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Mutlu M, Tekin C, Ak Aksoy S, Taskapilioglu MO, Kaya S, Balcin RN, Ocak PE, Kocaeli H, Bekar A, Tolunay S, Tunca B. Long non-coding RNAs as a predictive markers of group 3 medulloblastomas. Neurol Res 2021; 44:232-241. [PMID: 34533098 DOI: 10.1080/01616412.2021.1975223] [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] [Indexed: 12/21/2022]
Abstract
ObjectiveThe appropriate treatments for the different molecular subgroups of medulloblastomas are challenging to determine. Hence, this study aimed to examine the expression profiles of long non-coding RNAs (LncRNAs) to determine a marker that may be important for treatment selection in these subgroups.MethodsChanges in the expression of LncRNAs in the tissues of patients with medulloblastoma, which are classified into four subgroups according to their clinical characteristics and gene expression profiles, were examined via reverse transcription polymerase chain reaction. Moreover, there association with patient prognosis was evaluated.ResultsThe expression levels of MALAT1 and SNGH16 were significantly higher in patients with group 3 medulloblastoma than in those with other subtypes. Patients with high expression levels of MALAT1 and SNGH16 had a relatively shorter overall survival than those with low expression levels.ConclusionsPatients with group 3 medulloblastoma have a high MALAT1 level, which is associated with poor prognosis. Therefore, MALAT1 can be a new therapeutic target in medulloblastoma.
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Affiliation(s)
- Melis Mutlu
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Cagla Tekin
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Secil Ak Aksoy
- Inegol Vocation School, Bursa Uludag University, Bursa, Turkey
| | | | - Seckin Kaya
- Department of Neurosurgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Rabia Nur Balcin
- Department of Neurosurgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Pınar Eser Ocak
- Department of Neurosurgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Hasan Kocaeli
- Department of Neurosurgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Ahmet Bekar
- Department of Neurosurgery, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Sahsine Tolunay
- Department of Pathology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
| | - Berrin Tunca
- Department of Medical Biology, Faculty of Medicine, Bursa Uludag University, Bursa, Turkey
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102
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Lu C, Wei D, Zhang Y, Wang P, Zhang W. Long Non-Coding RNAs as Potential Diagnostic and Prognostic Biomarkers in Breast Cancer: Progress and Prospects. Front Oncol 2021; 11:710538. [PMID: 34527584 PMCID: PMC8436618 DOI: 10.3389/fonc.2021.710538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/09/2021] [Indexed: 01/05/2023] Open
Abstract
Breast cancer is the most common malignancy among women worldwide, excluding non-melanoma skin cancer. It is now well understood that breast cancer is a heterogeneous entity that exhibits distinctive histological and biological features, treatment responses and prognostic patterns. Therefore, the identification of novel ideal diagnostic and prognostic biomarkers is of utmost importance. Long non-coding RNAs (lncRNAs) are commonly defined as transcripts longer than 200 nucleotides that lack coding potential. Extensive research has shown that lncRNAs are involved in multiple human cancers, including breast cancer. LncRNAs with dysregulated expression can act as oncogenes or tumor-suppressor genes to regulate malignant transformation processes, such as proliferation, invasion, migration and drug resistance. Intriguingly, the expression profiles of lncRNAs tend to be highly cell-type-specific, tissue-specific, disease-specific or developmental stage-specific, which makes them suitable biomarkers for breast cancer diagnosis and prognosis.
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Affiliation(s)
- Cuicui Lu
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Duncan Wei
- Department of Pharmacy, The First Affiliated Hospital of Medical College of Shantou University, Shantou, China
| | - Yahui Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Peng Wang
- Department of Pharmacy, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Wen Zhang
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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103
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Qian Z, Chen L, Wang X, Kan Y, Wang Y, Yu Y, Wang X, Zhao Z, Yang H, Ge P, Ding T, Zhai Q, Zhao H. Increased MALAT1 expression predicts poor prognosis in primary gastrointestinal diffuse large B-cell lymphoma. Clin Exp Med 2021; 22:183-191. [PMID: 34427833 DOI: 10.1007/s10238-021-00748-2] [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: 02/23/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022]
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is involved in the pathogenesis and progression of several cancers. However, the potential effect of MALAT1 in primary gastrointestinal diffuse large B-cell lymphoma (PGI-DLBCL) has not been elucidated. This study aimed to explore the prognostic value of MALAT1 in patients with PGI-DLBCL. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to determine the expression of MALAT1 in 90 patients with PGI-DLBCL. MALAT1 was remarkably upregulated in PGI-DLBCL tissues compared to paired adjacent non-tumor tissues (P < 0.001), and the area under the receiver operating characteristic (ROC) curve (AUC) was 0.838. MALAT1 expression was further increased in the non-germinal center B-cell-like (non-GCB), advanced stage (stages IIE-IV) and International Prognostic Index (IPI) score (3-5) groups (P = 0.01, P < 0.001 and P < 0.001, respectively). Furthermore, Kaplan-Meier analysis showed that elevated MALAT1 expression correlated with inferior overall survival (OS) and progression-free survival in PGI-DLBCL patients (P < 0.001 and P < 0.001, respectively), and our multivariate analysis results suggested that upregulation of MALAT1 and high IPI score (3-5) were two unfavorable prognostic factors for PGI-DLBCL. In conclusion, our results demonstrate that MALAT1 may serve as a novel prognostic biomarker and an ideal therapeutic target for patients with PGI-DLBCL.
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Affiliation(s)
- Zhengzi Qian
- Key Laboratory of Cancer Prevention and Therapy, Department of Lymphoma, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Leiyuan Chen
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Xinyuan Wang
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Yutian Kan
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Yafei Wang
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Yong Yu
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Xiaofang Wang
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Zhigang Zhao
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Hongliang Yang
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China
| | - Peng Ge
- Key Laboratory of Cancer Prevention and Therapy, Department of Laboratory, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Tingting Ding
- Key Laboratory of Cancer Prevention and Therapy, Department of Pathology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Qiongli Zhai
- Key Laboratory of Cancer Prevention and Therapy, Department of Pathology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Haifeng Zhao
- Key Laboratory of Cancer Prevention and Therapy, Department of Hematology, National Clinical Research Center for Cancer, Tianjin Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, People's Republic of China.
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104
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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105
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Zhang C, Wang J, Guo L, Peng M. Long non-coding RNA MALAT1 regulates cell proliferation, invasion and apoptosis by modulating the Wnt signaling pathway in squamous cell carcinoma. Am J Transl Res 2021; 13:9233-9240. [PMID: 34540039 PMCID: PMC8430056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/26/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To explore the mechanisms by which long non-coding RNA, (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) regulates cell proliferation, invasion and apoptosis through signaling axes in cutaneous squamous cell carcinoma (CSCC) cells. METHODS A total of 60 CSCC samples and 15 normal skin tissue samples were collected. qRT-PCR was used to determine MALAT1 expression. After knockdown of MALAT1 expression in A431 cells, Transwell assay was performed to detect cell migration and invasion, CCK8 assay was used to detect cell proliferation, and Western blotting was used to detect EMT-related protein expression. RESULTS Compared with the normal group, the MALAT1 positive expression rate was significantly higher in the low, moderate, and high differentiation groups (P < 0.05). The expression of MALATl in A431 cells in the siMALATl-1 and siMALATl-2 groups was lower than that in siNC group (P < 0.05). A431 cell proliferation, invasion and apoptosis at 24 h, 48 h and 72 h in the siMALATl-1 and siMALATl-2 groups were all lower and the apoptosis rate of A431 cells were all higher than that of the siNC group (P < 0.05). E-cadherin expression was higher while the expression of β-catenin, vimentin, and Bcl-2 was lower in the siMALATl-1 and siMALATl-2 groups than those of the siNC group (P < 0.05). CONCLUSION Down-regulation of lncRNA MALAT1 expression may promote apoptosis of CSCC cells and inhibit cell migration, invasion and proliferation by regulating the Wnt signaling pathway.
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Affiliation(s)
- Chunhua Zhang
- Department of Dermatology, Shanghai Baoshan Hospital of Integerated Traditional Chinese and Western Medicine Shanghai 201999, China
| | - Jianchao Wang
- Department of Dermatology, Shanghai Baoshan Hospital of Integerated Traditional Chinese and Western Medicine Shanghai 201999, China
| | - Lian Guo
- Department of Dermatology, Shanghai Baoshan Hospital of Integerated Traditional Chinese and Western Medicine Shanghai 201999, China
| | - Mingxia Peng
- Department of Dermatology, Shanghai Baoshan Hospital of Integerated Traditional Chinese and Western Medicine Shanghai 201999, China
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106
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Zheng H, Talukder A, Li X, Hu H. A systematic evaluation of the computational tools for lncRNA identification. Brief Bioinform 2021; 22:6343529. [PMID: 34368833 DOI: 10.1093/bib/bbab285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/21/2021] [Accepted: 07/03/2021] [Indexed: 12/28/2022] Open
Abstract
The computational identification of long non-coding RNAs (lncRNAs) is important to study lncRNAs and their functions. Despite the existence of many computation tools for lncRNA identification, to our knowledge, there is no systematic evaluation of these tools on common datasets and no consensus regarding their performance and the importance of the features used. To fill this gap, in this study, we assessed the performance of 17 tools on several common datasets. We also investigated the importance of the features used by the tools. We found that the deep learning-based tools have the best performance in terms of identifying lncRNAs, and the peptide features do not contribute much to the tool accuracy. Moreover, when the transcripts in a cell type were considered, the performance of all tools significantly dropped, and the deep learning-based tools were no longer as good as other tools. Our study will serve as an excellent starting point for selecting tools and features for lncRNA identification.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Amlan Talukder
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
| | - Xiaoman Li
- Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, USA
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, FL, USA
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107
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Sharma A, Kansara S, Mahajan M, Yadav B, Garg M, Pandey AK. Long non-coding RNAs orchestrate various molecular and cellular processes by modulating epithelial-mesenchymal transition in head and neck squamous cell carcinoma. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166240. [PMID: 34363933 DOI: 10.1016/j.bbadis.2021.166240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 07/15/2021] [Accepted: 07/31/2021] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) regulate various hallmarks associated with the progression of human cancers through their binding with RNA, DNA, and proteins. Epithelial-Mesenchymal Transition (EMT) is a cardinal and multi-stage process where epithelial cells acquire a mesenchymal-like phenotype that is instrumental for tumor cells to initiate invasion and metastasis. LncRNAs can potentially promote tumor onset and progression as well as drug resistance by directly or indirectly altering the EMT program. Head and neck squamous cell carcinoma (HNSCC) are a dreadful malignancy affecting public health globally. The past few years have provided a better insight into the mechanism of EMT in HNSCC. The differential expression of the lncRNAs that can act either as promoters or suppressors in the process of EMT is of great importance. In this review, we aim to sum up, the highly structured mechanism with the diverse role of lncRNAs and their interaction with different molecules in the regulation of EMT. Moreover, discussing principal EMT pathways modulated by lncRNAs and their prospective potential value as therapeutic targets.
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Affiliation(s)
- Ayushi Sharma
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India.
| | - Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Mehul Mahajan
- Indian Institute of Technology, Roorkee, Uttarakhand, India
| | - Bhupender Yadav
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Sector-125, Noida 201313, India
| | - Amit Kumar Pandey
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India.
