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Elimam H, Eldeib MG, Kizilaslan EZ, Alhamshry NAA, Ashour AE, Elfar N, Abdel-Wahab MM, Zaki MB, Mohammed OA, Radwan AF, Abdel-Reheim MA, Moussa R, Doghish AS. Exploring the interplay of natural products and long non-coding RNAs in colorectal cancer: pathogenesis, diagnosis, and overcoming drug resistance. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03425-9. [PMID: 39287672 DOI: 10.1007/s00210-024-03425-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024]
Abstract
Colorectal cancer (CRC) is recognized as one of the most prevalent malignancies, both in terms of incidence and mortality rates. Current research into CRC has shed light on the molecular mechanisms driving its development. Several factors, including lifestyle, environmental influences, genetics, and diet, play significant roles in its pathogenesis. Natural compounds such as curcumin, tanshinone, lycorine, sinomenine, kaempferol, verbascoside, quercetin, berberine, and fisetin have shown great promise in the prevention and treatment of CRC. Research has also highlighted the significance of non-coding RNAs (ncRNAs) as biomarkers and therapeutic targets in CRC. Among these, long non-coding RNAs (lncRNAs) have been found to regulate the transcription of genes involved in cancer. LncRNAs contribute to cancer stem cell (CSC) proliferation, angiogenesis, epithelial-mesenchymal transition (EMT), and chemoresistance. Specific lncRNAs, including GAS5, LNC00337, HOTAIR, TPT1-AS1, cCSC1, BCAR4, TUG1, and Solh2, play crucial roles in these processes. They hold potential as novel biomarkers, detectable in bodily fluids and tissues, and could serve as therapeutic targets due to their involvement in drug resistance and sensitivity. These insights could improve CRC treatment strategies, addressing resistance to chemotherapy and radiotherapy. This review article aims to provide a comprehensive analysis of the current knowledge regarding the effectiveness of natural anti-cancer agents in CRC treatment. Additionally, it offers an in-depth evaluation of lncRNAs in CRC, their role in the disease's progression, and their potential applications in its management.
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Affiliation(s)
- Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt.
| | - Mahmoud Gomaa Eldeib
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Al-Azhar University, Nasr City, 11231, Cairo, Egypt
- Department of Biochemistry, Faculty of Pharmacy, Sinai University-Kantara Branch, Ismailia, 41636, Egypt
| | | | - Nora A A Alhamshry
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt
| | - Abdelkader E Ashour
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Salman International University, Ras Sudr, South Sinai, Egypt
| | - Nourhan Elfar
- School of Life and Medical Sciences, University of Hertfordshire Hosted By Global Academic Foundation, New Administrative Capital, 11578, Cairo, Egypt
- Egyptian Drug Authority, Ministry of Health and Population, Cairo, 11567, Egypt
| | - Maie M Abdel-Wahab
- Department of Biochemistry, Faculty of Pharmacy, Sinai University-Kantara Branch, Ismailia, 41636, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, 61922, Bisha, Saudi Arabia
| | - Abdullah F Radwan
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo, 11829, Egypt
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmacology, College of Pharmacy, Shaqra University, 11961, Shaqra, Saudi Arabia.
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, 62521, Egypt.
| | - Rewan Moussa
- Faculty of Medicine, Helwan University, Cairo, 11795, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo, Badr City, 11829, Cairo, Egypt
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, Al-Azhar University, Nasr City, 11231, Cairo, Egypt
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Tapia A, Liu X, Malhi NK, Yuan D, Chen M, Southerland KW, Luo Y, Chen ZB. Role of long noncoding RNAs in diabetes-associated peripheral arterial disease. Cardiovasc Diabetol 2024; 23:274. [PMID: 39049097 PMCID: PMC11271017 DOI: 10.1186/s12933-024-02327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024] Open
Abstract
Diabetes mellitus (DM) is a metabolic disease that heightens the risks of many vascular complications, including peripheral arterial disease (PAD). Various types of cells, including but not limited to endothelial cells (ECs), vascular smooth muscle cells (VSMCs), and macrophages (MΦs), play crucial roles in the pathogenesis of DM-PAD. Long non-coding RNAs (lncRNAs) are epigenetic regulators that play important roles in cellular function, and their dysregulation in DM can contribute to PAD. This review focuses on the developing field of lncRNAs and their emerging roles in linking DM and PAD. We review the studies investigating the role of lncRNAs in crucial cellular processes contributing to DM-PAD, including those in ECs, VSMCs, and MΦ. By examining the intricate molecular landscape governed by lncRNAs in these relevant cell types, we hope to shed light on the roles of lncRNAs in EC dysfunction, inflammatory responses, and vascular remodeling contributing to DM-PAD. Additionally, we provide an overview of the research approach and methodologies, from identifying disease-relevant lncRNAs to characterizing their molecular and cellular functions in the context of DM-PAD. We also discuss the potential of leveraging lncRNAs in the diagnosis and therapeutics for DM-PAD. Collectively, this review provides a summary of lncRNA-regulated cell functions contributing to DM-PAD and highlights the translational potential of leveraging lncRNA biology to tackle this increasingly prevalent and complex disease.
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Affiliation(s)
- Alonso Tapia
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, 91010, USA
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Xuejing Liu
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Naseeb Kaur Malhi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Dongqiang Yuan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Muxi Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Kevin W Southerland
- Division of Vascular and Endovascular Surgery, Department of Surgery, Duke University Medical Center, Durham, NC, 27710, USA
| | - Yingjun Luo
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA
| | - Zhen Bouman Chen
- Irell and Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA, 91010, USA.
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA, USA.
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3
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Doghish AS, Zaki MB, Eldeib MG, Radwan AF, Moussa R, Abdel-Wahab MM, Kizilaslan EZ, Alhamshry NAA, Ashour AE, Elimam H. The potential relevance of long non-coding RNAs in colorectal cancer pathogenesis and treatment: A review focus on signaling pathways. Pathol Res Pract 2024; 253:155044. [PMID: 38141573 DOI: 10.1016/j.prp.2023.155044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
Colorectal cancer (CRC) is one of the most frequent cancers in incidence and mortality. Despite advances in cancer biology, molecular genetics, and targeted treatments, CRC prognosis and survival have not kept pace. This is usually due to advanced staging and metastases at diagnosis. Thus, great importance has been placed upon understanding the molecular pathophysiology behind the development of CRC, which has highlighted the significance of non-coding RNA's role and associated intracellular signaling pathways in the pathogenesis of the disease. According to recent studies, long non-coding RNAs (lncRNA), a subtype of ncRNAs whose length exceeds 200 nucleotides, have been found to have regulatory functions on multiple levels. Their actions at the transcription, post-transcriptional, translational levels, and epigenetic regulation have made them prime modulators of gene expression. Due to their role in cellular cancer hallmarks, their dysregulation has been linked to several illnesses, including cancer. Furthermore, their clinical relevance has expanded due to their possible detection in blood which has cemented them as potential future biomarkers and thus, potential targets for new therapy. This review will highlight the importance of lncRNAs and related signaling pathways in the development of CRC and their subsequent clinical applications.
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Affiliation(s)
- Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Mahmoud Gomaa Eldeib
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Sinai University - Kantara Branch, 41636 Ismailia, Egypt
| | - Abdullah F Radwan
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo 11829, Egypt
| | - Rewan Moussa
- Faculty of Medicine, Helwan University, Cairo, Egypt
| | - Maie M Abdel-Wahab
- Department of Biochemistry, Faculty of Pharmacy, Sinai University - Kantara Branch, 41636 Ismailia, Egypt
| | | | - Nora A A Alhamshry
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt
| | - Abdelkader E Ashour
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, King Salman International University, Ras Sudr, South Sinai, Egypt
| | - Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City 32897, Egypt.
