymerase chain reaction (qRT-PCR) to assess TUG1 relative expression levels normalized to GAPDH endogenous control. Also, in silico data analysis was applied. Statistical Analysis Used The relative expression levels were calculated using the LIVAK method. The survival rates were assessed using the Kaplan-Meier curves and the Cox proportional model. P < 0.05 was considered statistically significant. Results TUG1expression in the colon cancer specimens was significantly overexpressed (median = 21.50, interquartile range [IQR]: 7.0-209.2; P = 0.001) relative to the noncancerous tissues. In silico analysis confirmed TUG1 upregulation in colon carcinoma (median = 13.92, IQR: 13.5-1432). There were no significant associations between TUG1 expression and clinicopathological characteristics, such as the site, grade, stage, histopathological type, or the rates of lymphovascular invasion and relapse. Similarly, Kaplan-Meir and Cox multivariate regression analyses showed that TUG1 expression could not predict the overall survival and progression-free survival in colon cancer patients of our population. Conclusions This study confirms the overexpression of TUG1 lncRNA in colon cancer tissues. Larger sample size is warranted to further elucidate the specific role of TUG1 in colon cancer.
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Affiliation(s)
| | - Shahad W Kattan
- Department of Medical Laboratory, College of Applied Medical Sciences, Taibah University, Yanbu, Saudi Arabia
| | - Hanadi T Ahmedah
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Rabegh, Saudi Arabia
| | - Eshrag Baothman
- Department of Medicine, Batterjee Medical Technology College, Jeddah, Saudi Arabia
| | - Sameerah Shaheen
- Anatomy Department and Stem Cell Unit, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Eman A Toraih
- Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, USA; Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Manal Said Fawzy
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt; Department of Biochemistry, Faculty of Medicine, Northern Border University, Saudi Arabia
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Ghafouri-Fard S, Safarzadeh A, Hussen BM, Taheri M, Rashnoo F. A concise review on the role of LINC00324 in different cancers. Pathol Res Pract 2022; 240:154192. [DOI: 10.1016/j.prp.2022.154192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022]
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Shi C, Ren S, Zhao X, Li Q. lncRNA MALAT1 regulates the resistance of breast cancer cells to paclitaxel via the miR-497-5p/ SHOC2 axis. Pharmacogenomics 2022; 23:973-985. [PMID: 36420706 DOI: 10.2217/pgs-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Aim: To explore the roles of lncRNA MALAT1 and SHOC2 in breast cancer, and the potential connections to chemotherapy resistance in breast cancer. Materials & methods: Paclitaxel-resistant breast cancer cells were induced by gradually increasing intermittent doses. Bioinformatic analyses were performed to predict the regulated miRNAs of MALAT1. Results: High expressions of MALAT1 and SHOC2 contribute to paclitaxel resistance in breast cancer cells. MALAT1 sponges miR-497-5p enhance SHOC2 expression in paclitaxel-resistant breast cancer cells and contribute to paclitaxel resistance in breast cancer cells. Conclusion: Patients with high expression of MALAT1 and SHOC2 have a poorer response to paclitaxel. Upregulation of miR-497-5p could improve the treatment response to paclitaxel in patients with breast cancer by inhibiting MALAT1 and SHOC2.
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Affiliation(s)
- Chang Shi
- The Fourth Department of General Surgery, the Second Hospital of Hebei Medical University
| | - Shuangjie Ren
- Department of Traditional Chinese Medicine Surgery, the Second Hospital of Hebei Medical University
| | - Xiaodong Zhao
- The Fourth Department of General Surgery, the Second Hospital of Hebei Medical University
| | - Qinghuai Li
- The Sixth Department of General Surgery, the Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, 050000, China
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Jia Y, Yan Q, Zheng Y, Li L, Zhang B, Chang Z, Wang Z, Tang H, Qin Y, Guan XY. Long non-coding RNA NEAT1 mediated RPRD1B stability facilitates fatty acid metabolism and lymph node metastasis via c-Jun/c-Fos/SREBP1 axis in gastric cancer. J Exp Clin Cancer Res 2022; 41:287. [PMID: 36171622 PMCID: PMC9520879 DOI: 10.1186/s13046-022-02449-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background Lymph node metastasis is one of most common determinants of the stage and prognosis of gastric cancer (GC). However, the key molecular events and mechanisms mediating lymph node metastasis remain elusive. Methods RNA sequencing was used to identify driver genes responsible for lymph node metastasis in four cases of gastric primary tumors, metastatic lesions of lymph nodes and matched normal gastric epithelial tissue. qRT–PCR and IHC were applied to examine RPRD1B expression. Metastatic functions were evaluated in vitro and in vivo. RNA-seq was used to identify target genes. ChIP, EMSA and dual luciferase reporter assays were conducted to identify the binding sites of target genes. Co-IP, RIP, MeRIP, RNA-FISH and ubiquitin assays were applied to explore the underlying mechanisms. Results The top 8 target genes (RPRD1B, MAP4K4, MCM2, TOPBP1, FRMD8, KBTBD2, ADAM10 and CXCR4) that were significantly upregulated in metastatic lymph nodes of individuals with GC were screened. The transcriptional cofactor RPRD1B (regulation of nuclear pre-mRNA domain containing 1B) was selected for further characterization. The clinical analysis showed that RPRD1B was significantly overexpressed in metastatic lymph nodes and associated with poor outcomes in patients with GC. The Mettl3-induced m6A modification was involved in the upregulation of RPRD1B. Functionally, RPRD1B promoted lymph node metastasis capabilities in vitro and in vivo. Mechanistic studies indicated that RPRD1B increased fatty acid uptake and synthesis by transcriptionally upregulating c-Jun/c-Fos and activating the c-Jun/c-Fos/SREBP1 axis. In addition, NEAT1 was upregulated significantly by c-Jun/c-Fos in RPRD1B-overexpressing cells. NEAT1, in turn, increased the stability of the RPRD1B mRNA by recruiting the m6A “reader” protein hnRNPA2B1 and reduced the degradation of the RPRD1B protein by inhibiting TRIM25-mediated ubiquitination. Notably, this functional circuitry was disrupted by an inhibitor of c-Jun/c-Fos/AP1 proteins (SR11302) and small interfering RNAs targeting NEAT1, leading to a preferential impairment of lymph node metastasis. Conclusions Based on these findings, RPRD1B facilitated FA metabolism and assisted primary tumor implantation in lymph nodes via the c-Jun/c-Fos/SREBP1 axis, which was enhanced by a NEAT1-mediated positive feedback loop, serving as a potential therapeutic target for GC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02449-4.