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108
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李 玉, 陈 婕, 罗 倩, 谈 勇. Research progress in lncRNA and its action as ceRNA in ovarian function as well as the relevant diseases. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:745-752. [PMID: 34382592 PMCID: PMC10930132 DOI: 10.11817/j.issn.1672-7347.2021.200622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Indexed: 11/03/2022]
Abstract
Long chain non-encoding RNA (lncRNA) can affect gene expression through transcription, post transcriptional regulation and epigenetic modification, and it is involved in regulating ovarian physiological function. LncRNA, as a competitive endogenous RNA, can affect the expression of target gene mRNA by competitively binding microRNA (miRNA), which are called lncRNA/miRNA/mRNA regulatory network. It plays an important role in the regulation of ovarian physiological function and the occurrence and development of ovarian reproductive disorders, expecting to become a new target and diagnostic index for the treatment of reproductive disorders.
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Affiliation(s)
| | | | | | - 勇 谈
- 谈勇,, ORCID: 0000-0003-3629-1789
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109
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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110
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Wang N, Cao S, Wang X, Zhang L, Yuan H, Ma X. lncRNA MALAT1/miR‑26a/26b/ST8SIA4 axis mediates cell invasion and migration in breast cancer cell lines. Oncol Rep 2021; 46:181. [PMID: 34278507 PMCID: PMC8273684 DOI: 10.3892/or.2021.8132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/03/2021] [Indexed: 12/25/2022] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA that is overexpressed in various human cancers, including breast cancer. Evidence has associated the function of the α-2,8-sialyltransferase (ST8SIA) family with breast cancer. The present study aimed to investigate the potential roles of MALAT1 in breast cancer development and progression using analyses of both breast cancer tissues and cell lines. The mRNA levels of MALAT1, microRNA (miR)-26a/26b and ST8SIA4 were detected by reverse transcription-quantitative PCR (RT-qPCR) and the protein level of ST8SIA4 was assessed by western blot analysis. Cell proliferation, invasion and migration were detected by CCK-8, wound healing and Transwell assays, respectively. Interactions between MALAT1 and miR-26a/26b were assessed using fluorescence in situ hybridization, RNA immunoprecipitation and luciferase reporter assays. Herein, different levels of MALAT1 were primarily observed in human breast cancer samples and cells. Upregulated MALAT1 was a crucial predictor of poor breast cancer prognosis. Altered MALAT1 modulated cell progression in breast cancer. Moreover, miR-26a/26b was confirmed as a direct regulator of MALAT1, and ST8SIA4 was predicted as a target of miR-26a/26b. Functional analysis in human breast cancer cell lines demonstrated that MALAT1 modulated breast cancer cell tumorigenicity by acting as a competing endogenous lncRNA (ceRNA) to regulate ST8SIA4 levels by sponging miR-26a/26b. The identification of the MALAT1/miR-26a/26b/ST8SIA4 axis which contributes to breast cancer progression may constitute a potential new therapeutic target.
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Affiliation(s)
- Nan Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Shengji Cao
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Lina Zhang
- Department of Radiology Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
| | - Hong Yuan
- Department of Clinical Laboratory Medicine, Dalian Municipal Central Hospital, Dalian, Liaoning 116033, P.R. China
| | - Xiaolu Ma
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116011, P.R. China
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111
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Huang XC, Pang FX, Ou SS, Wei XJ, Xu YJ, Lai YH. Risk Score Based on Two microRNAs as a Prognostic Marker of Hepatocellular Carcinoma and the Corresponding Competitive Endogenous RNA Network. Int J Gen Med 2021; 14:3377-3385. [PMID: 34285562 PMCID: PMC8286150 DOI: 10.2147/ijgm.s318516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/28/2021] [Indexed: 12/15/2022] Open
Abstract
Purpose Liver transplantation (LT) currently yields the best outcomes for hepatocellular carcinoma (HCC). However, tumor recurrence still occurs in some patients. Identifying markers that predict HCC recurrence after LT is an unmet medical need. Methods In this study, differential expression analysis was used to identify differentially expressed microRNAs (DEmiRs) between HCC and liver tissues in the The Cancer Genome Atlas database and in data from patients with recurrent or non-recurrent HCC in the GSE64989 dataset. The expression profiles of the overlap DEmiRs were used to construct an miRNA-based risk score to predict prognosis using Cox regression analysis. The target genes of the miRNAs of interest were predicted, and they were analyzed for functional enrichment. Furthermore, we used the miRNAs of interest to construct a competitive endogenous RNA (ceRNA) network of long non-coding RNAs (lncRNAs), miRs and mRNAs. Results Four up-regulated and three down-regulated miRNAs in HCC and recurrent HCC after LT were considered as candidate miRs. MiR-3200-3p and miR-3690 were selected to construct the miR-based risk score, which was found to be associated with poor overall survival and progression-free survival. Furthermore, it proved to be an independent prognostic factor after adjusting for other clinicopathological factors. The corresponding ceRNA networks of these two miRs that we constructed may help to understand their regulatory mechanisms in HCC. Conclusion We propose a risk score based on miR-3200-3p and miR-3690 that may be useful as a prognostic marker to predict HCC recurrence after LT. We generated a ceRNA network involving these miRNAs, which may help reveal their regulatory roles in HCC.
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Affiliation(s)
- Xiao-Chun Huang
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
| | - Fei-Xiong Pang
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
| | - Sheng-Song Ou
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
| | - Xiao-Jiao Wei
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
| | - Yu-Ju Xu
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
| | - Yan-Hua Lai
- Department of Transplantation, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, 530021, People's Republic of China.,Guangxi Academy Of Medical Sciences, Nanning, Guangxi, 530021, People's Republic of China
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Liu ZF, Ye QN, Yang J, Yang M, Pan DH, Dong MJ. Preclinical evaluation of [68Ga]Ga-MALAT-1-antisense oligonucleotides for specific PET imaging of MALAT-1 expressing tumours. Nucl Med Commun 2021; 42:782-791. [PMID: 33625181 DOI: 10.1097/mnm.0000000000001387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The present study was to explore the feasibility of developing positron molecular probes for the metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1), to evaluate the distribution and pharmacokinetics, and to explore whether the probe can be used for the imaging of malignant tumours with high MALAT-1 expression in vivo. METHODS [68Ga]Ga labelling of MALAT-1 antisense oligonucleotides ([68Ga]Ga-MALAT-1-ASO) was synthesized by the conjugation of MALAT-1-NOTA-ASO and [68Ga] Ga3+. The radiochemical purity was shown by radio-HPLC. Pharmacokinetic studies and cellular uptake studies were performed. The biodistribution and metabolism of [68Ga] Ga-MALAT-1-ASO in normal ICR and MHCC-LM3 xenograft-bearing nude mice were studied in vitro and in vivo. RESULTS [68Ga]Ga-MALAT-1-ASO was obtained in 98% radiochemical yield from a 10-min synthesis with 100 ± 50 MBq/nmol specific activity and >99% radiochemical purity. The Log D was -2.53 ± 0.19. The tracer displayed excellent stability in vitro. 68Ga-MALAT-1 ASO showed satisfactory binding ability to MHCC-LM3 cells; the biodistribution of [68Ga]Ga-MALAT-1-ASO in MHCC-LM3 tumour-bearing mice demonstrated specific uptake of the radiotracer (3.04 ± 0.11%ID/g). Micro-PET images of the MHCC-LM3 cell xenograft mouse model provided further evidence to support the hypothesis that [68Ga]Ga-MALAT-1-ASO can target tumours in vivo. CONCLUSIONS We conclude that [68Ga]Ga labelling of MALAT-1 ASO is a convenient approach. The high accumulation of [68Ga]Ga-MALAT-1-ASO for tumours expressing MALAT-1 suggests that this radio compound may be used as a potential positron molecular probe. Molecular structure optimization studies need to be more in-depth to further reduce its background uptake and enhance tumour targeting.
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Affiliation(s)
- Zhen-Feng Liu
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Qian-Ni Ye
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Jun Yang
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
| | - Min Yang
- Molecular Imaging Centre, Jiangsu institute of nuclear medicine, Jiangsu Province, China
| | - Dong-Hui Pan
- Molecular Imaging Centre, Jiangsu institute of nuclear medicine, Jiangsu Province, China
| | - Meng-Jie Dong
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou
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113
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Ding YF, Wen YC, Chuang CY, Lin CW, Yang YC, Liu YF, Chang WM, Chang LC, Yang SF, Chien MH. Combined Impacts of Genetic Variants of Long Non-Coding RNA MALAT1 and the Environmental Carcinogen on the Susceptibility to and Progression of Oral Squamous Cell Carcinoma. Front Oncol 2021; 11:684941. [PMID: 34268119 PMCID: PMC8276129 DOI: 10.3389/fonc.2021.684941] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/11/2021] [Indexed: 01/20/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common malignant tumor of the oral cavity, and long non-coding (lnc)RNA of metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) was recently reported to play a crucial role in OSCC development and progression. However, potential effects of genetic variants of MALAT1 on the development of OSCC are still unclear. Herein, we performed a case-control study in 1350 patients with OSCC and 1199 healthy controls to evaluate the association between functional single-nucleotide polymorphisms (SNPs) of MALAT1 and OSCC susceptibility, as well as its clinicopathologic characteristics. A TaqMan allelic discrimination assay was used to genotype four tagging SNPs, viz., rs3200401 C>T, rs619586 A>G, rs1194338 C>A, and rs7927113 G>A, and results showed that the MALAT1 rs3200401 T allele had a lower risk of OSCC (adjusted odds ratio (AOR): 0.779, 95% confidence interval (CI): 0.632~0.960, p=0.019) and a higher risk of developing moderately (grade II)/poorly (grade III) differentiated OSCC (AOR: 1.508-fold, 95% CI: 1.049~2.169, p=0.027) under a dominant model. According to environmental carcinogen exposure, patients with a betel quid-chewing habit who carried the T allele of rs3200401 more easily developed high-grade (II/III) OSCC (AOR: 1.588, 95% CI: 1.055~2.390, p=0.027), and patients with the same genotype but who did not chew betel quid had a lower risk of developing lymph node metastasis (AOR: 0.437, 95% CI: 0.255~0.749, p=0.003). In addition to rs3200401, the rs619586 AG/GG genotype was associated with increased risks of developing advanced stages (III+IV) and larger tumor sizes (>T2) compared to the AA genotype, especially in the subgroup of betel quid chewers. Furthermore, analyses of clinical datasets revealed that the MALAT1 expression level was upregulated in OSCC compared to normal tissues, especially in the betel quid-chewing population. These results indicated involvement of MALAT1 SNPs rs3200401 and rs619586 in the development of OSCC and support the interaction between MALAT1 gene polymorphisms and the environmental carcinogen as a predisposing factor for OSCC progression.