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Wang Q, Zheng C, Hou H, Bao X, Tai H, Huang X, Li Z, Li Z, Wang Q, Pan Q, Wang L, Zhou S, Bian Y, Pan Q, Gong A, Xu M. Interplay of Sphingolipid Metabolism in Predicting Prognosis of GBM Patients: Towards Precision Immunotherapy. J Cancer 2024; 15:275-292. [PMID: 38164288 PMCID: PMC10751665 DOI: 10.7150/jca.89338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/16/2023] [Indexed: 01/03/2024] Open
Abstract
Background: In spite of numerous existing bio-surveillance systems for predicting glioma (GBM) prognosis, enhancing the efficacy of immunotherapy remains an ongoing conundrum. The continual scrutiny of the dynamic interplay between the sphingolipid metabolic pathway and tumor immunophenotypes has unveiled potential implications. However, the intricate orchestration of functional and regulatory mechanisms by long non-coding RNAs (lncRNAs) in GBM, particularly in the context of sphingolipid metabolism, remains cryptic. Methods: We harnessed established R packages to intersect gene expression profiles of GBM patients within the The Cancer Genome Atlas (TCGA) database with the compilation of sphingolipid metabolism genes from GeneCards. This enabled us to discern markedly distinct lncRNAs, which were subsequently deployed to construct a robust prognostic model utilizing Lasso-Cox regression analysis. We then scrutinized the immune microenvironment across various risk strata using the ssGSEA and CIBERSORT algorithms. To evaluate mutation patterns and drug resistance profiles within patient subgroups, we devised the "Prophytic" and "Maftools" packages, respectively. Results: Our investigation scrutinized lncRNAs linked to sphingolipid metabolism, utilizing glioma specimens from TCGA. We meticulously curated 1224 sphingolipid-associated genes gleaned from GeneCards and pinpointed 272 differentially expressed mRNAs via transcriptomic analysis. Enrichment analyses underscored their significance in sphingolipid processes. A prognostic model founded on 17 meticulously selected lncRNAs was systematically constructed and validated. This model adeptly stratified GBM patients into high- and low-risk categories, yielding highly precise prognostic insights. We also discerned correlations between immune cell infiltration and genetic mutation discrepancies, along with distinct therapeutic responses through drug sensitivity analysis. Notably, computational findings were corroborated through experimental validation by RT-PCR. Conclusion: In summation, our exhaustive inquiry underscores the multifaceted utility of the sphingolipid metabolic pathway as an autonomous diagnostic and prognostic indicator for glioma patients. Furthermore, we amalgamate a profusion of substantiated evidence concerning immune infiltration and gene mutations, thereby reinforcing the proposition that sphingolipid metabolism may function as a pivotal determinant in the panorama of immunotherapeutic interventions.
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Affiliation(s)
- Qi Wang
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Chuanhua Zheng
- Department of Neurosurgery, the Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Hanjin Hou
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xin Bao
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Huading Tai
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Xufeng Huang
- Faculty of Dentistry, University of Debrecen, Debrecen, Hungary
| | - Zhengrui Li
- Department of Oral and Maxillofacial-Head and Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, College of Stomatology, Shanghai Jiao Tong University, Shanghai, China
- National Center for Stomatology & National Clinical Research Center for Oral Diseases, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai, China
| | - Zhangzuo Li
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Qiaowei Wang
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Qi Pan
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Longbin Wang
- Department of Clinical Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shujing Zhou
- Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Yanjie Bian
- Xinxiang Medical University, Xinxiang, China
| | - Qier Pan
- Department of Endocrinology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
| | - Aihua Gong
- Department of Cell Biology, School of Medicine, Jiangsu University, Zhenjiang, China
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China
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Tao S, Hou Y, Diao L, Hu Y, Xu W, Xie S, Xiao Z. Long noncoding RNA study: Genome-wide approaches. Genes Dis 2023; 10:2491-2510. [PMID: 37554208 PMCID: PMC10404890 DOI: 10.1016/j.gendis.2022.10.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 10/09/2022] [Accepted: 10/23/2022] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to play a crucial role in various biological processes across several species. Though many efforts have been devoted to the expansion of the lncRNAs landscape, much about lncRNAs is still unknown due to their great complexity. The development of high-throughput technologies and the constantly improved bioinformatic methods have resulted in a rapid expansion of lncRNA research and relevant databases. In this review, we introduced genome-wide research of lncRNAs in three parts: (i) novel lncRNA identification by high-throughput sequencing and computational pipelines; (ii) functional characterization of lncRNAs by expression atlas profiling, genome-scale screening, and the research of cancer-related lncRNAs; (iii) mechanism research by large-scale experimental technologies and computational analysis. Besides, primary experimental methods and bioinformatic pipelines related to these three parts are summarized. This review aimed to provide a comprehensive and systemic overview of lncRNA genome-wide research strategies and indicate a genome-wide lncRNA research system.
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Affiliation(s)
- Shuang Tao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yarui Hou
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Liting Diao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yanxia Hu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Wanyi Xu
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Shujuan Xie
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
- Institute of Vaccine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Zhendong Xiao
- The Biotherapy Center, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
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6
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Zhang Y, Wang W, Duan C, Li M, Gao L. Novel Long Non-Coding RNA (lncRNA) Transcript AL137782.1 Promotes the Migration of Normal Lung Epithelial Cells through Positively Regulating LMO7. Int J Mol Sci 2023; 24:13904. [PMID: 37762205 PMCID: PMC10530982 DOI: 10.3390/ijms241813904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
The role of long non-coding RNA (lncRNAs) in biological processes remains poorly understood, despite their significant impact. Our previous research discovered that the expression of AL137782.1, a long transcript of the novel lncRNA ENSG00000261553, is upregulated in lung epithelial cells upon exposure to microbes. Furthermore, the expression of AL137782.1 exhibits variability between para-cancerous and lung adenocarcinoma samples. These findings imply that this lncRNA may play a role in both normal lung epithelial cellular processes and pathophysiology. To elucidate the function of AL137782.1 in lung epithelial cells, we utilized bioinformatics retrieval and analysis to examine its expression. We then analyzed its subcellular localization using fluorescence in situ hybridization (FISH) and subcellular fractionation. Through rapid amplification of cDNA ends (RACE), we confirmed the presence of a 4401 nt lncRNA AL137782.1 in lung epithelial cells. Moreover, we discovered that this lncRNA positively regulates both mRNA and the protein expression of LMO7, a protein that may regulate the cell migration of normal lung epithelial cells. Although the overexpression of AL137782.1 has been shown to enhance the migration of both normal lung epithelial cells and lung adenocarcinoma cells in vitro, our study revealed that the expression of this lncRNA was significantly decreased in lung cancers compared to adjacent tissues. This suggests that the cell migration pattern regulated by the AL137782.1-LMO7 axis is more likely to occur in normal lung epithelial cells, rather than being a pathway that promotes lung cancer cell migration. Therefore, our study provides new insights into the mechanism underlying cell migration in human lung epithelial cells. This finding may offer a potential strategy to enhance normal lung epithelial cell migration after lung injury.
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Affiliation(s)
- Ying Zhang
- Life Science School, Ningxia University, Yinchuan 750001, China; (Y.Z.); (W.W.); (C.D.)
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan 750001, China
| | - Weili Wang
- Life Science School, Ningxia University, Yinchuan 750001, China; (Y.Z.); (W.W.); (C.D.)
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan 750001, China
| | - Chunchun Duan
- Life Science School, Ningxia University, Yinchuan 750001, China; (Y.Z.); (W.W.); (C.D.)
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan 750001, China
| | - Min Li
- Life Science School, Ningxia University, Yinchuan 750001, China; (Y.Z.); (W.W.); (C.D.)
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan 750001, China
| | - Liyang Gao
- Life Science School, Ningxia University, Yinchuan 750001, China; (Y.Z.); (W.W.); (C.D.)
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western, Ningxia University, Yinchuan 750001, China
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7
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Xu D, Tang L, Kapranov P. Complexities of mammalian transcriptome revealed by targeted RNA enrichment techniques. Trends Genet 2023; 39:320-333. [PMID: 36681580 DOI: 10.1016/j.tig.2022.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 01/21/2023]
Abstract
Studies using highly sensitive targeted RNA enrichment methods have shown that a large portion of the human transcriptome remains to be discovered and that most of the genome is transcribed in a complex, interleaved fashion characterized by a complex web of transcripts emanating from protein coding and noncoding loci. These results resonate with those from single-cell transcriptome profiling endeavors that reveal the existence of multiple novel, cell type-specific transcripts and clearly demonstrate that our understanding of the complexities of the human transcriptome is far from being complete. Here, we review the current status of the targeted RNA enrichment techniques, their application to the discovery of novel cell type-specific transcripts, and their impact on our understanding of the human genome and transcriptome.
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Affiliation(s)
- Dongyang Xu
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Lu Tang
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, 668 Jimei Road, Xiamen 361021, China.