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Mokhtari M. A review on the role of LINC01133 in cancers. Cancer Cell Int 2022; 22:270. [PMID: 36042493 PMCID: PMC9429693 DOI: 10.1186/s12935-022-02690-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Long Intergenic Non-Protein Coding RNA 1133 (LINC01133) is a long non-coding RNA (lncRNA) which interacts with miR-106a-3p, miR-576-5p, miR-495-3p, miR-205, miR-199a-5p, miR-4784, miR-30a-5p, miR-199a, miR-30b-5p, miR-216a -5p and miR-422a, thus increasing expression of mRNA targets of these miRNAs. LINC01133 can affect cancer metastasis through regulation of epithelial-mesenchymal transition program. Dysregulation of this lncRNA has been repeatedly detected in the process of tumorigenesis. In this review, we summarize the results of various studies that reported dysregulation of LINC01133 in different samples and described the role of this lncRNA as a marker for these disorders.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany. .,Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Mokhtari
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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lncRNA MEG3 Inhibits the Proliferation and Growth of Glioma Cells by Downregulating Bcl-xL in the PI3K/Akt/NF-κB Signal Pathway. BIOMED RESEARCH INTERNATIONAL 2022; 2022:3729069. [PMID: 35860793 PMCID: PMC9293524 DOI: 10.1155/2022/3729069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/24/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022]
Abstract
This study was conducted to investigate the impact and mechanisms of lncRNA MEG3 on glioma cells. lncRNA MEG3 was lowly expressed in glioma cells as compared to noncancer cells. Overexpression of MEG3 significantly downregulated the expression of Bcl-xL, slightly upregulated the expression of NF-κB p65 and IκBα, and reduced the proliferation of glioma cells with increased apoptosis and the migration and invasion ability. Subsequently, glioma cells overexpressing MEG3 had less tumorgenicity in xenograft mouse models. It is likely that MEG3 induces apoptosis in glioma cells via downregulating the Bcl-xL gene in the PI3K/Akt/NF-κB signal pathway to reduce the development of glioma.
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Wanowska E, Samorowska K, Szcześniak MW. Emerging Roles of Long Noncoding RNAs in Breast Cancer Epigenetics and Epitranscriptomics. Front Cell Dev Biol 2022; 10:922351. [PMID: 35865634 PMCID: PMC9294602 DOI: 10.3389/fcell.2022.922351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Breast carcinogenesis is a multistep process that involves both genetic and epigenetic changes. Epigenetics refers to reversible changes in gene expression that are not accompanied by changes in gene sequence. In breast cancer (BC), dysregulated epigenetic changes, such as DNA methylation and histone modifications, are accompanied by epitranscriptomic changes, in particular adenine to inosine modifications within RNA molecules. Factors that trigger these phenomena are largely unknown, but there is evidence for widespread participation of long noncoding RNAs (lncRNAs) that already have been linked to virtually any aspect of BC biology, making them promising biomarkers and therapeutic targets in BC patients. Here, we provide a systematic review of known and possible roles of lncRNAs in epigenetic and epitranscriptomic processes, along with methods and tools to study them, followed by a brief overview of current challenges regarding the use of lncRNAs in medical applications.
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Affiliation(s)
- Elżbieta Wanowska
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
| | - Klaudia Samorowska
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Michał Wojciech Szcześniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
- *Correspondence: Elżbieta Wanowska, ; Michał Wojciech Szcześniak,
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Ousati Ashtiani Z, Abbasi S, Pourmand G, Ghafouri-Fard S. Overexpression of long intergenic noncoding RNAs in bladder cancer: A new insight to cancer diagnosis. Pathol Res Pract 2022; 235:153961. [DOI: 10.1016/j.prp.2022.153961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/11/2022] [Accepted: 05/25/2022] [Indexed: 12/24/2022]
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Potentials of long non-coding RNAs as biomarkers of colorectal cancer. Clin Transl Oncol 2022; 24:1715-1731. [PMID: 35581419 DOI: 10.1007/s12094-022-02834-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/04/2022] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) is the third most common malignant tumor worldwide and the fourth major cause of cancer-related death, with high morbidity and increased mortality year by year. Although significant progress has been made in the therapy strategies for CRC, the great difficulty in early diagnosis, feeble susceptibility to radiotherapy and chemotherapy, and high recurrence rates have reduced therapeutic efficacy resulting in poor prognosis. Therefore, it is urgent to understand the pathogenesis of CRC and unravel novel biomarkers to improve the early diagnosis, treatment and prediction of CRC recurrence. Long non-coding RNAs (lncRNAs) are non-coding RNAs with a length of more than 200 nucleotides, which are abnormally expressed in tumor tissues and cell lines, activating or inhibiting specific genes through multiple mechanisms including transcription and translation. A growing number of studies have shown that lncRNAs are important regulators of microRNAs (miRNAs, miRs) expression in CRC and may be promising biomarkers and potential therapeutic targets in the research field of CRC. This review mainly summarizes the potential application value of lncRNAs as novel biomarkers in CRC diagnosis, radiotherapy, chemotherapy and prognosis. Additionally, the significance of lncRNA SNHGs family and lncRNA-miRNA networks in regulating the occurrence and development of CRC is mentioned, aiming to provide some insights for understanding the pathogenesis of CRC and developing new diagnostic and therapeutic strategies.