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Affiliation(s)
- Yi-Fang Ding
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Otolaryngology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Yu-Ching Wen
- Department of Urology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Department of Urology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Chun-Yi Chuang
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Otolaryngology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Yi-Chieh Yang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Department of Medical Research, Tungs' Taichung MetroHarbor Hospital, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, College of Medicine Sciences and Technology, Chung Shan Medical University, Taichung, Taiwan
| | - Wei-Min Chang
- School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan
| | - Lun-Ching Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL, United States
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Ming-Hsien Chien
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.,Traditional Herbal Medicine Research Center, Taipei Medical University Hospital, Taipei, Taiwan.,Taipei Medical University (TMU) Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
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114
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Liang T, Wang Y, Jiao Y, Cong S, Jiang X, Dong L, Zhang G, Xiao D. LncRNA MALAT1 Accelerates Cervical Carcinoma Proliferation by Suppressing miR-124 Expression in Cervical Tumor Cells. JOURNAL OF ONCOLOGY 2021; 2021:8836078. [PMID: 34221014 PMCID: PMC8221887 DOI: 10.1155/2021/8836078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 03/31/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022]
Abstract
Emerging studies have clarified the critical role of LncRNA MALAT1 in various pathological progressions. Here, we identified its positive relationship with cervical carcinoma proliferation. Cervical carcinoma has been considered as one of the most malignant tumors among female. Thus, our study was designed to investigate the underlying mechanism of LncRNA MALAT1 on cervical tumor cell proliferation. We observed that miR-124 was the potential target of LncRNA MALAT1 in cervical tumor cell lines (Hela, C-33A, Caski, and SiHa), the expression level of which is negatively correlated with LncRNA MALAT1 in cervical tumor cells, tissues of cervical patients, and mice. Gain- or loss-of-function analyses in cervical tumor cells have further verified the regulatory role of MALAT1 on miR-124. Additionally, the proliferation of cervical carcinoma was inhibited by miR-124 overexpression, whereas it was blocked by LV-MALAT1 transfection. In vivo assays, overexpression of miR-124, or knockdown of MALAT1 exhibited beneficial effects on tumor weight, size, and volume, together with elevating the survival rate, tightly related with the progression of cervical cancer. In conclusion, LncRNA MALAT1 disabled the effects of miR-124 as an inhibitory sponge, accelerating the progression of cervical carcinoma.
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Affiliation(s)
- Tian Liang
- Department of Obstetrics and Gynaecology, The 1st Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Yuchen Wang
- Department of Psychiatry, Qiqihar Medical University, 161006 Qiqihar, China
| | - Yu Jiao
- Department of Psychiatry, Qiqihar Medical University, 161006 Qiqihar, China
| | - Shanshan Cong
- Department of Obstetrics and Gynaecology, The 1st Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Xinyan Jiang
- Department of Obstetrics and Gynaecology, The 1st Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Lina Dong
- Department of Obstetrics and Gynaecology, The 1st Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Guangmei Zhang
- Department of Obstetrics and Gynaecology, The 1st Affiliated Hospital of Harbin Medical University, 150001 Harbin, China
| | - Dan Xiao
- Department of Psychiatry, Qiqihar Medical University, 161006 Qiqihar, China
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115
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François-Moutal L, Miranda VG, Mollasalehi N, Gokhale V, Khanna M. In Silico Targeting of the Long Noncoding RNA MALAT1. ACS Med Chem Lett 2021; 12:915-921. [PMID: 34141069 DOI: 10.1021/acsmedchemlett.1c00060] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/24/2021] [Indexed: 11/29/2022] Open
Abstract
RNA targeting has gained traction over the past decade. It has become clear that dysregulation of RNA can be linked to many diseases, leading to a need for new scaffolds recognizing RNA specifically. Long noncoding RNAs are emerging as key controllers of gene expression and potential therapeutic targets. However, traditional targeting methods have overwhelmingly been focused on proteins. In this study, we used a protein computational tool and found several possible targetable pockets in a structurally characterized long noncoding RNA, MALAT1. Screening against those identified pockets revealed several hit compounds. We tested the binding of those compounds to MALAT1 RNA and tRNA as a negative control, using SPR. While several compounds were nonspecific binders, others were able to recognize MALAT1 specifically. One of them, MTC07, has an apparent affinity of 400.2 ± 14.4 μM. Although it has weak affinity, MTC07 is the first compound targeting MALAT1 originating from in silico docking.
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Affiliation(s)
- Liberty François-Moutal
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center of Innovation in Brain Science, Tucson, Arizona 85721, United States
| | - Victor G. Miranda
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center of Innovation in Brain Science, Tucson, Arizona 85721, United States
| | - Niloufar Mollasalehi
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center of Innovation in Brain Science, Tucson, Arizona 85721, United States
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, United States
| | - Vijay Gokhale
- Bio5 Institute, University of Arizona, Tucson, Arizona 85721-0041, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States
- Center of Innovation in Brain Science, Tucson, Arizona 85721, United States
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116
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Association of MALAT1 and PVT1 Variants, Expression Profiles and Target miRNA-101 and miRNA-186 with Colorectal Cancer: Correlation with Epithelial-Mesenchymal Transition. Int J Mol Sci 2021; 22:ijms22116147. [PMID: 34200314 PMCID: PMC8201273 DOI: 10.3390/ijms22116147] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 05/28/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
The influence of PVT1 and MALAT1 variants on colorectal cancer (CRC) susceptibility and their impact on PVT1/miRNA-186/epithelial-mesenchymal transition (EMT) and MALAT1/miRNA-101/EMT axes in CRC are unknown. We investigated the influence of PVT1 rs13255292 and MALAT1 rs3200401 on the risk of CRC and adenomatous polyps (AP), their impact on the long noncoding RNAs PVT1 and MALAT1 expression and their target miRNA-186, miRNA-101/E-cadherin pathways, along with their potential as early CRC biomarkers. Overall, 280 individuals were recruited: 140 patients with CRC, 40 patients with AP, and 100 healthy volunteers. Genotyping and serum expression profiles were assessed using qPCR. The EMT biomarker, E-cadherin, was measured by ELISA. rs3200401 was associated with increased CRC risk, whereas rs13255292 was protective. Serum PVT1 and MALAT1 were upregulated in CRC and AP patients versus healthy controls, whereas, miRNA-186, miRNA-101 and E-cadherin were downregulated in CRC versus non-CRC groups. MALAT1 showed superior diagnostic potential for CRC and predicted CRC risk among non-CRC groups in the multivariate logistic analysis. PVT1, MALAT1, miRNA-186 and miRNA-101 levels were correlated with E-cadherin, tumor stage, lymph node and distant metastasis. E-cadherin was lost in metastatic vs. non-metastatic CRC. rs3200401CC genotype carriers showed higher E-cadherin levels than CC + CT carriers. rs3200401 was correlated with lymph node status. For the first time, rs13255292 and rs3200401 are potential genetic CRC predisposition markers, with rs3200401 possibly impacting the EMT process. Serum PVT1, MALAT1, miRNA-186 and miRNA-101 are novel non-invasive diagnostic biomarkers that could improve the clinical outcome of CRC.
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117
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Competing Endogenous RNAs in Cervical Carcinogenesis: A New Layer of Complexity. Processes (Basel) 2021. [DOI: 10.3390/pr9060991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by binding to complementary sequences within target mRNAs. Apart from working ‘solo’, miRNAs may interact in important molecular networks such as competing endogenous RNA (ceRNA) axes. By competing for a limited pool of miRNAs, transcripts such as long noncoding RNAs (lncRNAs) and mRNAs can regulate each other, fine-tuning gene expression. Several ceRNA networks led by different lncRNAs—described here as lncRNA-mediated ceRNAs—seem to play essential roles in cervical cancer (CC). By conducting an extensive search, we summarized networks involved in CC, highlighting the major impacts of such dynamic molecular changes over multiple cellular processes. Through the sponging of distinct miRNAs, some lncRNAs as HOTAIR, MALAT1, NEAT1, OIP5-AS1, and XIST trigger crucial molecular changes, ultimately increasing cell proliferation, migration, invasion, and inhibiting apoptosis. Likewise, several lncRNAs seem to be a sponge for important tumor-suppressive miRNAs (as miR-140-5p, miR-143-3p, miR-148a-3p, and miR-206), impairing such molecules from exerting a negative post-transcriptional regulation over target mRNAs. Curiously, some of the involved mRNAs code for important proteins such as PTEN, ROCK1, and MAPK1, known to modulate cell growth, proliferation, apoptosis, and adhesion in CC. Overall, we highlight important lncRNA-mediated functional interactions occurring in cervical cells and their closely related impact on cervical carcinogenesis.
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118
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The Role of lncRNAs in the Pathobiology and Clinical Behavior of Multiple Myeloma. Cancers (Basel) 2021; 13:cancers13081976. [PMID: 33923983 PMCID: PMC8074217 DOI: 10.3390/cancers13081976] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Multiple myeloma (MM), the second most common hematological neoplasm, is still considered an incurable disease. Long non-coding RNAs (lncRNAs), genes that do not encode proteins, participate in numerous biological processes, but their deregulation, like that of coding genes, can contribute to carcinogenesis. Increasing evidence points to the relevant role of lncRNAs in the development of human tumors, such that they emerge as attractive biomarkers and therapeutic targets for cancer treatment, including MM. Here we review the oncogenic or tumor-suppressor functions of lncRNAs in MM and provide an overview of novel therapeutic approaches based on lncRNAs that will help to improve the management of these patients. Abstract MM is a hematological neoplasm that is still considered an incurable disease. Besides established genetic alterations, recent studies have shown that MM pathogenesis is also characterized by epigenetic aberrations, such as the gain of de novo active chromatin marks in promoter and enhancer regions and extensive DNA hypomethylation of intergenic regions, highlighting the relevance of these non-coding genomic regions. A recent study described how long non-coding RNAs (lncRNAs) correspond to 82% of the MM transcriptome and an increasing number of studies have demonstrated the importance of deregulation of lncRNAs in MM. In this review we focus on the deregulated lncRNAs in MM, including their biological or functional mechanisms, their role as biomarkers to improve the prognosis and monitoring of MM patients, and their participation in drug resistance. Furthermore, we also discuss the evidence supporting the role of lncRNAs as therapeutic targets through different novel RNA-based strategies.
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119
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Khan S, Masood M, Gaur H, Ahmad S, Syed MA. Long non-coding RNA: An immune cells perspective. Life Sci 2021; 271:119152. [PMID: 33548285 DOI: 10.1016/j.lfs.2021.119152] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) were considered as accumulated genetic waste until they were found to be gene expression regulators by highly sensitive modern genomics platforms. It is a huge class of non-coding transcripts with an arbitrary length of >200 nucleotides, which has gained much attention in the past few years. Increasing evidence from several experimental studies unraveled the expression of lncRNA linked to immune response and disease progression. However, only a small number of lncRNAs have robust evidence of their function. Differential expression of lncRNAs in different immune cells is also evident. In this review, we focused on how lncRNAs expression assist in shaping immune cells (Macrophages, Dendritic cells, NK cells, T cells, B cells, eosinophils, neutrophils, and microglial cells) function and their response to the diseased conditions. Emerging evidence revealed lncRNAs may serve as key regulators in the innate and adaptive immune response system. So, the molecular mechanism insight into the function of lncRNAs in immune response may contribute to the development of potential therapeutic targets for various disease treatments. Therefore, it is imperative to explore the expression of lncRNAs and understand its relevance associated with the immune system.