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8
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Lopes M, Louzada S, Ferreira D, Veríssimo G, Eleutério D, Gama-Carvalho M, Chaves R. Human Satellite 1A analysis provides evidence of pericentromeric transcription. BMC Biol 2023; 21:28. [PMID: 36755311 PMCID: PMC9909926 DOI: 10.1186/s12915-023-01521-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/19/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Pericentromeric regions of human chromosomes are composed of tandem-repeated and highly organized sequences named satellite DNAs. Human classical satellite DNAs are classified into three families named HSat1, HSat2, and HSat3, which have historically posed a challenge for the assembly of the human reference genome where they are misrepresented due to their repetitive nature. Although being known for a long time as the most AT-rich fraction of the human genome, classical satellite HSat1A has been disregarded in genomic and transcriptional studies, falling behind other human satellites in terms of functional knowledge. Here, we aim to characterize and provide an understanding on the biological relevance of HSat1A. RESULTS The path followed herein trails with HSat1A isolation and cloning, followed by in silico analysis. Monomer copy number and expression data was obtained in a wide variety of human cell lines, with greatly varying profiles in tumoral/non-tumoral samples. HSat1A was mapped in human chromosomes and applied in in situ transcriptional assays. Additionally, it was possible to observe the nuclear organization of HSat1A transcripts and further characterize them by 3' RACE-Seq. Size-varying polyadenylated HSat1A transcripts were detected, which possibly accounts for the intricate regulation of alternative polyadenylation. CONCLUSION As far as we know, this work pioneers HSat1A transcription studies. With the emergence of new human genome assemblies, acrocentric pericentromeres are becoming relevant characters in disease and other biological contexts. HSat1A sequences and associated noncoding RNAs will most certainly prove significant in the future of HSat research.
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Affiliation(s)
- Mariana Lopes
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Sandra Louzada
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniela Ferreira
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Gabriela Veríssimo
- grid.12341.350000000121821287CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal ,grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Daniel Eleutério
- grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Margarida Gama-Carvalho
- grid.9983.b0000 0001 2181 4263BioISI – Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- CytoGenomics Lab, Department of Genetics and Biotechnology (DGB), University of Trás-Os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal. .,BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisbon, Portugal.
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9
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Yang W, Bai Q, Li Y, Chen J, Liu C. Epigenetic modifications: Allusive clues of lncRNA functions in plants. Comput Struct Biotechnol J 2023; 21:1989-1994. [PMID: 36950220 PMCID: PMC10025020 DOI: 10.1016/j.csbj.2023.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/13/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized. Moreover, the relationship between lncRNAs and other epigenetic modifications has not been systematically studied. In this mini-review, we briefly summarize the representative biological functions of lncRNAs in developmental programs and environmental responses in plants. In addition, we particularly discuss the intimate relationship between lncRNAs and other epigenetic modifications, and we outline the underlying avenues and challenges for future research on plant lncRNAs.
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Affiliation(s)
- Wenjing Yang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quanzi Bai
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan Li
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianghua Chen
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, China
- Corresponding author at: CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Yunnan Key Laboratory of Crop Wild Relatives Omics, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China.
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Pan H, Wang H, Zhang X, Yang F, Fan X, Zhang H. Chromosomal instability-associated MAT1 lncRNA insulates MLL1-guided histone methylation and accelerates tumorigenesis. Cell Rep 2022; 41:111829. [PMID: 36516779 DOI: 10.1016/j.celrep.2022.111829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
Acquired chromosomal instability, especially copy number variations (CNVs), has been considered an important determinant of cancer progression and clinical survival. However, the functional role of aberrant CNV-induced lncRNAs in tumorigenesis remains unexplored. Here, we identify a CNV-induced MSC-antisense-transcript 1 (MAT1) lncRNA that plays an oncogenic role in promoting tumorigenesis of uveal melanoma in orthotopic and metastatic xenografts. In addition, our data suggest that MAT1 interrupts the interaction between the MLL1 complex and the PCDH20 promoter by forming an RNA-DNA triplex structure, subsequently abolishing H3K4 trimethylation and inactivating transcription of tumor suppressor PCDH20 to accelerate tumorigenesis. Our data show an intriguing insulation pattern of H3K4 histone modification in tumorigenesis mediated by a lncRNA, thereby providing an alternative mechanism for noncoding blockers in gene regulation.
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Affiliation(s)
- Hui Pan
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Huixue Wang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xiaoyu Zhang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Fan Yang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China; Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P.R. China.
| | - He Zhang
- Institute for Regenerative Medicine of Shanghai East Hospital, Frontier Science Research Center for Stem Cells, School of Life Science and Technology, Tongji University, Shanghai 200092, China.
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11
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The Long Noncoding Transcript HNSCAT1 Activates KRT80 and Triggers Therapeutic Efficacy in Head and Neck Squamous Cell Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:4156966. [PMID: 35965679 PMCID: PMC9371835 DOI: 10.1155/2022/4156966] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/04/2022] [Indexed: 12/23/2022]
Abstract
Head and neck squamous carcinoma (HNSC) is the most prevalent malignancy of the head and neck regions. Long noncoding RNAs (lncRNAs) are vital in tumorigenesis regulation. However, the role of lncRNAs in HNSC requires further exploration. Herein, through bioinformatic assays using The Cancer Genome Atlas (TCGA) datasets, rapid amplification of cDNA ends (RACE) assays, and RNA-FISH, we revealed that a novel cytoplasmic transcript, HNSC-associated transcript 1 (HNSCAT1, previously recognized as linc01269), was downregulated in tumor samples and advanced tumor stages and was also associated with favorable outcomes in HNSC. Overexpression of HNSCAT1 triggered treatment efficacy in HNSCs both in vivo and in vitro. More importantly, through high-throughput transcriptome analysis (RNA-seq, in NODE database, OEZ007550), we identified KRT80, a tumor suppressor in HNSC, as the target of HNSCAT1. KRT80 expression was modulated by lncRNA HNSCAT1 and presented a positive correlation in tumor samples (R = 0.52, p < 0.001). Intriguingly, we identified that miR-1245 simultaneously interacts with KRT80 and HNSCAT1, which bridges the regulatory function between KRT80 and HNSCAT1. Conclusively, our study demonstrated that lncRNA HNSCAT1 functions as a necessary tumor inhibitor in HNSC, which provides a novel mechanism of lncRNA function and provides alternative targets for the diagnosis and treatment of HNSC.
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12
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Exploring the crosstalk between long non-coding RNAs and microRNAs to unravel potential prognostic and therapeutic biomarkers in β-thalassemia. Mol Biol Rep 2022; 49:7057-7068. [PMID: 35717472 DOI: 10.1007/s11033-022-07629-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
β-thalassemia is a prevalent monogenic disorder characterized by reduced or absent synthesis of the β-globin chain. Although great effort has been made to ameliorate the disease severity of β-thalassemic patients, progress has been stymied due to limited understanding of the detailed molecular mechanism of disease pathogenesis. Recently, non-coding RNAs have been established as key players in regulating various physiological and pathological processes. Many ncRNAs are involved in hematopoiesis and erythroid development. Furthermore, various studies have also reported the complex interplay between different ncRNAs, such as miRNA, lncRNAs, etc. in regulating disease progression and pathogenesis. Both lncRNAs and miRNAs have been identified as independent regulators of globin gene expression and are intricately involved in disease pathogenesis; yet accumulating evidence suggests that the cross-talk between lncRNAs and miRNAs is intricately involved in the underlying globin gene expression, fine-tuning the effect of their independent regulation. In this review, we summarize the current progress of research on the roles of lncRNAs and miRNAs implicated in β-thalassemia disease, including their interactions and regulatory networks. This can provide important insights into the detailed epigenetic regulation of globin gene switching and has the potential to develop novel therapeutic approaches against β-thalassemia.
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Zhang J, Cai B, Ma M, Kong S, Zhou Z, Zhang X, Nie Q. LncRNA SMARCD3-OT1 Promotes Muscle Hypertrophy and Fast-Twitch Fiber Transformation via Enhancing SMARCD3X4 Expression. Int J Mol Sci 2022; 23:ijms23094510. [PMID: 35562902 PMCID: PMC9105468 DOI: 10.3390/ijms23094510] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 11/21/2022] Open
Abstract
Long noncoding RNA (lncRNA) plays a crucial part in all kinds of life activities, especially in myogenesis. SMARCD3 (SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily d, member 3) is a member of the SWI/SNF protein complex and was reported to be required for cell proliferation and myoblast differentiation. In this study, we identified a new lncRNA named SMARCD3-OT1 (SMARCD3overlappinglncRNA), which strongly regulated the development of myogenesis by improving the expression of SMARCD3X4 (SMARCD3transcripts4). We overexpressed and knockdown the expression of SMARCD3-OT1 and SMARCD3X4 to investigate their function on myoblast proliferation and differentiation. Cell experiments proved that SMARCD3-OT1 and SMARCD3X4 promoted myoblast proliferation through the CDKN1A pathway and improved differentiation of differentiated myoblasts through the MYOD pathway. Moreover, they upregulated the fast-twitch fiber-related genes and downregulated the slow-twitch fiber-related genes, which indicated that they facilitated the slow-twitch fiber to transform into the fast-twitch fiber. The animals’ experiments supported the results above, demonstrating that SMARCD3-OT1 could induce muscle hypertrophy and fast-twitch fiber transformation. In conclusion, SMARCD3-OT1 can improve the expression of SMARCD3X4, thus inducing muscle hypertrophy. In addition, SMARCD3-OT1 can facilitate slow-twitch fibers to transform into fast-twitch fibers.