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Wang J, Hou F, Tang L, Xiao K, Yang T, Wang Z, Liu G. The interaction between long non-coding RNA LINC01564 and POU2F1 promotes the proliferation and metastasis of gastric cancer. J Transl Med 2022; 20:220. [PMID: 35562740 PMCID: PMC9101833 DOI: 10.1186/s12967-022-03391-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 02/23/2022] [Indexed: 12/24/2022] Open
Abstract
Background An increasing number of studies have demonstrated that long non-coding RNAs (lncRNAs) serve as key regulators in tumor development and progression. However, only a few lncRNAs have been functionally characterized in gastric cancer (GC). Methods Bioinformatics analysis was conducted to find lncRNAs that are associated with GC metastasis. RNA FISH, RIP, and RNA pull down assays were used to study the complementary binding of LINC01564 complementary to the 3′UTR of transcription factor POU2F1. The transcription activation of LINC01564 by POU2F1 as a transcription factor was examined by ChIP assay. In vitro assays such as MTT, cell invasion assay, and clonogenic assay were conducted to examined the impacts of LINC01564 and POU2F1 on GC cell proliferation and invasion. Experiments in vivo were performed to access the impacts of LINC01564 and POU2F1 on GC metastasis. Results The results showed that LINC01564 complementary bound to the 3′UTR of POU2F1 to form an RNA duplex, whereby stabilizing POU2F1 mRNA and increasing the enrichment in cells. The level of LINC01564 was also increased by POU2F1 through transcription activation. In vitro assays showed that LINC01564 promoted the proliferation, invasion and migration of GC cells through increasing POU2F1. In vivo experiments indicate the promotion of GC proliferation and metastasis by the interaction between LINC01564 and POU2F1. Conclusion Taken together, our results indicate that the interaction between LINC01564 and POU2F1 promotes the proliferation, migration and invasion of GC cells. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03391-x.
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Affiliation(s)
- Jixu Wang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Futao Hou
- Department of General Surgery, Hunan Provincial People's Hospital, First Affiliated Hospital of Hunan Normal University, 61 the West Jiefang Road, Furong District, Changsha, 410003, Hunan, China
| | - Lusheng Tang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Ke Xiao
- Department of Gastroduodenal and Pancreatic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Tengfei Yang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China
| | - Zhiqiang Wang
- Department of Interventional Vascular Surgery, Affiliated Hospital (Clinical College) of Xiangnan University and Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, 25 Renmin West Road, Chenzhou, 423000, Hunan, China.
| | - Gu Liu
- Department of Gastrointestinal Surgery, Chenzhou First People's Hospital and The First Affiliated Hospital of Xiangnan University, 102 Luojiajing, Chenzhou, 423000, Hunan, China.
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35
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Anti-cancer effect of LINC00478 in bladder cancer correlates with KDM1A-dependent MMP9 demethylation. Cell Death Dis 2022; 8:242. [PMID: 35504875 PMCID: PMC9065159 DOI: 10.1038/s41420-022-00956-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 02/22/2022] [Accepted: 03/16/2022] [Indexed: 11/18/2022]
Abstract
Accumulating evidence has highlighted the important roles of long intergenic non-coding RNAs (lincRNAs) during cancer progression. However, the involvement of LINC00478 in bladder cancer remains largely unclear. Accordingly, the current study sought to investigate the function of LINC00478 on malignant phenotypes of bladder cancer cells as well as the underlying mechanism. By integrating data from in silico analysis, we uncovered that LINC00478 was differentially expressed in bladder cancer. We further analyzed the expression of LINC00478 and matrix metalloprotein 9 (MMP9) in bladder cancer tissues and cell lines and observed a significant decline in LINC00478 expression and an elevation in MMP9 expression. In addition, chromatin immunoprecipitation, RNA-binding protein immunoprecipitation, and RNA pull-down assays predicted and validated that LINC00478 targeted lysine-specific demethylase-1 (KDM1A) and down-regulated the expression of MMP9 by decreasing the monomethylation on lysine 4 of histone H3 (H3K4me1) of MMP9 promoter. Treatment with KDM1A inhibitor tranylcypromine (TCP) also led to an increase in the enrichment of H3K4me1 in the MMP9 promoter region. Through gain- and loss-of-function approaches, we found that LINC00478 up-regulation diminished the malignant phenotype of bladder cancer cells in vitro, and further inhibited xenograft tumor growth and metastasis in vivo by repressing MMP9. Collectively, our findings unraveled a LINC00478-mediated inhibitory mechanism in bladder cancer via the recruitment of histone demethylation transferase KDM1A to the MMP9 promoter region, which can provide potential implications for novel therapeutic targets against bladder cancer.
