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Lyu QR, Zhang S, Zhang Z, Tang Z. Functional knockout of long non-coding RNAs with genome editing. Front Genet 2023; 14:1242129. [PMID: 37705609 PMCID: PMC10495571 DOI: 10.3389/fgene.2023.1242129] [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: 06/18/2023] [Accepted: 08/16/2023] [Indexed: 09/15/2023] Open
Abstract
An effective loss-of-function study is necessary to investigate the biological function of long non-coding RNA (lncRNA). Various approaches are available, including RNA silencing, antisense oligos, and CRISPR-based genome editing. CRISPR-based genome editing is the most widely used for inactivating lncRNA function at the genomic level. Knocking out the lncRNA function can be achieved by removing the promoter and the first exon (PE1), introducing pre-termination poly(A) signals, or deleting the entire locus, unlike frameshift strategies used for messenger RNA (mRNA). However, the intricate genomic interplay between lncRNA and neighbor genes makes it challenging to interpret lncRNA function accurately. This article discusses the advantages and disadvantages of each lncRNA knockout method and envisions the potential future directions to facilitate lncRNA functional study.
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Affiliation(s)
- Qing Rex Lyu
- Medical Research Center, Chongqing General Hospital, Chongqing, China
- Chongqing Academy of Medical Sciences, Chongqing, China
| | - Shikuan Zhang
- Key Lab in Healthy Science and Technology of Shenzhen, Tsinghua Shenzhen International Graduate School, Shenzhen, China
| | - Zhe Zhang
- Department of Chinese Medical Gastrointestinal of China-Japan Friendship Hospital, Beijing, China
| | - Zhiyu Tang
- Medical Research Center, Chongqing General Hospital, Chongqing, China
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Furtado CLM, da Silva Santos R, Sales SLA, Teixeira LPR, Pessoa CDÓ. Long Non-coding RNAs and CRISPR-Cas Edition in Tumorigenesis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1429:41-58. [PMID: 37486515 DOI: 10.1007/978-3-031-33325-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are one of the most abundant and heterogeneous transcripts with key roles in chromatin remodeling and gene regulation at the transcriptional and post-transcriptional levels. Due to their role in cell growth and differentiation, lncRNAs have emerged as an important biomarker in cancer diagnosis, prognosis, and targeted treatment. Recent studies have focused on elucidating lncRNA function during malignant transformation, tumor progression and drug resistance. The advent of the CRISPR system has made it possible to precisely edit complex genomic loci such as lncRNAs. Thus, we summarized the advances in CRISPR-Cas approaches for functional studies of lncRNAs including gene knockout, knockdown, overexpression and RNA targeting in tumorigenesis and drug resistance. Additionally, we highlighted the perspectives and potential applications of CRISPR approaches to treat cancer, as an emerging and promising target therapy.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- University of Fortaleza, Experimental Biology Center, Fortaleza, Ceara, Brazil.
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceara, Fortaleza, Brazil.
| | - Renan da Silva Santos
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | - Sarah Leyenne Alves Sales
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
| | | | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology, Drug Research and Development Center, Federal University of Ceara, Fortaleza, Brazil
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Emerging applications of CRISPR/Cas9 gene editing technology in reversing drug resistance in oral squamous cell carcinoma. Oral Oncol 2022; 134:106100. [PMID: 36063701 DOI: 10.1016/j.oraloncology.2022.106100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/21/2022]
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Hussen BM, Kheder RK, Abdullah ST, Hidayat HJ, Rahman HS, Salihi A, Taheri M, Ghafouri-Fard S. Functional interplay between long non-coding RNAs and Breast CSCs. Cancer Cell Int 2022; 22:233. [PMID: 35864503 PMCID: PMC9306174 DOI: 10.1186/s12935-022-02653-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 07/12/2022] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) represents aggressive cancer affecting most women’s lives globally. Metastasis and recurrence are the two most common factors in a breast cancer patient's poor prognosis. Cancer stem cells (CSCs) are tumor cells that are able to self-renew and differentiate, which is a significant factor in metastasis and recurrence of cancer. Long non-coding RNAs (lncRNAs) describe a group of RNAs that are longer than 200 nucleotides and do not have the ability to code for proteins. Some of these lncRNAs can be mainly produced in various tissues and tumor forms. In the development and spread of malignancies, lncRNAs have a significant role in influencing multiple signaling pathways positively or negatively, making them promise useful diagnostic and prognostic markers in treating the disease and guiding clinical therapy. However, it is not well known how the interaction of lncRNAs with CSCs will affect cancer development and progression. Here, in this review, we attempt to summarize recent findings that focus on lncRNAs affect cancer stem cell self-renewal and differentiation in breast cancer development and progression, as well as the strategies and challenges for overcoming lncRNA's therapeutic resistance.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil , Kurdistan Region, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Ramiar Kamal Kheder
- Department of Medical Analysis, Faculty of Science, Tishk International University, Erbil, Iraq.,Medical Laboratory Science, College of Science, University of Raparin, Rania, KGR, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Heshu Sulaiman Rahman
- Department of Physiology, College of Medicine, University of Sulaimani, Sulaimaniyah, Republic of Iraq.,Department of Medical Laboratory Sciences, Komar University of Science and Technology, Sulaimaniyah, Republic of Iraq
| | - Abbas Salihi
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Institute of Human Genetics, Jena University Hospital, Jena, Germany.