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Affiliation(s)
- Jing Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Manting Ma
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shaofen Kong
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhen Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (J.Z.); (B.C.); (M.M.); (S.K.); (Z.Z.); (X.Z.)
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- National-Local Joint Engineering Research Center for Livestock Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence:
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Adamopoulos PG, Tsiakanikas P, Stolidi I, Scorilas A. A versatile 5′ RACE-Seq methodology for the accurate identification of the 5′ termini of mRNAs. BMC Genomics 2022; 23:163. [PMID: 35219290 PMCID: PMC8881849 DOI: 10.1186/s12864-022-08386-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Technological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5′ ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5′ rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5′ ends of cDNAs. In the current study, we developed a 5′ RACE-seq method by coupling a custom template-switching and 5′ RACE assay with targeted nanopore sequencing, to accurately unveil 5′ termini of mRNA targets. Results The optimization of the described 5′ RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5′ RACE. Collectively, our results support the existence of two distinct 5′ termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5′ RACE-seq methodology to investigate the 5′ UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5′ UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones. Conclusions In this work we present an in-house developed 5′ RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5′ UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08386-y.
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15
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Roy S, Ganguly N, Banerjee S. Exploring clinical implications and role of non-coding RNAs in lung carcinogenesis. Mol Biol Rep 2022; 49:6871-6883. [PMID: 35076850 DOI: 10.1007/s11033-022-07159-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
Lung cancer is the utmost familiar category of cancer with greatest fatality rate worldwide and several regulatory mechanisms exercise cellular control on critical oncogenic trails implicated in lung associated carcinogenesis. The non-coding RNAs (ncRNAs) are shown to play a variety of regulatory roles, including stimulating cell proliferation, inhibiting programmed cell death, enhancing cancer cell metastatic ability and acquiring resistance to drugs. Furthermore, ncRNAs exhibit tissue-specific expression as well as great stability in bodily fluids. As a consequence, they are strong contenders for cancer based theragnostics. microRNA (miRNA) alters gene expression primarily by either degrading or interfering with the translation of targeted mRNA and long non-coding RNAs (lncRNAs) can influence gene expression by targeting transcriptional activators or repressors, RNA polymers and even DNA-duplex. lncRNAs are typically found to be dysregulated in lung cancer and hence targeting ncRNAs could be a viable strategy for developing potential therapies as well as for overcoming chemoresistance in lung cancer. The purpose of this review is to elucidate the role of ncRNAs, revisiting the recent studies in lung cancer.
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Affiliation(s)
- Swagata Roy
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India
| | - Neeldeep Ganguly
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India
| | - Satarupa Banerjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India.
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Li D, Huang Q, Huang L, Wen J, Luo J, Li Q, Peng Y, Zhang Y. Baiting out a full length sequence from unmapped RNA-seq data. BMC Genomics 2021; 22:857. [PMID: 34837950 PMCID: PMC8626966 DOI: 10.1186/s12864-021-08146-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 11/03/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As a powerful tool, RNA-Seq has been widely used in various studies. Usually, unmapped RNA-seq reads have been considered as useless and been trashed or ignored. RESULTS We develop a strategy to mining the full length sequence by unmapped reads combining with specific reverse transcription primers design and high throughput sequencing. In this study, we salvage 36 unmapped reads from standard RNA-Seq data and randomly select one 149 bp read as a model. Specific reverse transcription primers are designed to amplify its both ends, followed by next generation sequencing. Then we design a statistical model based on power law distribution to estimate its integrality and significance. Further, we validate it by Sanger sequencing. The result shows that the full length is 1556 bp, with insertion mutations in microsatellite structure. CONCLUSION We believe this method would be a useful strategy to extract the sequences information from the unmapped RNA-seq data. Further, it is an alternative way to get the full length sequence of unknown cDNA.
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Affiliation(s)
- Dongwei Li
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642 China
| | - Qitong Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
- Animal Breeding and Genomic, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Lei Huang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Jikai Wen
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, Guangdong 510642 China
| | - Jing Luo
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Qing Li
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yanling Peng
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Yubo Zhang
- Animal Functional Genomics Group, Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
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Carter JM, Ang DA, Sim N, Budiman A, Li Y. Approaches to Identify and Characterise the Post-Transcriptional Roles of lncRNAs in Cancer. Noncoding RNA 2021; 7:19. [PMID: 33803328 PMCID: PMC8005986 DOI: 10.3390/ncrna7010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/28/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
It is becoming increasingly evident that the non-coding genome and transcriptome exert great influence over their coding counterparts through complex molecular interactions. Among non-coding RNAs (ncRNA), long non-coding RNAs (lncRNAs) in particular present increased potential to participate in dysregulation of post-transcriptional processes through both RNA and protein interactions. Since such processes can play key roles in contributing to cancer progression, it is desirable to continue expanding the search for lncRNAs impacting cancer through post-transcriptional mechanisms. The sheer diversity of mechanisms requires diverse resources and methods that have been developed and refined over the past decade. We provide an overview of computational resources as well as proven low-to-high throughput techniques to enable identification and characterisation of lncRNAs in their complex interactive contexts. As more cancer research strategies evolve to explore the non-coding genome and transcriptome, we anticipate this will provide a valuable primer and perspective of how these technologies have matured and will continue to evolve to assist researchers in elucidating post-transcriptional roles of lncRNAs in cancer.
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Affiliation(s)
- Jean-Michel Carter
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Daniel Aron Ang
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Nicholas Sim
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Andrea Budiman
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
| | - Yinghui Li
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551, Singapore; (D.A.A.); (N.S.); (A.B.)
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
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18
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Mattox AK, Yang B, Douville C, Lo SF, Sciubba D, Wolinsky JP, Gokaslan ZL, Robison J, Blair C, Jiao Y, Bettegowda C. The mutational landscape of spinal chordomas and their sensitive detection using circulating tumor DNA. Neurooncol Adv 2021; 3:vdaa173. [PMID: 33543146 PMCID: PMC7850091 DOI: 10.1093/noajnl/vdaa173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Chordomas are the most common primary spinal column malignancy in the United States. The aim of this study was to determine whether chordomas may be detected by evaluating mutations in circulating tumor DNA (ctDNA). Methods Thirty-two patients with a biopsy-confirmed diagnosis of chordoma had blood drawn pre-operatively and/or at follow-up appointments. Mutations in the primary tumor were identified by whole exome sequencing and liquid biopsy by ddPCR and/or RACE-Seq was used to detect one or more of these mutations in plasma ctDNA at concurrent or later time points. Results At the time of initial blood draw, 87.1% of patients were ctDNA positive (P <.001). Follow-up blood draws in twenty of the patients suggest that ctDNA levels may reflect the clinical status of the disease. Patients with positive ctDNA levels were more likely to have greater mutant allele frequencies in their primary tumors (P = .004) and undergo radiotherapy (P = .02), and the presence of ctDNA may correlate with response to systemic chemotherapy and/or disease recurrence. Conclusions Detection of ctDNA mutations may allow for the detection and monitoring of disease progression for chordomas.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Beibei Yang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sheng-Fu Lo
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel Sciubba
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jean Paul Wolinsky
- Department of Neurosurgery, Northwestern University School of Medicine, Chicago, Illinois, USA
| | - Ziya L Gokaslan
- Department of Neurosurgery, Brown University School of Medicine, Providence, Rhode Island, USA
| | - Jamie Robison
- Department of Neurosurgery, Mayo Clinic, Jacksonville, Florida, USA
| | - Cherie Blair
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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19
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Rubino E, Cruciani M, Tchitchek N, Le Tortorec A, Rolland AD, Veli Ö, Vallet L, Gaggi G, Michel F, Dejucq-Rainsford N, Pellegrini S. Human Ubiquitin-Specific Peptidase 18 Is Regulated by microRNAs via the 3'Untranslated Region, A Sequence Duplicated in Long Intergenic Non-coding RNA Genes Residing in chr22q11.21. Front Genet 2021; 11:627007. [PMID: 33633774 PMCID: PMC7901961 DOI: 10.3389/fgene.2020.627007] [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: 11/07/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022] Open
Abstract
Ubiquitin-specific peptidase 18 (USP18) acts as gatekeeper of type I interferon (IFN) responses by binding to the IFN receptor subunit IFNAR2 and preventing activation of the downstream JAK/STAT pathway. In any given cell type, the level of USP18 is a key determinant of the output of IFN-stimulated transcripts. How the baseline level of USP18 is finely tuned in different cell types remains ill defined. Here, we identified microRNAs (miRNAs) that efficiently target USP18 through binding to the 3’untranslated region (3’UTR). Among these, three miRNAs are particularly enriched in circulating monocytes which exhibit low baseline USP18. Intriguingly, the USP18 3’UTR sequence is duplicated in human and chimpanzee genomes. In humans, four USP18 3’UTR copies were previously found to be embedded in long intergenic non-coding (linc) RNA genes residing in chr22q11.21 and known as FAM247A-D. Here, we further characterized their sequence and measured their expression profile in human tissues. Importantly, we describe an additional lincRNA bearing USP18 3’UTR (here linc-UR-B1) that is expressed only in testis. RNA-seq data analyses from testicular cell subsets revealed a positive correlation between linc-UR-B1 and USP18 expression in spermatocytes and spermatids. Overall, our findings uncover a set of miRNAs and lincRNAs, which may be part of a network evolved to fine-tune baseline USP18, particularly in cell types where IFN responsiveness needs to be tightly controlled.