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Shil R, Ghosh R, Banerjee AK, Mal C. LncRNA, miRNA and transcriptional co-regulatory network of breast and ovarian cancer reveals hub molecules. Meta Gene 2022. [DOI: 10.1016/j.mgene.2022.101024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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37
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Wang H, Chen Y, Liu Y, Li Q, Luo J, Wang L, Chen Y, Sang C, Zhang W, Ge X, Yao Z, Miao L, Liu X. The lncRNA ZFAS1 regulates lipogenesis in colorectal cancer by binding polyadenylate-binding protein 2 to stabilize SREBP1 mRNA. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:363-374. [PMID: 35036050 PMCID: PMC8728310 DOI: 10.1016/j.omtn.2021.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 12/08/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is the fourth leading cause of cancer-related mortality globally. Therefore, a better understanding of the early molecular events of this disease is needed. Long noncoding RNAs (lncRNAs) play a critical role in the regulation of tumorigenesis and cancer progression. In this study, we investigated the characteristics of ZFAS1 in CRC. We analyzed three independent microarray datasets of CRC tissues from GEO and found that ZFAS1 expression was remarkably upregulated in all three datasets. Moreover, we validated the overexpression of ZFAS1 in CRC tissues compared with normal tissues and found that ZFAS1 was positively correlated with tumor size and metastasis in CRC. Knockdown of ZFAS1 significantly suppressed the malignant phenotype and lipogenesis of CRC cells. Mechanistically, ZFAS1 binds polyadenylate-binding protein 2 (PABP2) to stabilize SREBP1 mRNA, thereby increasing the expression of SREBP1 and its target genes stearoyl-CoA desaturase (SCD1) and fatty acid synthase (FASN), thus promoting CRC lipid accumulation. These data demonstrated that ZFAS1 could act as an oncogene for CRC and that ZFAS1 reprograms lipid metabolism by binding with PABP2 to stabilize SREBP1 mRNA accumulation, implicating it as a novel and potent target for the treatment of CRC.
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Affiliation(s)
- Huishan Wang
- Department of Gastroenterology, Shanghai Songjiang District Central Hospital, Shanghai 210000, China
| | - Yuli Chen
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Yanwen Liu
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210000, China
| | - Qiuhui Li
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Jing Luo
- Department of Cardiothoracic Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing 210011, China
| | - Li Wang
- Department of Oncology, The Third Medical School of Nanjing Medical University, Nanjing 210011, China
| | - Yuanyuan Chen
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Chen Sang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow of University, Changzhou G 213003, China
| | - Wen Zhang
- Department of Oncology, Zhongda Hospital, Medical School of Southeast University, Nanjing 210000, China
| | - Xianxiu Ge
- Department of Gastroenterology, Shanghai Songjiang District Central Hospital, Shanghai 210000, China
| | - Zhifeng Yao
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow of University, Changzhou G 213003, China
| | - Lin Miao
- Medical Center for Digestive Diseases, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Xianghua Liu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
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Yao Q, Zhang X, Chen D. Emerging Roles and Mechanisms of lncRNA FOXD3-AS1 in Human Diseases. Front Oncol 2022; 12:848296. [PMID: 35280790 PMCID: PMC8914342 DOI: 10.3389/fonc.2022.848296] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/01/2022] [Indexed: 01/02/2023] Open
Abstract
Numerous long noncoding RNAs (lncRNAs) have been identified as powerful regulators of human diseases. The lncRNA FOXD3-AS1 is a novel lncRNA that was recently shown to exert imperative roles in the initialization and progression of several diseases. Emerging studies have shown aberrant expression of FOXD3-AS1 and close correlation with pathophysiological traits of numerous diseases, particularly cancers. More importantly, FOXD3-AS1 was also found to ubiquitously impact a range of biological functions. This study aims to summarize the expression, associated clinicopathological features, major functions and molecular mechanisms of FOXD3-AS1 in human diseases and to explore its possible clinical applications.
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Affiliation(s)
- Qinfan Yao
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Xiuyuan Zhang
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
| | - Dajin Chen
- Kidney Disease Center, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Kidney Disease Prevention and Control Technology, Hangzhou, China
- National Key Clinical Department of Kidney Diseases, Institute of Nephrology, Zhejiang University, Hangzhou, China
- Zhejiang Clinical Research Center of Kidney and Urinary System Disease, Hangzhou, China
- *Correspondence: Dajin Chen,
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Olabayo Olatubosun M, Abubakar MB, Batiha GES, Malami I, Ibrahim KG, Abubakar B, Bello MB, Alexiou A, Imam MU. LncRNA SNHG15: A potential therapeutic target in the treatment of colorectal cancer. Chem Biol Drug Des 2022; 101:1138-1150. [PMID: 35191201 DOI: 10.1111/cbdd.14036] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 01/20/2022] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
The global burden of colorectal cancer (CRC) is increasing annually. CRC could develop from genetic and phenotypic factors involving changes in gene expression. Incredibly, the human genome transcribes into non-coding RNAs, among which long non-coding RNAs (lncRNAs) signify the most crucial part of the transcriptome in multicellular organisms. lncRNAs affect gene expression at multiple levels, from transcription to protein localization and stability. Recent studies have implicated lncRNA small nucleolar RNA host gene 15 (SNHG15) in cancers occurrence and progression. Previously, an indication suggests SNHG15 overexpression triggers proliferation, metastasis, and impedes apoptosis in CRC. Further, through its activity of binding micro-RNAs, lncRNA SNHG15 modulates genes associated with CRC progression and promotes CRC resistance to chemotherapeutic drugs. Here we reviewed recent findings on the various mechanisms and roles of lncRNA SNHG15 implicated in CRC tumorigenesis. We further highlight how SNHG15 plays a vital role in regulating critical pathways linked to the development and progression of CRC. Finally, we highlight how SNHG15 can be modulated for CRC treatments and the various therapeutic strategies to be implored when targeting SNHG15 in the context of CRC treatments. Findings from these studies present SNHG15 as a potential therapeutic target for preventing and treating CRC.