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Affiliation(s)
- Salman Khan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Masood
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Harshita Gaur
- Department of Life Sciences, University of Glasgow, United Kingdom
| | - Shaniya Ahmad
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
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120
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Ma D, Wei J, Chen S, Wang H, Ning L, Luo SH, Liu CL, Song G, Yao Q. Fucoidan Inhibits the Progression of Hepatocellular Carcinoma via Causing lncRNA LINC00261 Overexpression. Front Oncol 2021; 11:653902. [PMID: 33928038 PMCID: PMC8078595 DOI: 10.3389/fonc.2021.653902] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/12/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) as a main type of primary liver cancers has become one of the most deadly tumors because of its high morbidity and poor prognosis. Fucoidan is a family of natural, heparin-like sulfated polysaccharides extracted from brown algae. It is not only a widely used dietary supplement, but also participates in many biological activities, such as anti-oxidation, anti-inflammation and anti-tumor. However, the mechanism of fucoidan induced inhibition of HCC is elusive. In our study, we demonstrated that fucoidan contributes to inhibiting cell proliferation in vivo and in vitro, restraining cell motility and invasion and inducing cell cycle arrest and apoptosis. According to High-Throughput sequencing of long-non-coding RNA (lncRNA) in MHCC-97H cells treated with 0.5 mg/mL fucoidan, we found that 56 and 49 lncRNAs were correspondingly up- and down-regulated. LINC00261, which was related to the progression of tumor, was highly expressed in fucoidan treated MHCC-97H cells. Moreover, knocking down LINC00261 promoted cell proliferation by promoting the expression level of miR-522-3p, which further decreased the expression level of downstream SFRP2. Taken together, our results verified that fucoidan effectively inhibits the progression of HCC via causing lncRNA LINC00261 overexpression.
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Affiliation(s)
- Danhui Ma
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Jiayi Wei
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Sinuo Chen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Heming Wang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Liuxin Ning
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Shi-Hua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chieh-Lun Liu
- Department of Clinical Research and Development, Hi-Q Marine Biotech International Ltd., Taipei, Taiwan
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
| | - Qunyan Yao
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai, China.,Shanghai Institute of Liver Diseases, Shanghai, China
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121
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Aurilia C, Donati S, Palmini G, Miglietta F, Iantomasi T, Brandi ML. The Involvement of Long Non-Coding RNAs in Bone. Int J Mol Sci 2021; 22:ijms22083909. [PMID: 33920083 PMCID: PMC8069547 DOI: 10.3390/ijms22083909] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/02/2021] [Accepted: 04/08/2021] [Indexed: 12/18/2022] Open
Abstract
A harmonious balance between osteoblast and osteoclast activity guarantees optimal bone formation and resorption, pathological conditions affecting the bone may arise. In recent years, emerging evidence has shown that epigenetic mechanisms play an important role during osteoblastogenesis and osteoclastogenesis processes, including long non-coding RNAs (lncRNAs). These molecules are a class of ncRNAs with lengths exceeding 200 nucleotides not translated into protein, that have attracted the attention of the scientific community as potential biomarkers to use for the future development of novel diagnostic and therapeutic approaches for several pathologies, including bone diseases. This review aims to provide an overview of the lncRNAs and their possible molecular mechanisms in the osteoblastogenesis and osteoclastogenesis processes. The deregulation of their expression profiles in common diseases associated with an altered bone turnover is also described. In perspective, lncRNAs could be considered potential innovative molecular biomarkers to help with earlier diagnosis of bone metabolism-related disorders and for the development of new therapeutic strategies.
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Affiliation(s)
- Cinzia Aurilia
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
| | - Simone Donati
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
| | - Gaia Palmini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
| | - Francesca Miglietta
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
| | - Teresa Iantomasi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
| | - Maria Luisa Brandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134 Florence, Italy; (C.A.); (S.D.); (G.P.); (F.M.); (T.I.)
- Fondazione Italiana Ricerca sulle Malattie dell’Osso (FIRMO Onlus), 50141 Florence, Italy
- Correspondence:
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Yamada H, Takahashi M, Watanuki M, Watanabe M, Hiraide S, Saijo K, Komine K, Ishioka C. lncRNA HAR1B has potential to be a predictive marker for pazopanib therapy in patients with sarcoma. Oncol Lett 2021; 21:455. [PMID: 33907565 PMCID: PMC8063340 DOI: 10.3892/ol.2021.12716] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/10/2021] [Indexed: 01/12/2023] Open
Abstract
Bone and soft-tissue sarcomas are rare and are highly heterogeneous mesenchymal malignancies. It is therefore challenging to acquire the clinical data of patients with specific histological subtypes of sarcoma using large clinical trials, and there is a need to further establish the diagnosis and treatment of sarcomas. The results of the current study revealed that long non-coding RNA (lncRNA) highly accelerated region 1B (HAR1B) may serve as a predictive biomarker for pazopanib treatment in bone and soft-tissue sarcomas. Using multiplex reverse transcription-quantitative PCR and microarray analyses, the results demonstrated that HAR1B and HOX transcript antisense RNA (HOTAIR) were differentially expressed in pazopanib-sensitive cells and responders. It was further revealed that small interfering RNA-knockdown of HAR1B led to an increased resistance to pazopanib in sarcoma cell lines. Gene expression profiles associated with pazopanib sensitivity included cellular molecular pathways, such as genes involved in von-Willebrand factor-related signaling. The current study demonstrated that lncRNA HAR1B expression in sarcoma cell lines affected cellular sensitivity to pazopanib in patients with sarcoma.
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Affiliation(s)
- Hideharu Yamada
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Masanobu Takahashi
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Munenori Watanuki
- Department of Orthopaedic Surgery, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
| | - Mika Watanabe
- Department of Pathology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Sakura Hiraide
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Ken Saijo
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Keigo Komine
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan
| | - Chikashi Ishioka
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi 980-8575, Japan.,Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi 980-8574, Japan.,Department of Clinical Oncology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan
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123
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Song Z, Lin J, Li Z, Huang C. The nuclear functions of long noncoding RNAs come into focus. Noncoding RNA Res 2021; 6:70-79. [PMID: 33898883 PMCID: PMC8053782 DOI: 10.1016/j.ncrna.2021.03.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/16/2022] Open
Abstract
Long noncoding RNAs (lncRNAs), defined as untranslated and tightly-regulated transcripts with a length exceeding 200 nt, are common outputs of the eukaryotic genome. It is becoming increasingly apparent that many lncRNAs likely serve as important regulators in a variety of biological processes. In particular, some of them accumulate in the nucleus and function in diverse nuclear events, including chromatin remodeling, transcriptional regulation, RNA processing, DNA damage repair, etc. Here, we unite recent progresses on the functions of nuclear lncRNAs and provide insights into the future research directions of this field.
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Affiliation(s)
- Zhenxing Song
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Jiamei Lin
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Zhengguo Li
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Chuan Huang
- School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Corresponding author. School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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Dias TR, Santos JMO, Gil da Costa RM, Medeiros R. Long non-coding RNAs regulate the hallmarks of cancer in HPV-induced malignancies. Crit Rev Oncol Hematol 2021; 161:103310. [PMID: 33781867 DOI: 10.1016/j.critrevonc.2021.103310] [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: 12/18/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023] Open
Abstract
High-risk human papillomavirus (HPV) is the most frequent sexually transmitted agent worldwide and is responsible for approximately 5% of human cancers. Identifying novel biomarkers and therapeutic targets for these malignancies requires a deeper understanding of the mechanisms involved in the progression of HPV-induced cancers. Long non-coding RNAs (lncRNAs) are crucial in the regulation of biological processes. Importantly, these molecules are key players in the progression of multiple malignancies and are able to regulate the development of the different hallmarks of cancer. This review highlights the action of lncRNAs in the regulation of cellular processes leading to the typical hallmarks of cancer. The regulation of lncRNAs by HPV oncogenes, their targets and also their mechanisms of action are also discussed, in the context of HPV-induced malignancies. Overall, accumulating data indicates that lncRNAs may have a significant potential to become useful tools for clinical practice as disease biomarkers or therapy targets.
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Affiliation(s)
- Tânia R Dias
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal; Research Department of the Portuguese League Against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal.
| | - Joana M O Santos
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal.
| | - Rui M Gil da Costa
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Center for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5001-911 Vila Real, Portugal; LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465, Porto, Portugal; Postgraduate Programme in Adult Health (PPGSAD), Tumour and DNA Biobank, Federal University of Maranhão (UFMA), 65080-805, São Luís, Brazil.
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; Faculty of Medicine of the University of Porto (FMUP), 4200-319, Porto, Portugal; Research Department of the Portuguese League Against Cancer-Regional Nucleus of the North (Liga Portuguesa Contra o Cancro-Núcleo Regional do Norte), 4200-177, Porto, Portugal; Virology Service, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072, Porto, Portugal; CEBIMED, Faculty of Health Sciences of the Fernando Pessoa University, 4249-004, Porto, Portugal.
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125
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Miao C, Bai L, Yang Y, Huang J. Dysregulation of lncRNAs in Rheumatoid Arthritis: Biomarkers, Pathogenesis and Potential Therapeutic Targets. Front Pharmacol 2021; 12:652751. [PMID: 33776780 PMCID: PMC7994855 DOI: 10.3389/fphar.2021.652751] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease of unknown etiology, mainly manifested by persistent abnormal proliferation of fibroblast-like synoviocytes (FLSs), inflammation, synovial hyperplasia and cartilage erosion, accompanied by joint swelling and joint destruction. Abnormal expression or function of long noncoding RNAs (lncRNAs) are closely related to human diseases, including cancers, mental diseases, autoimmune diseases and others. The abnormal sequence and spatial structure of lncRNAs, the disorder expression and the abnormal interaction with the binding protein will lead to the change of gene expression in the way of epigenetic modification. Increasing evidence demonstrated that lncRNAs were involved in the activation of FLSs, which played a key role in the pathogenesis of RA. In this review, the research progress of lncRNAs in the pathogenesis of RA was systematically summarized, including the role of lncRNAs in the diagnosis of RA, the regulatory mechanism of lncRNAs in the pathogenesis of RA, and the intervention role of lncRNAs in the treatment of RA. Furthermore, the activated signal pathways, the role of DNA methylation and other mechanism have also been overview in this review.
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Affiliation(s)
- Chenggui Miao
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China.,Anhui Provincial Key Laboratory of Chinese Medicine Compound, Anhui University of Chinese Medicine, Hefei, China.,Department of Pharmacy, School of Life and Health Sciences, Anhui University of Science and Technology, Fengyang, China
| | - Liangliang Bai
- Department of Biomedical Engineering, School of Biomedical Engineering, Anhui Medical University, Hefei, China
| | - Yaru Yang
- Department of Pharmacy, First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Jinling Huang
- Department of Pharmacology, School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
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126
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Brisotto G, Guerrieri R, Colizzi F, Steffan A, Montico B, Fratta E. Long Noncoding RNAs as Innovative Urinary Diagnostic Biomarkers. Methods Mol Biol 2021; 2292:73-94. [PMID: 33651353 DOI: 10.1007/978-1-0716-1354-2_7] [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] [Indexed: 02/06/2023]
Abstract
The characterization of circulating tumor cells (CTCs) is now widely studied as a promising source of cancer-derived biomarkers because of their role in tumor formation and progression. However, CTCs analysis presents some limitations and no standardized method for CTCs isolation from urine has been defined so far. In fact, besides blood, urine represents an ideal source of noninvasive biomarkers, especially for the early detection of genitourinary tumors. Besides CTCs, long noncoding RNAs (lncRNAs) have also been proposed as potential noninvasive biomarkers, and the evaluation of the diagnostic accuracy of urinary lncRNAs has dramatically increased over the last years, with many studies being published. Therefore, this review provides an update on the clinical utility of urinary lncRNAs as novel biomarkers for the diagnosis of bladder and prostate cancers.