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Affiliation(s)
- Erminia Rubino
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France.,École Doctorale Physiologie, Physiopathologie et Thérapeutique, ED394, Sorbonne Université, Paris, France
| | - Melania Cruciani
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Nicolas Tchitchek
- École Doctorale Physiologie, Physiopathologie et Thérapeutique, ED394, Sorbonne Université, Paris, France.,i3 research unit, Hôpital Pitié-Salpêtrière-Sorbonne Université, Paris, France
| | - Anna Le Tortorec
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Antoine D Rolland
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Önay Veli
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Leslie Vallet
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Giulia Gaggi
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Frédérique Michel
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
| | - Nathalie Dejucq-Rainsford
- UMR_S1085, Institut de recherche en santé, environnement et travail (Irset), EHESP, Inserm, Univ Rennes, Rennes, France
| | - Sandra Pellegrini
- Unit of Cytokine Signaling, Institut Pasteur, INSERM U1221, Paris, France
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20
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Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2021; 27:80-98. [PMID: 33055239 PMCID: PMC7749630 DOI: 10.1261/rna.074724.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
High-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify lncRNA more efficiently and accurately, they may produce inconsistent results, making selection a confusing issue. We compared the performance of 41 analysis models based on 14 software packages and different data sets, including high-quality data and low-quality data from 33 species. In addition, computational efficiency, robustness, and joint prediction of the models were explored. As a practical guidance, key points for lncRNA identification under different situations were summarized. In this investigation, no one of these models could be superior to others under all test conditions. The performance of a model relied to a great extent on the source of transcripts and the quality of assemblies. As general references, FEELnc_all_cl, CPC, and CPAT_mouse work well in most species while COME, CNCI, and lncScore are good choices for model organisms. Since these tools are sensitive to different factors such as the species involved and the quality of assembly, researchers must carefully select the appropriate tool based on the actual data. Alternatively, our test suggests that joint prediction could behave better than any single model if proper models were chosen. All scripts/data used in this research can be accessed at http://bioinfo.ihb.ac.cn/elit.
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Affiliation(s)
- You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
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21
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Gao N, Li Y, Li J, Gao Z, Yang Z, Li Y, Liu H, Fan T. Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers. Front Oncol 2020; 10:598817. [PMID: 33392092 PMCID: PMC7775490 DOI: 10.3389/fonc.2020.598817] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Na Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Yueheng Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhengfan Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhenzhen Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Translational Medicine Research Center, People’s Hospital of Zhengzhou, Zhengzhou, China
| | - Yong Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
- Faculty of Medicine, St George and Sutherland Clinical School, St George Hospital, The University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Hongtao Liu
- Laboratory for Cell Biology, College of Life Sciences of Zhengzhou University, Zhengzhou, China
| | - Tianli Fan
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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22
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Abstract
Metazoan genomes produce thousands of long-noncoding RNAs (lncRNAs), of which just a small fraction have been well characterized. Understanding their biological functions requires accurate annotations, or maps of the precise location and structure of genes and transcripts in the genome. Current lncRNA annotations are limited by compromises between quality and size, with many gene models being fragmentary or uncatalogued. To overcome this, the GENCODE consortium has developed RNA capture long-read sequencing (CLS), an approach combining targeted RNA capture with third-generation long-read sequencing. CLS provides accurate annotations at high-throughput rates. It eliminates the need for noisy transcriptome assembly from short reads, and requires minimal manual curation. The full-length transcript models produced are of quality comparable to present-day manually curated annotations. Here we describe a detailed CLS protocol, from probe design through long-read sequencing to creation of final annotations.
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23
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Pei Y, Tao C, Ling Z, Yu Z, Ji J, Khan A, Mamtimin T, Liu P, Li X. Exploring novel Cr(VI) remediation genes for Cr(VI)-contaminated industrial wastewater treatment by comparative metatranscriptomics and metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140435. [PMID: 32623159 DOI: 10.1016/j.scitotenv.2020.140435] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/17/2020] [Accepted: 06/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial remediation is a promising method to treat Cr(VI) in industrial wastewater. The remediation efficiency and stress-resistance ability of Cr(VI) remediation genes in microbes are the limiting factors for their application in industrial wastewater treatment. To screen novel highly efficient Cr(VI) remediation genes, comparative metatranscriptomic and metagenomic analyses were performed on long-term Cr(VI)-contaminated riparian soil with/without additional Cr(VI) treatment. The most suitable Cr(VI) treatment time was determined to be 30 min according to the high quality RNA yield and fold changes in gene expression. Six novel genes, which had complete open reading frames (ORFs) in metagenomic libraries, were identified from unculturable microbes. In the phenotypic functional assay, all novel genes enhanced the Cr(VI) resistance/reduction ability of E. coli. In the industrial wastewater treatment, E-mcr and E-gsr presented at least 50% Cr(VI) removal efficiencies in the presence of 200-600 μM of Cr(VI), without a decrease in efficiency over 17 days. The stress resistance assay showed that gsr increased the growth rate of E. coli by at least 30% under different extreme conditions, and thus, gsr was identified as a general stress-response gene. In the Cr valence distribution assay, E-mcr presented ~40 μM higher extracellular Cr (III) compared to E-yieF. Additionally, transmission electron microscopy (TEM) of E-mcr showed bulk black agglomerates on the cell surface. Thus, mcr was identified as a membrane chromate reductase gene. This research provides a new idea for studying novel highly efficient contaminant remediation genes from unculturable microbes.
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Affiliation(s)
- Yaxin Pei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China
| | - Chen Tao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Shuangqinglu #18, Beijing 100085, China
| | - Zhenmin Ling
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China
| | - Zhengsheng Yu
- Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China
| | - Jing Ji
- Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China
| | - Aman Khan
- Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China
| | - Tursunay Mamtimin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China; Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China
| | - Pu Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou 730000, Gansu, China; Key Laboratory for Resources Utilization Technology of Unconventional Water of Gansu province, Gansu Academy of Membrane Science and Technology, Duanjiatanlu #1272, Lanzhou 730000, Gansu, China.
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Zhang Z, Wan J, Liu X, Zhang W. Strategies and technologies for exploring long noncoding RNAs in heart failure. Biomed Pharmacother 2020; 131:110572. [PMID: 32836073 DOI: 10.1016/j.biopha.2020.110572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/23/2020] [Accepted: 07/26/2020] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNA (lncRNA) was once considered to be the "noise" of genome transcription without biological function. However, increasing evidence shows that lncRNA is dynamically expressed in developmental stage or disease status, playing a regulatory role in the process of gene expression and translation. In recent years, lncRNA is considered to be a core node of functional regulatory networks that controls cardiac and also involves in multiple process of heart failure such as myocardial hypertrophy, fibrosis, angiogenesis, etc., which would be a therapeutic target for diseases. In fact, it is the development of technology that has improved our understanding of lncRNAs and broadened our perspective on heart failure. From transcriptional "noise" to star molecule, progress of lncRNAs can't be achieved without the combination of multidisciplinary technologies, especially the emergence of high-throughput approach. Thus, here, we review the strategies and technologies available for the exploration lncRNAs and try to yield insights into the prospect of lncRNAs in clinical diagnosis and treatment in heart failure.
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Affiliation(s)
- Zhen Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jingjing Wan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Xia Liu
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Weidong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai, China; School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
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25
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Chen L, Zhu QH, Kaufmann K. Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. PLANTA 2020; 252:92. [PMID: 33099688 PMCID: PMC7585572 DOI: 10.1007/s00425-020-03480-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/22/2020] [Indexed: 05/14/2023]
Abstract
MAIN CONCLUSION Long non-coding RNAs modulate gene activity in plant development and stress responses by various molecular mechanisms. Long non-coding RNAs (lncRNAs) are transcripts larger than 200 nucleotides without protein coding potential. Computational approaches have identified numerous lncRNAs in different plant species. Research in the past decade has unveiled that plant lncRNAs participate in a wide range of biological processes, including regulation of flowering time and morphogenesis of reproductive organs, as well as abiotic and biotic stress responses. LncRNAs execute their functions by interacting with DNA, RNA and protein molecules, and by modulating the expression level of their targets through epigenetic, transcriptional, post-transcriptional or translational regulation. In this review, we summarize characteristics of plant lncRNAs, discuss recent progress on understanding of lncRNA functions, and propose an experimental framework for functional characterization.