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Affiliation(s)
- Mutolib Olabayo Olatubosun
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, Usmanu Danfodiyo University, P.M.B 2346, Sokoto, Nigeria.,Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria
| | - Murtala Bello Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B, 2254, Sokoto, Nigeria
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Ibrahim Malami
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Pharmacognosy and Ethnopharmacy, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B 2346, Sokoto, Nigeria
| | - Kasimu Ghandi Ibrahim
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B, 2254, Sokoto, Nigeria
| | - Bilyaminu Abubakar
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, Usmanu Danfodiyo University, P.M.B 2346, Sokoto, Nigeria
| | - Muhammad Bashir Bello
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Veterinary Microbiology, Faculty of Veterinary Medicine, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria
| | - Athanasios Alexiou
- Novel Global Community Educational Foundation, Hebersham, Australia.,AFNP Med Austria, Wien, Austria
| | - Mustapha Umar Imam
- Centre for Advanced Medical Research and Training, Usmanu Danfodiyo University, P.M.B. 2346, Sokoto, Nigeria.,Department of Medical Biochemistry, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, P.M.B, 2254, Sokoto, Nigeria
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Xiao L, Yuan W, Huang C, Luo Q, Xiao R, Chen ZH. LncRNA PCAT19 induced by SP1 and acted as oncogene in gastric cancer competitively binding to miR429 and upregulating DHX9. J Cancer 2022; 13:102-111. [PMID: 34976174 PMCID: PMC8692695 DOI: 10.7150/jca.61961] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 11/02/2021] [Indexed: 12/24/2022] Open
Abstract
Increasing evidence suggests that long non-coding RNAs (lncRNAs) are crucial in cancer biological processes. To investigate if lncRNA contributes to gastric cancer (GC), we conducted a bioinformatics analysis in human microarray datasets, and the results showed that lncRNA prostate cancer-associated transcript 19 (PCAT19) was upregulated in GC. Quantitative reverse-transcriptase PCR and in situ hybridization assays also revealed that PCAT19 was upregulated in GC tissues. The PCAT19 expression in GC was significantly related to tumor size, lymph node metastasis, and pathological stage. Moreover, patients with higher PCAT19 expression levels were more likely to have a poor prognosis for overall survival. The knockdown of PCAT19 by siRNA significantly suppressed the proliferation and invasion of GC cells. The cell distribution of PCAT19 in GC cells was examined by fluorescence in situ hybridization assay, and the results showed that it was mainly located in the cytoplasm. Mechanistically, PCAT19 sponges miR-429 and promotes DHX9 expression. In addition, the transcription factor SP1 is involved in PCAT19 activation. Our results demonstrate that lncRNA PCAT19 is induced by SP1 and acts as an oncogene in GC that competitively binds to miR429 and upregulates DHX9.
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Affiliation(s)
- Lei Xiao
- Department of Gastrointestinal, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Weijie Yuan
- Department of Gastrointestinal, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Changhao Huang
- Department of Gastrointestinal, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qingqing Luo
- Department of Oncology, Hunan Provincial People's Hospital, Changsha 410002, China
| | - Runsha Xiao
- Department of Gastrointestinal, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zi-Hua Chen
- Department of Gastrointestinal, Xiangya Hospital, Central South University, Changsha 410008, China
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41
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V SKP, Thahsin A, M M, G G. A Heterogeneous Information Network Model for Long Non-Coding RNA Function Prediction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:255-266. [PMID: 32750859 DOI: 10.1109/tcbb.2020.3000518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Exciting information on the functional roles played by long non-coding RNA (lncRNA) has drawn substantial research attention these days. With the advent of techniques such as RNA-Seq, thousands of lncRNAs are identified in very short time spans. However, due to the poor annotation rate, only a few of them are functionally characterised. The wet lab experiments to elucidate lncRNA functions are challenging, slow progressing and sometimes prohibitively expensive. This work attempts to solve the crucial problem of developing computational methods to predict lncRNA functions. The model presented here, predicts the functions of lncRNAs by making use of a meta-path based measure, AvgSim on a Heterogeneous Information Network (HIN). The network is constructed from existing protein and function association data of lncRNAs, lncRNA co-expression data and protein protein interaction data. Out of the 2,758 lncRNA considered for the experiment, the proposed method predicts possible functions for 2,695 lncRNAs with an accuracy of 73.68 percent and found to perform better than the other state-of-the-art approaches for an independent test set. A case study of two well-known lncRNAs (HOTAIR and H19) is conducted and the associated functions are identified. The results were validated using experimental evidence from the literature. The script and data used for the implementation of the model is freely available at: http://bdbl.nitc.ac.in/LncFunPred/index.html.