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Tellez-Gabriel M, Tekpli X, Reine TM, Hegge B, Nielsen SR, Chen M, Moi L, Normann LS, Busund LTR, Calin GA, Mælandsmo GM, Perander M, Theocharis AD, Kolset SO, Knutsen E. Serglycin Is Involved in TGF-β Induced Epithelial-Mesenchymal Transition and Is Highly Expressed by Immune Cells in Breast Cancer Tissue. Front Oncol 2022; 12:868868. [PMID: 35494005 PMCID: PMC9047906 DOI: 10.3389/fonc.2022.868868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 12/03/2022] Open
Abstract
Serglycin is a proteoglycan highly expressed by immune cells, in which its functions are linked to storage, secretion, transport, and protection of chemokines, proteases, histamine, growth factors, and other bioactive molecules. In recent years, it has been demonstrated that serglycin is also expressed by several other cell types, such as endothelial cells, muscle cells, and multiple types of cancer cells. Here, we show that serglycin expression is upregulated in transforming growth factor beta (TGF-β) induced epithelial-mesenchymal transition (EMT). Functional studies provide evidence that serglycin plays an important role in the regulation of the transition between the epithelial and mesenchymal phenotypes, and it is a significant EMT marker gene. We further find that serglycin is more expressed by breast cancer cell lines with a mesenchymal phenotype as well as the basal-like subtype of breast cancers. By examining immune staining and single cell sequencing data of breast cancer tissue, we show that serglycin is highly expressed by infiltrating immune cells in breast tumor tissue.
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Affiliation(s)
- Marta Tellez-Gabriel
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Trine M. Reine
- Department of Interphase Genetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - Beate Hegge
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Stephanie R. Nielsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Meng Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Line Moi
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - Lisa Svartdal Normann
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Department of Research and Innovation, Vestre Viken Hospital Trust, Drammen, Norway
| | - Lill-Tove R. Busund
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Clinical Pathology, University Hospital of North Norway, Tromsø, Norway
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Gunhild M. Mælandsmo
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria Perander
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Achilleas D. Theocharis
- Biochemistry, Biochemical Analysis & Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece
| | | | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
- Centre for Clinical Research and Education, University Hospital of North Norway, Tromsø, Norway
- *Correspondence: Erik Knutsen,
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Liu Y, Chen X, Che Y, Li H, Zhang Z, Peng W, Yang J. LncRNAs as the Regulators of Brain Function and Therapeutic Targets for Alzheimer’s Disease. Aging Dis 2022; 13:837-851. [PMID: 35656102 PMCID: PMC9116922 DOI: 10.14336/ad.2021.1119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/19/2021] [Indexed: 11/13/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common type of dementia and a serious threat to the health and safety of the elderly population. It has become an emerging public health problem and a major economic and social burden. However, there is currently no effective treatment for AD. Although the mechanism of AD pathogenesis has been investigated substantially, the full range of molecular factors that contribute to its development remain largely unclear. In recent years, accumulating evidence has revealed that long non-coding RNAs (lncRNAs), a type of non-coding RNA longer than 200 nucleotides, play important roles in multiple biological processes involved in AD pathogenesis. With the further exploration of genomics, the role of lncRNA in the pathogenesis of AD has been phenotypically or mechanistically studied. Herein, we systematically review the current knowledge about lncRNAs implicated in AD and elaborate on their main regulatory pathways, which may contribute to the discovery of novel therapeutic targets and drugs for AD.
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Affiliation(s)
- Yuqing Liu
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
| | - Xin Chen
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Yutong Che
- Xiangya School of Medicine, Central South University, Changsha, Hunan, China.
| | - Hongli Li
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zheyu Zhang
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Weijun Peng
- Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Inter-disciplinary Research Center of Language Intelligence and Cultural Heritages, Hunan University, Changsha, Hunan, China.
- Correspondence should be addressed to: Dr. Weijun Peng (E-mail: ) and Ms. Jingjing Yang (), Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Jingjing Yang
- Teaching and Research Section of Clinical Nursing, Xiangya Hospital, Central South University, Changsha, China.
- Xiangya Nursing School, Central South University, Changsha, China.
- Correspondence should be addressed to: Dr. Weijun Peng (E-mail: ) and Ms. Jingjing Yang (), Department of Integrated Traditional Chinese & Western Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
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