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Affiliation(s)
- Li Chen
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Kerstin Kaufmann
- Institute for Biology, Plant Cell and Molecular Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
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26
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Birkó Z, Nagy B, Klekner Á, Virga J. Novel Molecular Markers in Glioblastoma-Benefits of Liquid Biopsy. Int J Mol Sci 2020; 21:ijms21207522. [PMID: 33053907 PMCID: PMC7589793 DOI: 10.3390/ijms21207522] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/03/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma is a primary Central Nervous System (CNS) malignancy with poor survival. Treatment options are scarce and despite the extremely heterogeneous nature of the disease, clinicians lack prognostic and predictive markers to characterize patients with different outcomes. Certain immunohistochemistry, FISH, or PCR-based molecular markers, including isocitrate dehydrogenase1/2 (IDH1/2) mutations, epidermal growth factor receptor variant III (EGFRvIII) mutation, vascular endothelial growth factor overexpression (VEGF) overexpression, or (O6-Methylguanine-DNA methyltransferase promoter) MGMT promoter methylation status, are well-described; however, their clinical usefulness and accuracy is limited, and tumor tissue samples are always necessary. Liquid biopsy is a developing field of diagnostics and patient follow up in multiple types of cancer. Fragments of circulating nucleic acids are collected in various forms from different bodily fluids, including serum, urine, or cerebrospinal fluid in order to measure the quality and quantity of these markers. Multiple types of nucleic acids can be analyzed using liquid biopsy. Circulating cell-free DNA, mitochondrial DNA, or the more stable long and small non-coding RNAs, circular RNAs, or microRNAs can be identified and measured by novel PCR and next-generation sequencing-based methods. These markers can be used to detect the previously described alterations in a minimally invasive method. These markers can be used to differentiate patients with poor or better prognosis, or to identify patients who do not respond to therapy. Liquid biopsy can be used to detect recurrent disease, often earlier than using imaging modalities. Liquid biopsy is a rapidly developing field, and similarly to other types of cancer, measuring circulating tumor-derived nucleic acids from biological fluid samples could be the future of differential diagnostics, patient stratification, and follow up in the future in glioblastoma as well.
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Affiliation(s)
- Zsuzsanna Birkó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
- Correspondence:
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - Álmos Klekner
- Department of Neurosurgery, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
| | - József Virga
- Department of Oncology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary;
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27
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Kong L, Liu G, Deng M, Lian Z, Han Y, Sun B, Guo Y, Liu D, Li Y. Growth retardation-responsive analysis of mRNAs and long noncoding RNAs in the liver tissue of Leiqiong cattle. Sci Rep 2020; 10:14254. [PMID: 32868811 PMCID: PMC7459292 DOI: 10.1038/s41598-020-71206-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/10/2020] [Indexed: 12/15/2022] Open
Abstract
As an important type of non-coding RNA molecule, long non-coding RNAs (lncRNAs) have varied roles in many biological processes, and have been studied extensively over the past few years. However, little is known about lncRNA-mediated regulation during cattle growth and development. Therefore, in the present study, RNA sequencing was used to determine the expression level of mRNAs and lncRNAs in the liver of adult Leiqiong cattle under the condition of growth retardation and normal growth. We totally detected 1,124 and 24 differentially expressed mRNAs and lncRNAs, respectively. The differentially expressed mRNAs were mainly associated with growth factor binding, protein K63-linked ubiquitination and cellular protein metabolic process; additionally, they were significantly enriched in the growth and development related pathways, including PPAR signaling pathway, vitamin B6 metabolism, glyoxylate and dicarboxylate metabolism. Combined analysis showed that the co-located differentially expressed lncRNA Lnc_002583 might positively influence the expression of the corresponding genes IFI44 and IFI44L, exerting co-regulative effects on Leiqiong cattle growth and development. Thus, we made the hypothesis that Lnc_002583, IFI44 and IFI44L might function synergistically to regulate the growth of Leiqiong cattle. This study provides a catalog of Leiqiong cattle liver mRNAs and lncRNAs, and will contribute to a better understanding of the molecular mechanism underlying growth regulataion.
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Affiliation(s)
- Lingxuan Kong
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Zhiquan Lian
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Yinru Han
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China.
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China.
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, GD, China.
- National Local Joint Engineering Research Center of Livestock and Poutry, South China Agricultural University, Guangzhou, 510642, GD, China.
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28
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Deng Y, Luo H, Yang Z, Liu L. LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers. Brief Bioinform 2020; 22:5895039. [PMID: 32820322 DOI: 10.1093/bib/bbaa179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/05/2023] Open
Abstract
Accumulating studies demonstrated that the roles of lncRNAs for tumorigenesis were isoform-dependent and their aberrant splicing patterns in cancers contributed to function specificity. However, there is no existing database focusing on cancer-related alternative splicing of lncRNAs. Here, we developed a comprehensive database called LncAS2Cancer, which collected 5335 bulk RNA sequencing and 1826 single-cell RNA sequencing samples, covering over 30 cancer types. By applying six state-of-the-art splicing algorithms, 50 859 alternative splicing events for 8 splicing types were identified and deposited in the database. In addition, the database contained the following information: (i) splicing patterns of lncRNAs under seven different conditions, such as gene interference, which facilitated to infer potential regulators; (ii) annotation information derived from eight sources and manual curation, to understand the functional impact of affected sequences; (iii) survival analysis to explore potential biomarkers; as well as (iv) a suite of tools to browse, search, visualize and download interesting information. LncAS2Cancer could not only confirm the known cancer-associated lncRNA isoforms but also indicate novel ones. Using the data deposited in LncAS2Cancer, we compared gene model and transcript overlap between lncRNAs and protein-coding genes and discusses how these factors, along with sequencing depth, affected the interpretation of splicing signals. Based on recurrent signals and potential confounders, we proposed a reliable score to prioritize splicing events for further elucidation. Together, with the broad collection of lncRNA splicing patterns and annotation, LncAS2Cancer will provide important new insights into the diverse functional roles of lncRNA isoforms in human cancers. LncAS2Cancer is freely available at https://lncrna2as.cd120.com/.
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Affiliation(s)
- Yulan Deng
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Hao Luo
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Zhenyu Yang
- Department of Thoracic Surgery, West China Hospital, Sichuan University
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University
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29
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Adamopoulos PG, Koukouzeli FΕ, Kontos CK, Scorilas A. Identification of six novel alternative transcripts of the human kallikrein-related peptidase 15 (KLK15), using 3'RACE and high-throughput sequencing. Gene 2020; 749:144708. [PMID: 32334022 DOI: 10.1016/j.gene.2020.144708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 11/18/2022]
Abstract
The kallikrein-related peptidase 15 (KLK15) gene is a member of the largest cluster of serine proteases in the human genome. Exhibiting trypsin-like activity, KLK15 is most likely involved in the activation of prostate-specific antigen (PSA; also known as KLK3), an established biomarker for the diagnosis and screening of prostate cancer. High mRNA expression levels of KLK15 have already been reported in ovarian and prostate cancer, in contrast with breast cancer, where KLK15 has been proposed as a biomarker of favorable prognosis. In this study, we exploited the next-generation sequencing (NGS) technology along with 3' rapid amplification of cDNA ends (3' RACE) to discover alternative KLK15 splice variants. Extensive computational analysis of the obtained NGS data revealed the existence of novel splice junctions, thus supporting the existence of novel KLK15 transcripts. Six novel KLK15 splice variants were identified and verified by Sanger sequencing. Two of them (KLK15 v.11 and v.12) contain an open reading frame and are hence predicted to encode two novel KLK15 protein isoforms. Expression analysis of each KLK15 splice variant in sixteen cDNA pools from malignant cell lines and in normal cell lines (HEK293, HaCaT, and BJ cells) revealed very different expression profiles of particular KLK15 transcripts. Moreover, the new KLK15 splice variants were shown to be expressed in breast, ovarian, prostate, urinary bladder, colon, and renal tissue specimens. Due to the prominent clinical value of KLK15 mRNA expression, the novel KLK15 transcripts appear as candidate cancer biomarkers for diagnostic and/or prognostic purposes and, therefore, merit further investigation.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Fotini Ε Koukouzeli
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece.