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Affiliation(s)
- Giulia Brisotto
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Roberto Guerrieri
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Francesca Colizzi
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Barbara Montico
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy.
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Ren J, Zhang FJ, Wang JH, Tang JD. LINC01315 promotes the aggressive phenotypes of papillary thyroid cancer cells by sponging miR-497-5p. Kaohsiung J Med Sci 2021; 37:459-467. [PMID: 33611825 DOI: 10.1002/kjm2.12369] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 12/29/2022] Open
Abstract
Dysregulation of the long intergenic noncoding RNA 01315 (LINC01315) has recently been demonstrated in cancer. However, the role of LINC01315 in papillary thyroid cancer (PTC) has not been determined. We attempted to determine the function of LINC01315 in PTC. The levels of LINC01315 were higher in thyroid carcinoma tissues and cell lines compared with that in noncancerous tissues or normal cells, respectively. LINC01315 knockdown significantly inhibited the in vitro colony formation and invasion of PTC cells. Upregulation of LINC01315 produced opposite effects. Bioinformatic analysis and luciferase reporter assays indicated direct binding of miR-497-5p to LINC01315. Gain- and loss-of-function assays indicated that miR-497-5p acts as a suppressive miRNA in PTC. Furthermore, LINC01315 facilitated the growth and invasion of PTC cells by sponging miR-497-5p. Our results demonstrated the critical role of the LINC01315-miR-497-5p axis in the growth and invasion of PTC cells.
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Affiliation(s)
- Jian Ren
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Feng-Jiao Zhang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Jing-Hong Wang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
| | - Jian-Dong Tang
- Department of Endocrinology, Zhengzhou Central Hospital Affiliated to ZhengZhou University, Zhengzhou, China
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128
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Boija A, Klein IA, Young RA. Biomolecular Condensates and Cancer. Cancer Cell 2021; 39:174-192. [PMID: 33417833 PMCID: PMC8721577 DOI: 10.1016/j.ccell.2020.12.003] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022]
Abstract
Malignant transformation is characterized by dysregulation of diverse cellular processes that have been the subject of detailed genetic, biochemical, and structural studies, but only recently has evidence emerged that many of these processes occur in the context of biomolecular condensates. Condensates are membrane-less bodies, often formed by liquid-liquid phase separation, that compartmentalize protein and RNA molecules with related functions. New insights from condensate studies portend a profound transformation in our understanding of cellular dysregulation in cancer. Here we summarize key features of biomolecular condensates, note where they have been implicated-or will likely be implicated-in oncogenesis, describe evidence that the pharmacodynamics of cancer therapeutics can be greatly influenced by condensates, and discuss some of the questions that must be addressed to further advance our understanding and treatment of cancer.
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Affiliation(s)
- Ann Boija
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Isaac A Klein
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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129
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Huang Z, Qin Q, Xia L, Lian B, Tan Q, Yu Y, Mo Q. Significance of Oncotype DX 21-Gene Test and Expression of Long Non-Coding RNA MALAT1 in Early and Estrogen Receptor-Positive Breast Cancer Patients. Cancer Manag Res 2021; 13:587-593. [PMID: 33519238 PMCID: PMC7837574 DOI: 10.2147/cmar.s276795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/04/2020] [Indexed: 12/21/2022] Open
Abstract
Objective To investigate the association between the recurrence score (RS) obtained by Oncotype DX 21-gene test and long non-coding RNA (lncRNA) MALAT1 expression in early and estrogen receptor-positive (ER+) breast cancer. Materials and Methods The Oncotype DX 21-gene test and MALAT1 expression detection were performed in tumor samples from 76 ER+ and early breast cancer patients with the Surplex liquid chip. The RS value was calculated based on the expression of total 21 genes. The level of MALAT1 was measured in both tumor tissue and para-tumor tissue, and relatively quantified with an internal control gene. Mann–Whitney U-test or Kruskal–Wallis test were used to analyze the association between MALAT1 level and different clinical pathological characteristics, including age, tumor stage, disease grade, lymph node status, Ki-67 expression, and progesterone receptor (PR) status. The association between the RS and different characteristics was analyzed by Wilcoxon rank-sum test. Correlation between two parameters was analyzed by Spearman’s rank correlation analysis. Results The expression of MALAT1 was more abundant in tumor tissue (2.992 ± 2.256) than that in adjacent normal tissue (1.641±1.438, Z=−2.594, p=0.009), and it was not correlated with any clinical pathological characteristics. According to the old criteria for RS stratification, 52.7% of patients were in low risk (RS<18), 36.8% of patients were in medium risk (18≤RS≤30), and 10.5% of patients were in high risk (RS>30). While under the new criteria, 18.4% were in low risk group (RS<11), 63.2% were in a medium risk group (11≤RS≤26), and 18.4% were in a high risk group (RS>26). The Oncotype DX 21-gene results only correlated with Ki-67 expression under both new and old criteria, and it was not related with other cancer characteristics. The expression of lncRNA MALAT1 was significantly correlated with the Oncotype DX 21-gene results under the old criteria. Conclusion MALAT1 is a novel breast cancer biomarker independent of tumor stage, disease grade and lymph node status. MALAT1 level is associated with the Oncotype DX 21-gene RS value. Therefore, combination of MALAT1 and the Oncotype DX 21-gene test may be used to predict prognosis in ER+ and early stage breast cancer.
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Affiliation(s)
- Zhen Huang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qinghong Qin
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Longjie Xia
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Bin Lian
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qixing Tan
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Yinghua Yu
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qinguo Mo
- Department of Breast Surgery, The Affiliated Tumor Hospital of Guangxi Medical University, Nanning, People's Republic of China
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130
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Li G, Deng L, Huang N, Sun F. The Biological Roles of lncRNAs and Future Prospects in Clinical Application. Diseases 2021; 9:diseases9010008. [PMID: 33450825 PMCID: PMC7838801 DOI: 10.3390/diseases9010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Chemo and radiation therapies are the most commonly used therapies for cancer, but they can induce DNA damage, resulting in the apoptosis of host cells. DNA double-stranded breaks (DSBs) are the most lethal form of DNA damage in cells, which are constantly caused by a wide variety of genotoxic agents, both environmentally and endogenously. To maintain genomic integrity, eukaryotic organisms have developed a complex mechanism for the repair of DNA damage. Researches reported that many cellular long noncoding RNAs (lncRNAs) were involved in the response of DNA damage. The roles of lncRNAs in DNA damage response can be regulated by the dynamic modification of N6-adenosine methylation (m6A). The cellular accumulation of DNA damage can result in various diseases, including cancers. Additionally, lncRNAs also play roles in controlling the gene expression and regulation of autophagy, which are indirectly involved with individual development. The dysregulation of these functions can facilitate human tumorigenesis. In this review, we summarized the origin and overview function of lncRNAs and highlighted the roles of lncRNAs involved in the repair of DNA damage.
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Affiliation(s)
- Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
| | - Liang Deng
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
- Correspondence: ; Tel.: +86-021-6630-6909
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131
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Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq. Sci Rep 2021; 11:1175. [PMID: 33441968 PMCID: PMC7806670 DOI: 10.1038/s41598-020-80846-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
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132
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Goyal B, Yadav SRM, Awasthee N, Gupta S, Kunnumakkara AB, Gupta SC. Diagnostic, prognostic, and therapeutic significance of long non-coding RNA MALAT1 in cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188502. [PMID: 33428963 DOI: 10.1016/j.bbcan.2021.188502] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/30/2020] [Accepted: 01/02/2021] [Indexed: 12/20/2022]
Abstract
Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) is a widely studied lncRNA in cancer. Although dispensable for normal physiology, MALAT1 is important for cancer-related pathways regulation. It is localized in the nuclear speckles periphery along with centrally located pre-RNA splicing factors. MALAT1 associated cancer signaling pathways include MAPK/ERK, PI3K/AKT, β-catenin/Wnt, Hippo, VEGF, YAP, etc. Molecular tools such as immunoprecipitation, RNA pull-down, reporter assay, Northern blotting, microarray, and q-RT-PCR has been used to elucidate MALAT1's function in cancer pathogenesis. MALAT1 can regulate multiple steps in the development of tumours. The diagnostic and prognostic significance of MALAT1 has been demonstrated in cancers of the breast, cervix, colorectum, gallbladder, lung, ovary, pancreas, prostate, glioma, hepatocellular carcinoma, and multiple myeloma. MALAT1 has also emerged as a novel therapeutic target for solid as well as hematological malignancies. In experimental models, siRNA and antisense oligonucleotide (ASO) based strategy has been used for targeting MALAT1. The lncRNA has also been targeted for the chemosensitization and radiosensitization of cancer cells. However, most studies have been performed in preclinical models. How the cross-talk of MALAT1 with other signaling pathways affect cancer pathogenesis is the focus of this article. The diagnostic, prognostic, and therapeutic significance of MALAT1 in multiple cancer types are discussed.
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Affiliation(s)
- Bela Goyal
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Shashi Ranjan Mani Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Nikee Awasthee
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Sweety Gupta
- Department of Radiation Oncology, All India Institute of Medical Sciences, Rishikesh, Uttarakhand, India
| | - Ajaikumar B Kunnumakkara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India
| | - Subash Chandra Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Cáceres-Durán MÁ, Ribeiro-dos-Santos Â, Vidal AF. Roles and Mechanisms of the Long Noncoding RNAs in Cervical Cancer. Int J Mol Sci 2020; 21:ijms21249742. [PMID: 33371204 PMCID: PMC7766288 DOI: 10.3390/ijms21249742] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer (CC) continues to be one of the leading causes of death for women across the world. Although it has been determined that papillomavirus infection is one of the main causes of the etiology of the disease, genetic and epigenetic factors are also required for its progression. Among the epigenetic factors are included the long noncoding RNAs (lncRNAs), transcripts of more than 200 nucleotides (nt) that generally do not code for proteins and have been associated with diverse functions such as the regulation of transcription, translation, RNA metabolism, as well as stem cell maintenance and differentiation, cell autophagy and apoptosis. Recently, studies have begun to characterize the aberrant regulation of lncRNAs in CC cells and tissues, including Homeobox transcript antisense RNA (HOTAIR), H19, Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), Cervical Carcinoma High-Expressed 1 (CCHE1), Antisense noncoding RNA in the inhibitors of cyclin-dependent kinase 4 (ANRIL), Growth arrest special 5 (GAS5) and Plasmacytoma variant translocation 1 (PVT1). They have been associated with several disease-related processes such as cell growth, cell proliferation, cell survival, metastasis and invasion as well as therapeutic resistance, and are novel potential biomarkers for diagnosis and prognosis in CC. In this review, we summarize the current literature regarding the knowledge we have about the roles and mechanisms of the lncRNAs in cervical neoplasia.
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Affiliation(s)
- Miguel Ángel Cáceres-Durán
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil; (M.Á.C.-D.); (Â.R.-d.-S.)