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Zhou H, Gao Y, Li X, Shang S, Wang P, Zhi H, Guo S, Sun D, Liu H, Li X, Zhang Y, Ning S. Identifying and characterizing lincRNA genomic clusters reveals its cooperative functions in human cancer. J Transl Med 2021; 19:509. [PMID: 34906173 PMCID: PMC8672572 DOI: 10.1186/s12967-021-03179-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/03/2021] [Indexed: 02/01/2023] Open
Abstract
Background Emerging evidence has revealed that some long intergenic non-coding RNAs (lincRNAs) are likely to form clusters on the same chromosome, and lincRNA genomic clusters might play critical roles in the pathophysiological mechanism. However, the comprehensive investigation of lincRNA clustering is rarely studied, particularly the characterization of their functional significance across different cancer types. Methods In this study, we firstly constructed a computational method basing a sliding window approach for systematically identifying lincRNA genomic clusters. We then dissected these lincRNA genomic clusters to identify common characteristics in cooperative expression, conservation among divergent species, targeted miRNAs, and CNV frequency. Next, we performed comprehensive analyses in differentially-expressed patterns and overall survival outcomes for patients from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) across multiple cancer types. Finally, we explored the underlying mechanisms of lincRNA genomic clusters by functional enrichment analysis, pathway analysis, and drug-target interaction. Results We identified lincRNA genomic clusters according to the algorithm. Clustering lincRNAs tended to be co-expressed, highly conserved, targeted by more miRNAs, and with similar deletion and duplication frequency, suggesting that lincRNA genomic clusters may exert their effects by acting in combination. We further systematically explored conserved and cancer-specific lincRNA genomic clusters, indicating they were involved in some important mechanisms of disease occurrence through diverse approaches. Furthermore, lincRNA genomic clusters can serve as biomarkers with potential clinical significance and involve in specific pathological processes in the development of cancer. Moreover, a lincRNA genomic cluster named Cluster127 in DLK1-DIO3 imprinted locus was discovered, which contained MEG3, MEG8, MEG9, MIR381HG, LINC02285, AL132709.5, and AL132709.1. Further analysis indicated that Cluster127 may have the potential for predicting prognosis in cancer and could play their roles by participating in the regulation of PI3K-AKT signaling pathway. Conclusions Clarification of the lincRNA genomic clusters specific roles in human cancers could be beneficial for understanding the molecular pathogenesis of different cancer types. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03179-5.
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Affiliation(s)
- Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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Wang Y, Yi K, Liu X, Tan Y, Jin W, Li Y, Zhou J, Wang H, Kang C. HOTAIR Up-Regulation Activates NF-κB to Induce Immunoescape in Gliomas. Front Immunol 2021; 12:785463. [PMID: 34887871 PMCID: PMC8649724 DOI: 10.3389/fimmu.2021.785463] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/05/2021] [Indexed: 12/20/2022] Open
Abstract
Background Checkpoint blockade therapies targeting programmed death ligand 1 (PD-L1) and its receptor programmed cell death 1 promote T cell-mediated immune surveillance against tumors and have been associated with significant clinical benefit in cancer patients. The long-stranded non-coding RNA HOTAIR is highly expressed and associated with metastasis in a variety of cancer types and promotes tumor metastasis at least in part through association with the PRC2 complex that induces redirection to hundreds of genes involved in tumor metastasis. Here, we report that HOTAIR is an activator lncRNA of the NF-κB pathway and demonstrate that its apparent upregulation promotes inflammatory signaling and immune escape in glioma cells. Methods Bioinformatics analysis was used to elucidate the relationship between HOTAIR and NF-κB pathway in HOTAIR knockdown glioma cells. At the cytological level, protein hybridization and immunofluorescence were used to detect the response of proteins in the NF-κB signaling pathway to HOTAIR regulation. ChIP and ChIRP experiments identified HOTAIR target genes. Animal experiments verified alterations in inflammation and immune escape following HOTAIR knockdown and activity inhibition. Results HOTAIR activated the expression of proteins involved in NF-κB, TNFα, MAPK and other inflammatory signaling pathways. In addition, HOTAIR induced various proteins containing protein kinase structural domains and promoted the enrichment of proteins and complexes of important inflammatory signaling pathways, such as the TNFα/NF-κB signaling protein complex, the IκB kinase complex, and the IKKA-IKKB complex. In addition, HOTAIR aberrantly activated biological processes involved in glioma immune responses, T-cell co-stimulation and transcription initiation by RNA polymerase II. HOTAIR facilitated the induction of IκBα phosphorylation by suppressing the expression of the NF-κB upstream protein UBXN1, promoting NF-κB phosphorylation and nuclear translocation. In vivo, reduction of HOTAIR decreased PD-L1 protein expression, indicating that cells are more likely to be targeted by immune T cells. Conclusion In conclusion, our results provide convincing evidence that lncRNA HOTAIR drives aberrant gene transcription and immune escape from tumor cells through the NF-κB pathway.
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Affiliation(s)
- Yunfei Wang
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Kaikai Yi
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China.,Department of Neuro-Oncology and Neurosurgery, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Clinical Research Center for Cancer, Tianjin, China
| | - Xing Liu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yanli Tan
- Department of Pathology, Hebei University Medical College, Baoding, China.,Department of Pathology, Affiliated Hospital of Hebei University, Baoding, China
| | - Weili Jin
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Yansheng Li
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Junhu Zhou
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
| | - Hongjun Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chunsheng Kang
- Laboratory of Neuro-Oncology, Department of Neurosurgery, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China.,Key Laboratory of Post-Neuro Injury Neuro-Repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin, China
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Ng KH, Subrayan V, Ramachandran V, Ismail F. Screening of single nucleotide polymorphisms among fuchs’ endothelial corneal dystrophy subjects in Malaysia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2021. [DOI: 10.1186/s43042-021-00193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The pathophysiology underlying Fuchs' Endothelial Corneal Dystrophy (FECD), especially in older individuals, remains unclear, with a genetic predisposition being reported as the single best predictor of the disease. Genetic studies have shown that several genes in various loci such as COL8A2, SLC4A11, TCF8/ZEB1 and TCF4 are associated with FECD in different populations and ethnicities. A case–control study was conducted to determine the association between genetic variants and FECD in a tertiary care setting in Malaysia. A total number of 12 patients with clinically diagnosed FECD and 12 age, gender and race matched control subjects were recruited. Extracted genomic DNA were genotyped using Infinium Global Screening Array (GSA)-24 version 1.0 BeadChip with iScan high-throughput system. Illumina GenomeStudio 2.0 Data Analysis and PLINK version 1.9 software were used to perform association tests and determine the distribution of obtained variants among the cases and controls.