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30
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Castandet B, Germain A, Hotto AM, Stern DB. Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana reveals >200 transcription initiation sites and the extensive imprints of RNA-binding proteins and secondary structures. Nucleic Acids Res 2020; 47:11889-11905. [PMID: 31732725 PMCID: PMC7145512 DOI: 10.1093/nar/gkz1059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/02/2019] [Accepted: 11/05/2019] [Indexed: 12/23/2022] Open
Abstract
Chloroplast transcription requires numerous quality control steps to generate the complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we systematically mapped transcript ends by developing a protocol called Terminome-seq. Using Arabidopsis thaliana as a model, we catalogued >215 primary 5′ ends corresponding to transcription start sites (TSS), as well as 1628 processed 5′ ends and 1299 3′ ends. While most termini were found in intergenic regions, numerous abundant termini were also found within coding regions and introns, including several major TSS at unexpected locations. A consistent feature was the clustering of both 5′ and 3′ ends, contrasting with the prevailing description of discrete 5′ termini, suggesting an imprecision of the transcription and/or RNA processing machinery. Numerous termini correlated with the extremities of small RNA footprints or predicted stem-loop structures, in agreement with the model of passive RNA protection. Terminome-seq was also implemented for pnp1–1, a mutant lacking the processing enzyme polynucleotide phosphorylase. Nearly 2000 termini were altered in pnp1–1, revealing a dominant role in shaping the transcriptome. In summary, Terminome-seq permits precise delineation of the roles and regulation of the many factors involved in organellar transcriptome quality control.
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Affiliation(s)
- Benoît Castandet
- Boyce Thompson Institute, Ithaca, NY 14853, USA.,Institut des Sciences des Plantes de Paris Saclay (IPS2), UEVE, INRA, CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91192 Gif sur Yvette, France.,Université de Paris, IPS2, F-91192 Gif sur Yvette, France
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31
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Abou Alezz M, Celli L, Belotti G, Lisa A, Bione S. GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. Front Genet 2020; 11:488. [PMID: 32499820 PMCID: PMC7242645 DOI: 10.3389/fgene.2020.00488] [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: 12/13/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are recognized as an important class of regulatory molecules involved in a variety of biological functions. However, the regulatory mechanisms of long non-coding genes expression are still poorly understood. The characterization of the genomic features of lncRNAs is crucial to get insight into their function. In this study, we exploited recent annotations by GENCODE to characterize the genomic and splicing features of long non-coding genes in comparison with protein-coding ones, both in human and mouse. Our analysis highlighted differences between the two classes of genes in terms of their gene architecture. Significant differences in the splice sites usage were observed between long non-coding and protein-coding genes (PCG). While the frequency of non-canonical GC-AG splice junctions represents about 0.8% of total splice sites in PCGs, we identified a significant enrichment of the GC-AG splice sites in long non-coding genes, both in human (3.0%) and mouse (1.9%). In addition, we found a positional bias of GC-AG splice sites being enriched in the first intron in both classes of genes. Moreover, a significant shorter length and weaker donor and acceptor sites were found comparing GC-AG introns to GT-AG introns. Genes containing at least one GC-AG intron were found conserved in many species, more prone to alternative splicing and a functional analysis pointed toward their enrichment in specific biological processes such as DNA repair. Our study shows for the first time that GC-AG introns are mainly associated with lncRNAs and are preferentially located in the first intron. Additionally, we discovered their regulatory potential indicating the existence of a new mechanism of non-coding and PCGs expression regulation.
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Affiliation(s)
| | | | | | | | - Silvia Bione
- Computational Biology Unit, Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, National Research Council, Pavia, Italy
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32
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Huang PS, Lin YH, Chi HC, Tseng YH, Chen CY, Lin TK, Yeh CT, Lin KH. Dysregulated FAM215A Stimulates LAMP2 Expression to Confer Drug-Resistant and Malignant in Human Liver Cancer. Cells 2020; 9:cells9040961. [PMID: 32295144 PMCID: PMC7227021 DOI: 10.3390/cells9040961] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and aggressive human malignancies worldwide. Long non-coding (lnc) RNAs regulate complex cellular functions, such as cell growth, differentiation, metabolism, and metastasis. Although deregulation of lncRNA expression has been detected in HCC, many of the hepato-carcinogenesis-associated lncRNAs remain yet unidentified. Here, we aimed to investigate the involvement of a specific HCC-dysregulated lncRNA, FAM215A, and characterize its molecular regulation mechanism. We show for the first time that FAM215A is overexpressed in HCC, and its expression level correlates with tumor size, vascular invasion, and pathology stage. Overexpression of FAM215A accelerates cell proliferation and metastasis in HCC cells. According to Gene Expression Omnibus Dataset analysis, FAM215A is induced in doxorubicin (DOX)-resistant HCC cells. Overexpression of FAM215A increases DOX resistance in two HCC cell lines, and this is associated with enhanced expression of lysosome-associated membrane protein 2 (LAMP2). FAM215A interacts with LAMP2 to protect it from ubiquitination. Together, our results show that the lncRNA, FAM215A, is highly expressed in HCC, where it interacts with and stabilizes LAMP2 to increase tumor progression while decreasing doxorubicin sensitivity.
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MESH Headings
- Animals
- Antibiotics, Antineoplastic/pharmacology
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Doxorubicin/pharmacology
- Drug Resistance, Neoplasm
- Gene Knockdown Techniques
- Humans
- Liver Neoplasms/drug therapy
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- Lysosomal-Associated Membrane Protein 2/genetics
- Lysosomal-Associated Membrane Protein 2/metabolism
- Mice
- Mice, SCID
- Neoplasm Metastasis
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Transfection
- Up-Regulation
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Po-Shuan Huang
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan, (H.-C.C.)
| | - Yang-Hsiang Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan, (C.-T.Y.)
| | - Hsiang-Cheng Chi
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan, (H.-C.C.)
| | - Yi-Hsin Tseng
- Institute of Stem Cell and Translational Cancer Research, Chang Gung Memorial Hospital at Linkou, and Chang Gung University, Taoyuan 333, Taiwan;
| | - Cheng Yi Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Tzu-Kang Lin
- Neurosurgery, Fu Jen Catholic University Hospital and School of Medicine, Fu Jen Catholic University, New Taipei City 24205, Taiwan;
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan, (C.-T.Y.)
| | - Kwang-Huei Lin
- Department of Biochemistry, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan, (H.-C.C.)
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan 333, Taiwan, (C.-T.Y.)
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: (K.-H.L.); Tel./Fax: +886-3-2118263 (K.-H.L.)
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33
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Matveishina E, Antonov I, Medvedeva YA. Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction. Int J Mol Sci 2020; 21:E830. [PMID: 32012884 PMCID: PMC7037363 DOI: 10.3390/ijms21030830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play a key role in many cellular processes including chromatin regulation. To modify chromatin, lncRNAs often interact with DNA in a sequence-specific manner forming RNA:DNA triple helices. Computational tools for triple helix search do not always provide genome-wide predictions of sufficient quality. Here, we used four human lncRNAs (MEG3, DACOR1, TERC and HOTAIR) and their experimentally determined binding regions for evaluating triplex parameters that provide the highest prediction accuracy. Additionally, we combined triplex prediction with the lncRNA secondary structure and demonstrated that considering only single-stranded fragments of lncRNA can further improve DNA-RNA triplexes prediction.
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Affiliation(s)
- Elena Matveishina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
| | - Ivan Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, 117971 Moscow, Russia
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34
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Lloret-Llinares M, Jensen TH. Global Identification of Human Exosome Substrates Using RNA Interference and RNA Sequencing. Methods Mol Biol 2020; 2062:127-145. [PMID: 31768975 DOI: 10.1007/978-1-4939-9822-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
The RNA exosome is involved in RNA processing and quality control. In humans, it consists of an enzymatically inactive nine-subunit core, with ribonucleolytic activity contributed by one or two additional components. Moreover, several protein cofactors interact with the exosome to enable and specify its recruitment to a wide range of substrates. A common strategy to identify these substrates has been to deplete an exosome subunit or a cofactor and subsequently interrogate which transcripts become stabilized. Here, we describe an experimental pipeline including siRNA-mediated depletion of the RNA exosome or its cofactors in HeLa cells, confirmation of the knockdown efficiencies, and the manual or high-throughput identification of exosome targets.