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil; (M.Á.C.-D.); (Â.R.-d.-S.)
- Graduate Program in Oncology and Medical Sciences, Center of Oncology Researches, Federal University of Pará, Belém 66073-005, Brazil
| | - Amanda Ferreira Vidal
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém 66075-110, Brazil; (M.Á.C.-D.); (Â.R.-d.-S.)
- Correspondence: ; Tel.: +55-91-3201-7843
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134
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Zhang J, Liu H, Zhang W, Li Y, Fan Z, Jiang H, Luo J. Identification of lncRNA-mRNA Regulatory Module to Explore the Pathogenesis and Prognosis of Melanoma. Front Cell Dev Biol 2020; 8:615671. [PMID: 33392203 PMCID: PMC7773644 DOI: 10.3389/fcell.2020.615671] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/24/2020] [Indexed: 12/21/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is an aggressive form of skin cancer that results in high mortality rate worldwide. It is vital to discover effective prognostic biomarkers and therapeutic targets for the treatment of melanoma. Long non-coding RNA (lncRNA) has been verified to play an essential role in the regulation of gene expression in diseases and tumors. Therefore, it is significant to explore the function of lncRNAs in the development and progression of SKCM. In this paper, a set of differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) were first screened out using 471 cutaneous melanoma samples and 813 normal skin samples. Gene Ontology and KEGG pathway enrichment analysis were performed to obtain the significant function annotations and pathways of DEmRNAs. We also ran survival analysis on both DElncRNAs and DEmRNAs to identify prognostic-related lncRNAs and mRNAs. Next, a set of hub genes derived from protein-protein interaction (PPI) network analysis and lncRNA target genes screened from starbase-ENCORI database were integrated to construct a lncRNA-mRNA regulatory module, which includes 6 lncRNAs 4 target mRNAs. We further checked the capacity of these lncRNA and mRNA in the diagnosis of melanoma, and found that single lncRNA can effectively distinguish tumor and normal tissue. Moreover, we ran CMap analysis to select a list of small molecule drugs for SKCM, such as EGFR inhibitor AG-490, growth factor receptor inhibitor GW-441756 and apoptosis stimulant betulinic-acid, which have shown therapeutic effect in the treatment of melanoma.
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Affiliation(s)
- Jiaqi Zhang
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China.,Department of Dermatology, Graduate School of Dalian Medical University, Dalian, China
| | - Hui Liu
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Wenhao Zhang
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Yinfang Li
- Aliyun School of Big Data, Changzhou University, Changzhou, China
| | - Zhigang Fan
- Department of Oncology, Affiliated 3201 Hospital of Xi'an Jiaotong University, Hanzhong, China
| | - Hua Jiang
- Department of Oncology, The Affiliated Changzhou No.2 People's Hospital of Nanjing Medical University, Changzhou, China
| | - Judong Luo
- Department of Radiotherapy, The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University, Changzhou, China
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135
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Extracellular Vesicles from Adipose Tissue Stem Cells in Diabetes and Associated Cardiovascular Disease; Pathobiological Impact and Therapeutic Potential. Int J Mol Sci 2020; 21:ijms21249598. [PMID: 33339409 PMCID: PMC7766415 DOI: 10.3390/ijms21249598] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023] Open
Abstract
Adipose tissue-derived stem cells (ADSCs) are pluripotent mesenchymal stem cells found in relatively high percentages in the adipose tissue and able to self-renew and differentiate into many different types of cells. “Extracellular vesicles (EVs), small membrane vesicular structures released during cell activation, senescence, or apoptosis, act as mediators for long distance communication between cells, transferring their specific bioactive molecules into host target cells”. There is a general consensus on how to define and isolate ADSCs, however, multiple separation and characterization protocols are being used in the present which complicate the results’ integration in a single theory on ADSCs’ and their derived factors’ way of action. Metabolic syndrome and type 2 diabetes mellitus (T2DM) are mainly caused by abnormal adipose tissue size, distribution and metabolism and so ADSCs and their secretory factors such as EVs are currently investigated as therapeutics in these diseases. Moreover, due to their relatively easy isolation and propagation in culture and their differentiation ability, ADSCs are being employed in preclinical studies of implantable devices or prosthetics. This review aims to provide a comprehensive summary of the current knowledge on EVs secreted from ADSCs both as diagnostic biomarkers and therapeutics in diabetes and associated cardiovascular disease, the molecular mechanisms involved, as well as on the use of ADSC differentiation potential in cardiovascular tissue repair and prostheses.
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136
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NIMBus: a negative binomial regression based Integrative Method for mutation Burden Analysis. BMC Bioinformatics 2020; 21:474. [PMID: 33092526 PMCID: PMC7580035 DOI: 10.1186/s12859-020-03758-1] [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: 11/18/2019] [Accepted: 09/16/2020] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Identifying frequently mutated regions is a key approach to discover DNA elements influencing cancer progression.
However, it is challenging to identify these burdened regions due to mutation rate heterogeneity across the genome and across different individuals. Moreover, it is known that this heterogeneity partially stems from genomic confounding factors, such as replication timing and chromatin organization. The increasing availability of cancer whole genome sequences and functional genomics data from the Encyclopedia of DNA Elements (ENCODE) may help address these issues.
Results
We developed a negative binomial regression-based Integrative Method for mutation Burden analysiS (NIMBus). Our approach addresses the over-dispersion of mutation count statistics by (1) using a Gamma–Poisson mixture model to capture the mutation-rate heterogeneity across different individuals and (2) estimating regional background mutation rates by regressing the varying local mutation counts against genomic features extracted from ENCODE. We applied NIMBus to whole-genome cancer sequences from the PanCancer Analysis of Whole Genomes project (PCAWG) and other cohorts. It successfully identified well-known coding and noncoding drivers, such as TP53 and the TERT promoter. To further characterize the burdening of non-coding regions, we used NIMBus to screen transcription factor binding sites in promoter regions that intersect DNase I hypersensitive sites (DHSs). This analysis identified mutational hotspots that potentially disrupt gene regulatory networks in cancer. We also compare this method to other mutation burden analysis methods.
Conclusion
NIMBus is a powerful tool to identify mutational hotspots. The NIMBus software and results are available as an online resource at github.gersteinlab.org/nimbus.
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137
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Jin KT, Lu ZB, Lv JQ, Zhang JG. The role of long non-coding RNAs in mediating chemoresistance by modulating autophagy in cancer. RNA Biol 2020; 17:1727-1740. [PMID: 32129701 PMCID: PMC7714480 DOI: 10.1080/15476286.2020.1737787] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/13/2022] Open
Abstract
Cancer is a complex process in which protein-coding and non-coding genes play essential roles. Long noncoding RNAs (lncRNAs), as a subclass of noncoding genes, are implicated in various cancer processes including growth, proliferation, metastasis, and angiogenesis. Due to presence in body fluids such as blood and urine, lncRNAs have become novel biomarkers in cancer detection, diagnosis, progression, and therapy response. Remarkably, increasing evidence has verified that lncRNAs play essential roles in chemoresistance by targeting different signalling pathways. Autophagy, a highly conserved process in response to environmental stresses such as starvation and hypoxia, plays a paradoxical role in inducing resistance or sensitivity to chemotherapy agents. In this regard, we reviewed chemoresistance, the role of lncRNAs in cancer, and the role of lncRNAs in chemoresistance by modulating autophagy.
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Affiliation(s)
- Ke-Tao Jin
- Department of Colorectal Surgery, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, Zhejiang Province, P.R. China
| | - Ze-Bei Lu
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital (People’s Hospital of Hangzhou Medical College), Hangzhou, Zhejiang Province, P.R. China
| | - Jie-Qing Lv
- Department of Colorectal Surgery, Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, Zhejiang Province, P.R. China
| | - Jun-Gang Zhang
- Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital (People’s Hospital of Hangzhou Medical College), Hangzhou, Zhejiang Province, P.R. China
- Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital (People’s Hospital of Hangzhou Medical College), Hangzhou, Zhejiang Province, P.R. China
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138
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Marzano F, Caratozzolo MF, Consiglio A, Licciulli F, Liuni S, Sbisà E, D'Elia D, Tullo A, Catalano D. Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. Front Genet 2020; 11:552490. [PMID: 33193626 PMCID: PMC7531330 DOI: 10.3389/fgene.2020.552490] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/20/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are ubiquitous regulators of gene expression, evolutionarily conserved in plants and mammals. In recent years, although a growing number of papers debate the role of plant miRNAs on human gene expression, the molecular mechanisms through which this effect is achieved are still not completely elucidated. Some evidence suggest that this interaction might be sequence specific, and in this work, we investigated this possibility by transcriptomic and bioinformatics approaches. Plant and human miRNA sequences from primary databases were collected and compared for their similarities (global or local alignments). Out of 2,588 human miRNAs, 1,606 showed a perfect match of their seed sequence with the 5′ end of 3,172 plant miRNAs. Further selections were applied based on the role of the human target genes or of the miRNA in cell cycle regulation (as an oncogene, tumor suppressor, or a biomarker for prognosis, or diagnosis in cancer). Based on these criteria, 20 human miRNAs were selected as potential functional analogous of 7 plant miRNAs, which were in turn transfected in different cell lines to evaluate their effect on cell proliferation. A significant decrease was observed in colorectal carcinoma HCT116 cell line. RNA-Seq demonstrated that 446 genes were differentially expressed 72 h after transfection. Noteworthy, we demonstrated that the plant mtr-miR-5754 and gma-miR4995 directly target the tumor-associated long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and nuclear paraspeckle assembly transcript 1 (NEAT1) in a sequence-specific manner. In conclusion, according to other recent discoveries, our study strengthens and expands the hypothesis that plant miRNAs can have a regulatory effect in mammals by targeting both protein-coding and non-coding RNA, thus suggesting new biotechnological applications.
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Affiliation(s)
- Flaviana Marzano
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Mariano Francesco Caratozzolo
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Arianna Consiglio
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Flavio Licciulli
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Sabino Liuni
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Elisabetta Sbisà
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Domenica D'Elia
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
| | - Apollonia Tullo
- Department of Biomedical Sciences, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy
| | - Domenico Catalano
- Department of Biomedical Sciences, Institute for Biomedical Technologies, Bari, Italy
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139
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Luo G, He K, Xia Z, Liu S, Liu H, Xiang G. Regulation of microRNA-497 expression in human cancer. Oncol Lett 2020; 21:23. [PMID: 33240429 PMCID: PMC7681205 DOI: 10.3892/ol.2020.12284] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/28/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs/miRs) are a type of non-coding single-stranded RNA, with a length of ~22 nt, which are encoded by endogenous genes and are involved in the post-transcriptional regulation of gene expression in animals and plants. Studies have demonstrated that miRNAs play an important role in the occurrence, development, metastasis, diagnosis and treatment of cancer. In recent years, miR-497 has been identified as one of the key miRNAs in a variety of cancer types and has been shown to be downregulated in a variety of solid tumors. However, the regulation of miR-497 expression involves a complex network, which is affected by several factors. The aim of the present review was to summarize the mechanism of regulation of miR-497 expression at the pre-transcriptional and transcriptional levels in cancer, as well as the role of miR-497 expression imbalance in cancer diagnosis, treatment and prognosis. The regulatory mechanisms of miR-497 expression may aid in our understanding of the causes of miR-497 expression imbalance and provide a reference value for further research on the diagnosis and treatment of cancer.