Results
A significant novel genetic variant, rs11626651, a variant of the LOC105370676 gene or known as the LINC02320 gene, located at chromosome 14, has been identified as a suggestive association with FECD (p < 5 × 10−6). Further analysis in this study suggested that candidate genes such as COL8A2, ZEB1/TCF8, TCF4 and SLC4A11 had no significant associations with FECD.
Conclusions
The discovery of a novel variant may influence the underlying pathogenic basis of FECD in Malaysia. The current study is the first genetic study on FECD to use Infinium GSA. It is the first comprehensive report in Malaysia to provide genetic information of potential relevance to FECD, which may pave the way for new therapeutic strategies in the future. A detailed analysis with a larger sample size is recommended for further evaluation.
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Integrative analysis of long non-coding RNAs and mRNAs associated with tumorigenesis of salivary gland pleomorphic adenoma. Arch Oral Biol 2021; 133:105303. [PMID: 34775268 DOI: 10.1016/j.archoralbio.2021.105303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 10/23/2021] [Accepted: 10/30/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The current study investigated long non-coding RNA (lncRNA) and mRNA profiles of the human salivary gland pleomorphic adenoma (SGPA). DESIGN Microarray analysis was used to study the expression of lncRNAs and mRNAs and the differentially expressed lncRNAs in human SGPA (all from parotid gland) were identified. The differentially expressed lncRNAs were subjected to qRT-PCR to verify and quantify their expression and a lncRNA-mRNA co-expression network was constructed. The lncRNAs correlated to pleomorphic adenoma gene 1 (PLAG1), a known key transcription factor, were identified and analyzed. RESULTS In the present study, 17,382 lncRNAs and 8132 mRNAs were found to be significantly differentially expressed in SGPA (fold change > 2, P < 0.05). The expression of three lncRNAs (NR_110874, NR_110875 and T087085) was significantly altered in SGPA compared to the corresponding healthy tissues, and it was confirmed using the lncRNA-mRNA co-expression network analysis that several lncRNAs interact with 5 key regulators (PLAG1, CTNNB1, CCND1, IGF2, and TP53). Furthermore, T042819 was significantly upregulated in SGPA, which may upregulate PLAG1 by sponging has-miR195-5p. CONCLUSION These data suggested that the differently expressed lncRNAs may contribute to the tumorigenesis of SGPA, and analyzing the differences in the lncRNA expression profiles may provide novel insights into the pathogenesis of SGPA.
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Shaath H, Elango R, Alajez NM. Molecular Classification of Breast Cancer Utilizing Long Non-Coding RNA (lncRNA) Transcriptomes Identifies Novel Diagnostic lncRNA Panel for Triple-Negative Breast Cancer. Cancers (Basel) 2021; 13:cancers13215350. [PMID: 34771513 PMCID: PMC8582428 DOI: 10.3390/cancers13215350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Breast cancer is the most commonly diagnosed cancer in women today and accounts for thousands of cancer-related deaths each year. While some breast cancer subtypes can be easily diagnosed and targeted for therapy, triple-negative breast cancer, which lacks receptor expression, is the most challenging to diagnose and treat. In this study, we use multiple RNA sequencing data to look specifically at long non-coding RNA (lncRNA) expression portraits at the transcript level and to identify lncRNA-based biomarkers associated with each breast cancer subtype. Receiver operating characteristic (ROC) analysis was used to validate their diagnostic potential, which was validated in two independent cohorts. Several lncRNA transcripts were found to be enriched in TNBC across all validation cohorts. Binary regression analysis identified a four lncRNA transcript signature with the highest diagnostic power for TNBC as potential novel biomarkers for diagnostic and therapeutic intervention. Interestingly, several of the identified lncRNAs were shown to have prognostic potential in TNBC. Abstract Breast cancer remains the world’s most prevalent cancer, responsible for around 685,000 deaths globally despite international research efforts and advances in clinical management. While estrogen receptor positive (ER+), progesterone receptor positive (PR+), and human epidermal growth factor receptor positive (HER2+) subtypes are easily classified and can be targeted, there remains no direct diagnostic test for triple-negative breast cancer (TNBC), except for the lack of receptors expression. The identification of long non-coding RNAs (lncRNAs) and the roles they play in cancer progression has recently proven to be beneficial. In the current study, we utilize RNA sequencing data to identify lncRNA-based biomarkers associated with TNBC, ER+ subtypes, and normal breast tissue. The Marker Finder algorithm identified the lncRNA transcript panel most associated with each molecular subtype and the receiver operating characteristic (ROC) analysis was used to validate the diagnostic potential (area under the curve (AUC) of ≥8.0 and p value < 0.0001). Focusing on TNBC, findings from the discovery cohort were validated in an additional two cohorts, identifying 13 common lncRNA transcripts enriched in TNBC. Binary regression analysis identified a four lncRNA transcript signature (ENST00000425820.1, ENST00000448208.5, ENST00000521666.1, and ENST00000650510.1) with the highest diagnostic power for TNBC. The ENST00000671612.1 lncRNA transcript correlated with worse refractory free survival (RFS). Our data provides a step towards finding a novel diagnostic lncRNA-based panel for TNBC with potential therapeutic implications.