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Affiliation(s)
- Guanshui Luo
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China.,Department of Postgraduate Studies, The Second Clinical College of Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Ke He
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China
| | - Zhenglin Xia
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China
| | - Shuai Liu
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China
| | - Hong Liu
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China
| | - Guoan Xiang
- Department of General Surgery, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong 510317, P.R. China
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140
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Fu S, Wang Y, Li H, Chen L, Liu Q. Regulatory Networks of LncRNA MALAT-1 in Cancer. Cancer Manag Res 2020; 12:10181-10198. [PMID: 33116873 PMCID: PMC7575067 DOI: 10.2147/cmar.s276022] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/03/2020] [Indexed: 12/18/2022] Open
Abstract
Long noncoding (lnc)RNAs are a group of RNAs with a length greater than 200 nt that do not encode a protein but play an essential role in regulating the expression of target genes in normal biological contexts as well as pathologic processes including tumorigenesis. The lncRNA metastasis-associated lung adenocarcinoma transcript (MALAT)-1 has been widely studied in cancer. In this review, we describe the known functions of MALAT-1; its mechanisms of action; and associated signaling pathways and their clinical significance in different cancers. In most malignancies, including lung, colorectal, thyroid, and other cancers, MALAT-1 functions as an oncogene and is upregulated in tumors and tumor cell lines. MALAT-1 has a distinct mechanism of action in each cancer type and is thus at the center of large gene regulatory networks. Dysregulation of MALAT-1 affects cellular processes such as alternative splicing, epithelial–mesenchymal transition, apoptosis, and autophagy, which ultimately results in the abnormal cell proliferation, invasion, and migration that characterize cancers. In other malignancies, such as glioma and endometrial carcinoma, MALAT-1 functions as a tumor suppressor and thus forms additional regulatory networks. The current evidence indicates that MALAT-1 and its associated signaling pathways can serve as diagnostic or prognostic biomarker or therapeutic target in the treatment of many cancers.
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Affiliation(s)
- Shijian Fu
- The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Yanhong Wang
- Department of Laboratory Medicine, Yuebei People's Hospital of Shaoguan, The Affiliated Hospital of Shantou University, Shaoguan 512025, People's Republic of China
| | - Hang Li
- The First Affiliated Hospital of Harbin Medical University, Harbin 150081, People's Republic of China
| | - Leilei Chen
- Department of Cardiology, Beijing Anzhen Hospital, Beijing Institute of Heart Lung and Blood Vessel Disease, Capital Medical University, Beijing 100029, People's Republic of China
| | - Quanzhong Liu
- Department of Medical Genetics, Harbin Medical University, Harbin 150081, People's Republic of China
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141
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Jiang T, Cai Z, Ji Z, Zou J, Liang Z, Zhang G, Liang Y, Lin H, Tan M. The lncRNA MALAT1/miR-30/Spastin Axis Regulates Hippocampal Neurite Outgrowth. Front Cell Neurosci 2020; 14:555747. [PMID: 33192306 PMCID: PMC7606917 DOI: 10.3389/fncel.2020.555747] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 09/23/2020] [Indexed: 11/13/2022] Open
Abstract
Spastin, a microtubule-severing enzyme, is important for neurite outgrowth. However, the mechanisms underlying the post-transcriptional regulation of spastin during microtubule-related processes are largely unknown. We demonstrated that the spastin expression level is controlled by a long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/microRNA-30 (miR-30) axis during neurite outgrowth. The miR-30 expression level decreased in hippocampal neurons with increasing days in culture, and miR-30 overexpression suppressed while miR-30 inhibition promoted neurite outgrowth in hippocampal neurons. Spastin was validated as a target gene of miR-30 using the luciferase reporter assay. The protein expression, microtubule severing activity, and neurite promoting effect of spastin were suppressed by the overexpression of miR-30 mimics and increased by miR-30 inhibitors. MALAT1 expression increased during neurite outgrowth and MALAT1 silencing impaired neurite outgrowth. miR-30 was a sponge target of MALAT1 and MALAT1/miR-30 altered neurite outgrowth in hippocampal neurons. MALAT1 overexpression reversed the inhibitory effect of miR-30 on the activity of a luciferase reporter construct containing spastin, as well as spastin mRNA and protein expression, indicating that spastin was a downstream effector of MALAT1/miR-30. The MALAT1/miR-30 cascade also modulated spastin-induced microtubule severing, and the MALAT1/miR-30/spastin axis regulated neurite outgrowth in hippocampal neurons. This study suggests a new mechanism governing neurite outgrowth in hippocampal neurons involving MALAT1/miR-30-regulated spastin expression.
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Affiliation(s)
- Tao Jiang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Orthopaedics, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Zhenbin Cai
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhisheng Ji
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jianyu Zou
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zhi Liang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Guowei Zhang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yaozhong Liang
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Hongsheng Lin
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Minghui Tan
- Department of Orthopaedics, The First Affiliated Hospital of Jinan University, Guangzhou, China
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142
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Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Sci Rep 2020; 10:17597. [PMID: 33077815 PMCID: PMC7572424 DOI: 10.1038/s41598-020-74483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/30/2020] [Indexed: 01/25/2023] Open
Abstract
Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.
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143
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Zhang Z, Zhang W, Wen QW, Wang TH, Qin W, Huang H, Mo YJ, Wu XD, Cen H. Associations of genetic polymorphisms within MALAT1, UCA1, FAM211A-AS1 and AC000111.6 with genetic susceptibility to rheumatoid arthritis. Autoimmunity 2020; 53:408-414. [PMID: 32909867 DOI: 10.1080/08916934.2020.1818230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Recently, several long non-coding RNAs (lncRNAs) including MALAT1, UCA1, ENST00000483588, and ENST00000456270 have been implicated in the pathogenesis of rheumatoid arthritis (RA), and we hypothesized that polymorphisms within these lncRNA genes might be genetic modifiers for the development of RA. A total of 10 potentially functional single-nucleotide polymorphisms (SNPs) were selected and genotyped in 1198 participants, including 594 RA patients and 604 healthy controls. Significant associations of FAM211A-AS1 rs2882581 (G vs. A, OR = 1.31, 95%CI 1.07-1.62, p = .01; G/G + A/G vs. A/A, OR = 1.40, 95%CI 1.08-1.83, p = .01), rs3744281 (T vs. A, OR = 1.25, 95%CI 1.02-1.54, p = .03; T/T vs. A/T + A/A, OR = 1.69, 95%CI 1.01-2.82, p = 4.59 × 10-2), and rs3760235 (A vs. G, OR = 1.32, 95%CI 1.04-1.68, p = .02; A/A vs. A/G + G/G, OR = 1.32, 95%CI 1.00-1.74, p = 4.89 × 10-2) with RF-positive RA were found. Functional annotation results indicated that these identified polymorphisms might regulate the expression of FAM211A-AS1 and nearby genes via impacting on transcription factor binding. Taken together, our results indicated that FAM211A-AS1 rs2882581, rs3744281, and rs3760235 were involved in the genetic background of RF-positive RA.
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Affiliation(s)
- Zhen Zhang
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Wei Zhang
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo, Zhejiang, PR China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang, PR China
| | - Qin-Wen Wen
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Ting-Hui Wang
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Wen Qin
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Hua Huang
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Yi-Jun Mo
- Department of Physical Examination, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, China
| | - Xiu-Di Wu
- Department of Rheumatology, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, Zhejiang, PR China
| | - Han Cen
- Department of Preventive Medicine, Medical School of Ningbo University, Ningbo, Zhejiang, PR China.,Zhejiang Provincial Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, Zhejiang, PR China
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144
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Rong F, Liu L, Zou C, Zeng J, Xu Y. MALAT1 Promotes Cell Tumorigenicity Through Regulating miR-515-5p/EEF2 Axis in Non-Small Cell Lung Cancer. Cancer Manag Res 2020; 12:7691-7701. [PMID: 32943920 PMCID: PMC7468487 DOI: 10.2147/cmar.s242425] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 08/06/2020] [Indexed: 12/12/2022] Open
Abstract
Background Previous studies suggested long noncoding RNA metastasis associated with lung adenocarcinoma transcript 1 (lncRNA MALAT1) acted as a tumor promoter to promote cell carcinogenesis in non-small cell lung cancer (NSCLC). MALAT1 was found to exist in serum exosomes of several cancers. However, the role of exosomal-derived MALAT1 in NSCLC remains poorly understood. Materials and Methods Exosomes were isolated using the ExoQuick precipitation kit. Western blot was used to detect the protein expression of CD3, CD63, apoptosis- and metastasis-related protein. The expression of MALAT1, microRNA (miR)-515-5p and eukaryotic elongation factor 2 (EEF2) mRNA was detected using quantitative real-time polymerase chain reaction. Cell viability, apoptosis, or invasion were measured using 3-(4, 5)-dimethylthiahiazo (-z-y1)-3, 5-di-phenytetrazoliumromide (MTT) assay, flow cytometry or transwell assay, respectively. The interaction between miR-515-5p and MALAT1 or EEF2 was confirmed by dual-luciferase reporter assay. In vivo experiments were conducted through the murine xenograft model. Results MALAT1 was highly expressed in serum and cell exosomes from NSCLC patients. MALAT1 knockdown repressed cell proliferation, invasion and induced cell apoptosis in vitro as well as inhibited tumor growth in vivo in NSCLC. Subsequently, we confirmed that MALAT1 was a sponge of miR-515-5p, and EEF2 was a target of miR-515-5p. Furthermore, MALAT1 served as a sponge of miR-515-5p to regulate EEF2 expression in NSCLC cells. More importantly, MALAT1 deletion performed anti-tumor effects by interacting with miR-515-5p/EEF2 axis in vitro and in vivo in NSCLC. Conclusion MALAT1 knockdown repressed NSCLC tumorigenicity by inhibiting cell proliferation, invasion and promoting apoptosis through regulating miR-515-5p/EEF2, besides, MALAT1 was highly enriched in exosomes of NSCLC, suggesting a possible molecular-targeted therapy for NSCLC patients.