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Affiliation(s)
- Hibah Shaath
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar;
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar;
| | - Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar;
| | - Nehad M. Alajez
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar;
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha P.O. Box 34110, Qatar;
- Correspondence: ; Tel.: +974-4454-7252; Fax: +974-4454-0281
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Chandra K, Banerjee A, Das M. Epigenetic and transcriptional regulation of GnRH gene under altered metabolism and ageing. THE NUCLEUS 2021. [DOI: 10.1007/s13237-021-00374-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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Wu C, Bian X, Zhang L, Hu Y, Wu Y, Pei T, Han X. Long noncoding RNA LINC00968 inhibits proliferation, migration and invasion of lung adenocarcinoma through targeting miR-22-5p/CDC14A axis. 3 Biotech 2021; 11:433. [PMID: 34603911 PMCID: PMC8440738 DOI: 10.1007/s13205-021-02981-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 09/01/2021] [Indexed: 12/13/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a high aggressive human cancer which usually diagnosed at advanced stages. Accumulating evidences indicate that long noncoding RNAs (lncRNAs) are crucial participants in LUAD progression. In the present study, we found that lncRNA LINC00968 was significantly down-regulated in LUAD tissues and cell lines. LINC00968 level was positively correlated to survival rate, and negatively correlated to tumor node metastasis (TNM) stage, tumor size and lymph node metastasis of LUAD patients. We over-expressed LINC00968 in LUAD cells using lentivirus, inhibited proliferation and cell cycle arrest at G1 phase were detected. LINC00968 over-expression also suppressed migration, invasion and epithelial mesenchymal transition. We further validated that LINC00968 localized in cytoplasm and acted as an upstream regulator of microRNA miR-22-5p, which was up-regulated in LUAD tissues and cell lines. Besides, elevated miR-22-5p expression abolished the effect of LINC00968 over-expression on LUAD progression including in vivo tumor growth. In addition, we first validated that cell division cycle 14A (CDC14A), which was down-regulated in LUAD tissues, was a downstream target of miR-22-5p. We over-expressed CDC14A in LUAD cells and miR-22-5p induced LUAD progression was partially reversed. In conclusion, our study demonstrated that LINC00968 inhibited proliferation, migration and invasion of LUAD by sponging miR-22-5p and further restoring CDC14A. This novel regulatory axis might provide us with promising diagnostic and therapeutic target in LUAD treatment.
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Affiliation(s)
- Chao Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Xuzhao Bian
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Liyuan Zhang
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yuanyuan Hu
- Medical College, Xijing University, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Yang Wu
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - Tianli Pei
- Department of Medical Quality Management, Xi’an International Medical Center Hospital, Xi’an, 710100 Shaanxi People’s Republic of China
| | - XinPeng Han
- Department of Respiratory Medicine of Thoracic Hospital, Xi’an International Medical Center Hospital, No.777 Xitai Road, Gaoxin District, Xi’an, 710100 Shaanxi People’s Republic of China
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Rao M, Xu S, Zhang Y, Liu Y, Luan W, Zhou J. Long non-coding RNA ZFAS1 promotes pancreatic cancer proliferation and metastasis by sponging miR-497-5p to regulate HMGA2 expression. Cell Death Dis 2021; 12:859. [PMID: 34552050 PMCID: PMC8458532 DOI: 10.1038/s41419-021-04123-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 01/10/2023]
Abstract
The lncRNA ZFAS1 plays a carcinogenic regulatory role in many human tumours, but it is rarely reported in pancreatic cancer. We identify the role and molecular mechanisms of ZFAS1 in pancreatic cancer. The expression of ZFAS1, miR-497-5p and HMGA2 in pancreatic cancer tissues was detected by qRT-PCR. Pancreatic cancer data in The Cancer Genome Atlas were also included in this study. CCK8, EdU, transwell and scratch wound assays were used to investigate the biological effects of ZFAS1 in pancreatic cancer cells. MS2-RIP, RNA pull-down, RNA-ChIP and luciferase reporter assays were used to clarify the molecular biological mechanisms of ZFAS1 in pancreatic cancer. The role of ZFAS1 in vivo was also confirmed via xenograft experiments. ZFAS1 was overexpressed in pancreatic cancer tissues. ZFAS1 promoted the growth and metastasis of pancreatic cancer cells, and miR-497-5p acted as a tumour suppressor gene in pancreatic cancer by targeting HMGA2. We also demonstrated that ZFAS1 exerts its effects by promoting HMGA2 expression through decoying miR-497-5p. We also found that ZFAS1 promoted the progression of pancreatic cancer in vivo by modulating the miR-497-5p/HMGA2 axis. In conclusion, this study revealed a new role for and the molecular mechanisms of ZFAS1 in pancreatic cancer, identifying ZFAS1 as a novel target for the diagnosis and treatment of pancreatic cancer.
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Affiliation(s)
- Min Rao
- Hepatobiliary surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Song Xu
- Hepatobiliary surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Yong Zhang
- Hepatobiliary surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Yifan Liu
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wenkang Luan
- Department of Plastic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Junjing Zhou
- Hepatobiliary surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China.
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Non-coding RNAs: The key regulators in NLRP3 inflammasome-mediated inflammatory diseases. Int Immunopharmacol 2021; 100:108105. [PMID: 34481143 DOI: 10.1016/j.intimp.2021.108105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 08/03/2021] [Accepted: 08/26/2021] [Indexed: 02/07/2023]
Abstract
Inflammasomes are multiprotein complexes responding to various microbes and endogenous danger signals, contributing to initiating the innate protective response of inflammatory diseases. NLRP3 inflammasome is a crucial regulator of pro-inflammatory cytokines (IL-1β and IL-18) production through activating caspase-1. Non-coding RNAs (ncRNAs) are a class of RNA transcripts lacking the ability to encode peptides or proteins. Its dysregulation leads to the development and progression of inflammation in diseases. Recently, accumulating evidence has indicated that NLRP3 inflammasome activation could be modulated by ncRNAs (lncRNAs, miRNAs, and circRNAs) in a variety of inflammatory diseases. This review focuses on the substantial role and function of ncRNAs in the NLRP3 inflammasome activation, providing novel insight for the future therapeutic approach of inflammatory diseases.
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