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Affiliation(s)
- Feng Rong
- Department of Respiratory, Xiantao First People's Hospital Affiliated to Changjiang University, Xiantao, Hubei, People's Republic of China
| | - Liang Liu
- Department of Respiratory, Xiantao First People's Hospital Affiliated to Changjiang University, Xiantao, Hubei, People's Republic of China
| | - Can Zou
- Department of Respiratory, Xiantao First People's Hospital Affiliated to Changjiang University, Xiantao, Hubei, People's Republic of China
| | - Jing Zeng
- Department of Respiratory, Xiantao First People's Hospital Affiliated to Changjiang University, Xiantao, Hubei, People's Republic of China
| | - Yasheng Xu
- Department of Respiratory, Xiantao First People's Hospital Affiliated to Changjiang University, Xiantao, Hubei, People's Republic of China
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145
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Donlic A, Zafferani M, Padroni G, Puri M, Hargrove A. Regulation of MALAT1 triple helix stability and in vitro degradation by diphenylfurans. Nucleic Acids Res 2020; 48:7653-7664. [PMID: 32667657 PMCID: PMC7430642 DOI: 10.1093/nar/gkaa585] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/18/2020] [Accepted: 07/09/2020] [Indexed: 12/23/2022] Open
Abstract
Small molecule-based modulation of a triple helix in the long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been proposed as an attractive avenue for cancer treatment and a model system for understanding small molecule:RNA recognition. To elucidate fundamental recognition principles and structure-function relationships, we designed and synthesized nine novel analogs of a diphenylfuran-based small molecule DPFp8, a previously identified lead binder of MALAT1. We investigated the role of recognition modalities in binding and in silico studies along with the relationship between affinity, stability and in vitro enzymatic degradation of the triple helix. Specifically, molecular docking studies identified patterns driving affinity and selectivity, including limited ligand flexibility, as observed by ligand preorganization and 3D shape complementarity for the binding pocket. The use of differential scanning fluorimetry allowed rapid evaluation of ligand-induced thermal stabilization of the triple helix, which correlated with decreased in vitro degradation of this structure by the RNase R exonuclease. The magnitude of stabilization was related to binding mode and selectivity between the triple helix and its precursor stem loop structure. Together, this work demonstrates the value of scaffold-based libraries in revealing recognition principles and of raising broadly applicable strategies, including functional assays, for small molecule-RNA targeting.
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Affiliation(s)
- Anita Donlic
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Martina Zafferani
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Giacomo Padroni
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Malavika Puri
- Department of Chemistry, Duke University, 124 Science Drive, Durham, NC 27708, USA
| | - Amanda E Hargrove
- To whom correspondence should be addressed. Tel: +1 919 660 1522; Fax: +1 919 660 1522;
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146
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LncRNA MALAT1 inhibits apoptosis of endometrial stromal cells through miR-126-5p-CREB1 axis by activating PI3K-AKT pathway. Mol Cell Biochem 2020; 475:185-194. [PMID: 32809092 DOI: 10.1007/s11010-020-03871-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/01/2020] [Indexed: 12/13/2022]
Abstract
Endometriosis is a common, chronic and painful disease in women, whose pathogenesis remains not entirely clear. Long non-coding RNA (lncRNA) MALAT1 participates in the development of endometriosis. This study further investigated the regulation of MALAT1-miR-126-5p-CREB1 axis in the pathological process of endometriosis. MALAT1, miR-126-5p, and CREB1 levels in human endometrial stromal cells (HESCs) were detected by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Protein levels were determined by Western blotting. Cell viability and apoptosis was assessed by MTT assay and annexin V-FITC staining, respectively. The interactivity between miR-126-5p and MALAT1 (or CREB1) was assessed by dual luciferase reporter system. Knockdown of MALAT1 or CREB1 restrained proliferation and induced apoptosis as confirmed by upregulating cleaved caspase-3 and Bax, and down-regulating Bcl-2 in HESCs, while inhibition of miR-126-5p presented the opposite results. Moreover, silencing of MALAT1 triggered apoptosis of HESCs via targeting miR-126-5p. In addition, miR-126-5p directly regulated CREB1 expression via binding to its 3' non-coding region. Finally, miR-126-5p inhibitor-mediated apoptosis inhibition was restrained by CREB1 silencing via inactivation of PI3K-AKT pathway in HESCs. Taken together, our study firstly demonstrates that MALAT1 regulates apoptosis of HESCs through miR-126-5p/CREB1 axis mediated PI3K/AKT pathway. Our findings explained the pathogenesis of endometriosis and offered promising therapeutic option for endometriosis.
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147
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Tsurumi A, Li WX. Aging mechanisms-A perspective mostly from Drosophila. ADVANCED GENETICS (HOBOKEN, N.J.) 2020; 1:e10026. [PMID: 36619249 PMCID: PMC9744567 DOI: 10.1002/ggn2.10026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 04/04/2020] [Accepted: 04/08/2020] [Indexed: 01/11/2023]
Abstract
A mechanistic understanding of the natural aging process, which is distinct from aging-related disease mechanisms, is essential for developing interventions to extend lifespan or healthspan. Here, we discuss current trends in aging research and address conceptual and experimental challenges in the field. We examine various molecular markers implicated in aging with an emphasis on the role of heterochromatin and epigenetic changes. Studies in model organisms have been advantageous in elucidating conserved genetic and epigenetic mechanisms and assessing interventions that affect aging. We highlight the use of Drosophila, which allows controlled studies for evaluating genetic and environmental contributors to aging conveniently. Finally, we propose the use of novel methodologies and future strategies using Drosophila in aging research.
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Affiliation(s)
- Amy Tsurumi
- Department of SurgeryMassachusetts General Hospital, and Harvard Medical SchoolBostonMassachusettsUSA,Department of Microbiology and ImmunologyHarvard Medical SchoolBostonMassachusettsUSA,Shriners Hospitals for Children‐Boston®BostonMassachusettsUSA
| | - Willis X. Li
- Department of MedicineUniversity of California at San DiegoLa JollaCaliforniaUSA
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148
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Nozawa RS, Yamamoto T, Takahashi M, Tachiwana H, Maruyama R, Hirota T, Saitoh N. Nuclear microenvironment in cancer: Control through liquid-liquid phase separation. Cancer Sci 2020; 111:3155-3163. [PMID: 32594560 PMCID: PMC7469853 DOI: 10.1111/cas.14551] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
The eukaryotic nucleus is not a homogenous single‐spaced but a highly compartmentalized organelle, partitioned by various types of membraneless structures, including nucleoli, PML bodies, paraspeckles, DNA damage foci and RNA clouds. Over the past few decades, these nuclear structures have been implicated in biological reactions such as gene regulation and DNA damage response and repair, and are thought to provide “microenvironments,” facilitating these reactions in the nucleus. Notably, an altered morphology of these nuclear structures is found in many cancers, which may relate to so‐called “nuclear atypia” in histological examinations. While the diagnostic significance of nuclear atypia has been established, its nature has remained largely enigmatic and awaits characterization. Here, we review the emerging biophysical principles that govern biomolecular condensate assembly in the nucleus, namely, liquid‐liquid phase separation (LLPS), to investigate the nature of the nuclear microenvironment. In the nucleus, LLPS is typically driven by multivalent interactions between proteins with intrinsically disordered regions, and is also facilitated by protein interaction with nucleic acids, including nuclear non–coding RNAs. Importantly, an altered LLPS leads to dysregulation of nuclear events and epigenetics, and often to tumorigenesis and tumor progression. We further note the possibility that LLPS could represent a new therapeutic target for cancer intervention.
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Affiliation(s)
- Ryu-Suke Nozawa
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Tatsuro Yamamoto
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Motoko Takahashi
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Hiroaki Tachiwana
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Reo Maruyama
- Project for Cancer Epigenomics, The Cancer Institute of JFCR, Tokyo, Japan
| | - Toru Hirota
- Division of Experimental Pathology, The Cancer Institute of JFCR, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, Japan
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149
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Yu J, Jin T, Zhang T. Suppression of Long Non-Coding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 (MALAT1) Potentiates Cell Apoptosis and Drug Sensitivity to Taxanes and Adriamycin in Breast Cancer. Med Sci Monit 2020; 26:e922672. [PMID: 32623440 PMCID: PMC7357251 DOI: 10.12659/msm.922672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/04/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is expressed highly in various types of tumors. Moreover, the tumor-initiating role of MALAT1 has been probed in the context of breast cancer. This study was set to investigate the regulatory role of MALAT1 on the chemosensitivity of breast cancer cells to taxanes (Tax) and adriamycin (Adr). MATERIAL AND METHODS Following the measurement of MALAT1 expression in patients with breast cancer by means of qRT-PCR, the connection between the MALAT1 expression pattern and the prognosis of breast cancer patients as well as the molecular typing of breast cancer patients was analyzed using Kaplan-Meier survival analysis and receiver operating characteristic (ROC) curves. Next, the analysis between the expression of MALAT1 and the clinical symptoms of breast cancer patients was carried out. Subsequently, we generated taxane-resistant MCF-7 cells (MCF-7/Tax) and purchased Adr-resistant MCF-7 cells (MCF-7/Adr). Finally, the proliferation, apoptosis and drug resistance of resistant and parental cells were evaluated after transfection of silencing MALAT1 into these cells. RESULTS MALAT1 was highly expressed in the breast cancer tissues. Moreover, patients with relative overexpression of MALAT1 had worse prognosis. MALAT1 expression was remarkably promoted in MCF-7/Tax and MCF-7/Adr cells, whose sensitivity to Tax and Adr was enhanced following MALAT1 knockdown. CONCLUSIONS MALAT1 was elevated in breast cancer tissues and MCF-7-resistant cells, relative to corresponding controls and downregulation of MALAT1 inhibited the growth and chemoresistance of breast cancer cells to Tax and Adr.
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Affiliation(s)
- Jie Yu
- Department of General Surgery I, Zhuji Central Hospital, Zhuji, Zhejiang, P.R. China
| | - Taobo Jin
- Department of Thyroid and Breast Surgery, Zhuji People’s Hospital, Zhuji, Zhejiang, P.R. China
| | - Tianya Zhang
- Department of Thyroid and Breast Surgery, Zhuji People’s Hospital, Zhuji, Zhejiang, P.R. China
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Kesherwani V, Shukla M, Coulter DW, Sharp JG, Joshi SS, Chaturvedi NK. Long non-coding RNA profiling of pediatric Medulloblastoma. BMC Med Genomics 2020; 13:87. [PMID: 32591022 PMCID: PMC7318516 DOI: 10.1186/s12920-020-00744-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Background Medulloblastoma (MB) is one of the most common malignant cancers in children. MB is primarily classified into four subgroups based on molecular and clinical characteristics as (1) WNT (2) Sonic-hedgehog (SHH) (3) Group 3 (4) Group 4. Molecular characteristics used for MB classification are based on genomic and mRNAs profiles. MB subgroups share genomic and mRNA profiles and require multiple molecular markers for differentiation from each other. Long non-coding RNAs (lncRNAs) are more than 200 nucleotide long RNAs and primarily involve in gene regulation at epigenetic and post-transcriptional levels. LncRNAs have been recognized as diagnostic and prognostic markers in several cancers. However, the lncRNA expression profile of MB is unknown. Methods We used the publicly available gene expression datasets for the profiling of lncRNA expression across MB subgroups. Functional analysis of differentially expressed lncRNAs was accomplished by Ingenuity pathway analysis (IPA). Results In the current study, we have identified and validated the lncRNA expression profile across pediatric MB subgroups and associated molecular pathways. We have also identified the prognostic significance of lncRNAs and unique lncRNAs associated with each MB subgroup. Conclusions Identified lncRNAs can be used as single biomarkers for molecular identification of MB subgroups that warrant further investigation and functional validation.
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Affiliation(s)
- Varun Kesherwani
- Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE, 69198, USA
| | - Mamta Shukla
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 69198, USA
| | - Don W Coulter
- Department of Pediatrics, Hematology and Oncology Division, University of Nebraska Medical Center, Omaha, NE, 986395, USA
| | - J Graham Sharp
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 69198, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 69198, USA
| | - Nagendra K Chaturvedi
- Department of Pediatrics, Hematology and Oncology Division, University of Nebraska Medical Center, Omaha, NE, 986395, USA. .,Nebraska Medical Center, Omaha, NE, USA.
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