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Affiliation(s)
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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35
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Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, der Laan MHPV, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol 2019; 17:108. [PMID: 31884969 PMCID: PMC6936065 DOI: 10.1186/s12915-019-0726-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 11/19/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RESULTS RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. CONCLUSIONS We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
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Affiliation(s)
- Sylvain Foissac
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Sarah Djebali
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Kylie Munyard
- Curtin University, School of Pharmacy & Biomedical Sciences, CHIRI Biosciences, Perth, 24105 Australia
| | - Nathalie Vialaneix
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Andrea Rau
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Kevin Muret
- PEGASE, Agrocampus-Ouest, INRA, Saint-Gilles Cedex, F-35590 France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
- INRA, US1426, GeT-PlaGe, Genotoul, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Matthias Zytnicki
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Fany Blanc
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Cédric Cabau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Elisa Crisci
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Sophie Dhorne-Pollet
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Ignacio Gonzalez
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Adeline Goubil
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | | | - Sylvain Marthey
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Maria Marti-Marimon
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Florence Mompart
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - David Robelin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Magali San Cristobal
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Christophe Klopp
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Hervé Acloque
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | - Elisabetta Giuffra
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
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36
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Zhu HR, Yu XN, Zhang GC, Shi X, Bilegsaikhan E, Guo HY, Liu LL, Cai Y, Song GQ, Liu TT, Dong L, Janssen HLA, Weng SQ, Wu J, Shen XZ, Zhu JM. Comprehensive analysis of long non‑coding RNA‑messenger RNA‑microRNA co‑expression network identifies cell cycle‑related lncRNA in hepatocellular carcinoma. Int J Mol Med 2019; 44:1844-1854. [PMID: 31485608 PMCID: PMC6777664 DOI: 10.3892/ijmm.2019.4323] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/24/2019] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to contribute to progression and prognosis of hepatocellular carcinoma (HCC). However, expression profiling and interaction of lncRNAs with messenger RNAs (mRNAs) and microRNAs (miRNAs) remain largely unknown in HCC. The expression profiling of lncRNAs, mRNA and miRNAs was obtained using microarray. The Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to characterize potential functions of differentially expressed mRNAs. Cytoscape was applied to construct an lncRNA-miRNA-mRNA co-expression network and candidate lncRNAs were validated via quantitative PCR in 30 pairs of HCC and adjacent tumor-free tissues. In this study, 1,056 upregulated and 1,288 downregulated lncRNAs were identified, while 2,687 mRNAs and 6 miRNAs were aberrantly expressed in HCC compared with adjacent tumor-free tissues. Potential functions of differentially expressed mRNAs were demonstrated to significantly participate in modulating critical genes in the cell cycle, such as cyclin E1 and cyclin B2. After screening, 95 lncRNAs, 5 miRNAs and 36 mRNAs were recruited for construction of lncRNA-mRNA-miRNA co-expression network in the cell cycle pathway. Subsequently, the top 5 lncRNAs that potentially modulate critical genes in the cell cycle were selected as the candidates for further verification. Kaplan-Meier curves using the Cancer Genome Atlas database showed that 13 targeted mRNAs were associated with overall survival of HCC patients. Finally, three lncRNAs, including ENST00000522221, lnc-HACE1-6:1 and lnc-ICOSLG-11:1, are significantly upregulated in HCC tissues compared with adjacent tumor-free tissues. These findings suggest that lncRNAs play essential roles in the pathogenesis of HCC via regulating coding genes and miRNAs, and may be important targets for diagnosis and treatment of this disease.
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Affiliation(s)
- Hai-Rong Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Xiang-Nan Yu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Guang-Cong Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Xuan Shi
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Enkhnaran Bilegsaikhan
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Hong-Ying Guo
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Li-Li Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Yu Cai
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Guang-Qi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Tao-Tao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Harry L A Janssen
- Division of Gastroenterology, University of Toronto and University Health Network, Toronto, ON M5G 2C4, Canada
| | - Shu-Qiang Weng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Jian Wu
- Shanghai Institute of Liver Diseases, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Xi-Zhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
| | - Ji-Min Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital of Fudan University, Shanghai 200032, P.R. China
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37
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Antonov IV, Mazurov E, Borodovsky M, Medvedeva YA. Prediction of lncRNAs and their interactions with nucleic acids: benchmarking bioinformatics tools. Brief Bioinform 2019; 20:551-564. [PMID: 29697742 DOI: 10.1093/bib/bby032] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/26/2018] [Indexed: 01/22/2023] Open
Abstract
The genomes of mammalian species are pervasively transcribed producing as many noncoding as protein-coding RNAs. There is a growing body of evidence supporting their functional role. Long noncoding RNA (lncRNA) can bind both nucleic acids and proteins through several mechanisms. A reliable computational prediction of the most probable mechanism of lncRNA interaction can facilitate experimental validation of its function. In this study, we benchmarked computational tools capable to discriminate lncRNA from mRNA and predict lncRNA interactions with other nucleic acids. We assessed the performance of 9 tools for distinguishing protein-coding from noncoding RNAs, as well as 19 tools for prediction of RNA-RNA and RNA-DNA interactions. Our conclusions about the considered tools were based on their performances on the entire genome/transcriptome level, as it is the most common task nowadays. We found that FEELnc and CPAT distinguish between coding and noncoding mammalian transcripts in the most accurate manner. ASSA, RIBlast and LASTAL, as well as Triplexator, turned out to be the best predictors of RNA-RNA and RNA-DNA interactions, respectively. We showed that the normalization of the predicted interaction strength to the transcript length and GC content may improve the accuracy of inferring RNA interactions. Yet, all the current tools have difficulties to make accurate predictions of short-trans RNA-RNA interactions-stretches of sparse contacts. All over, there is still room for improvement in each category, especially for predictions of RNA interactions.
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Affiliation(s)
- Ivan V Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | | | - Mark Borodovsky
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, Moscow, Russian Federation.,Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation.,Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, Moscow, Russian Federation
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38
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Kong Y, Lu Z, Liu P, Liu Y, Wang F, Liang EY, Hou FF, Liang M. Long Noncoding RNA: Genomics and Relevance to Physiology. Compr Physiol 2019; 9:933-946. [PMID: 31187897 DOI: 10.1002/cphy.c180032] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mammalian cell expresses thousands of long noncoding RNAs (lncRNAs) that are longer than 200 nucleotides but do not encode any protein. lncRNAs can change the expression of protein-coding genes through both cis and trans mechanisms, including imprinting and other types of transcriptional regulation, and posttranscriptional regulation including serving as molecular sponges. Deep sequencing, coupled with analysis of sequence characteristics, is the primary method used to identify lncRNAs. Physiological roles of specific lncRNAs can be examined using genetic targeting or knockdown with modified oligonucleotides. Identification of nucleic acids or proteins with which an lncRNA interacts is essential for understanding the molecular mechanism underlying its physiological role. lncRNAs have been reported to contribute to the regulation of physiological functions and disease development in several organ systems, including the cardiovascular, renal, muscular, endocrine, digestive, nervous, respiratory, and reproductive systems. The physiological role of the majority of lncRNAs, many of which are species and tissue specific, remains to be determined. © 2019 American Physiological Society. Compr Physiol 9:933-946, 2019.
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Affiliation(s)
- Yiwei Kong
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zeyuan Lu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Sir Run Run Shaw Hospital, Institute of Translational Medicine, Zhejiang University, Zhejiang, China
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Feng Wang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Nephrology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Eugene Y Liang
- Center for Advancing Population Science, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Fan Fan Hou
- National Clinical Research Center for Kidney Disease, State Key Laboratory of Organ Failure Research, Guangzhou Regenerative Medicine and Health - Guangdong Laboratory, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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39
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Agliano F, Rathinam VA, Medvedev AE, Vanaja SK, Vella AT. Long Noncoding RNAs in Host-Pathogen Interactions. Trends Immunol 2019; 40:492-510. [PMID: 31053495 DOI: 10.1016/j.it.2019.04.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/28/2019] [Accepted: 04/02/2019] [Indexed: 02/08/2023]
Abstract
Long noncoding RNAs (lncRNAs) are key molecules that regulate gene expression in a variety of organisms. LncRNAs can drive different transcriptional and post-transcriptional events that impact cellular functions. Recent studies have identified many lncRNAs associated with immune cell development and activation; however, an understanding of their functional role in host immunity to infection is just emerging. Here, we provide a detailed and updated review of the functional roles of lncRNAs in regulating mammalian immune responses during host-pathogen interactions, because these functions may be either beneficial or detrimental to the host. With increased mechanistic insight into the roles of lncRNAs, it may be possible to design and/or improve lncRNA-based therapies to treat a variety of infectious and inflammatory diseases.
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Affiliation(s)
- Federica Agliano
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Vijay A Rathinam
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Andrei E Medvedev
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Sivapriya Kailasan Vanaja
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
| | - Anthony T Vella
- Department of Immunology, School of Medicine, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA.
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40
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Abstract
Biomarker-driven personalized cancer therapy is a field of growing interest, and several molecular tests have been developed to detect biomarkers that predict, e.g., response of cancers to particular therapies. Identification of these molecules and understanding their molecular mechanisms is important for cancer prognosis and the development of therapeutics for late stage diseases. In the past, significant efforts have been placed on the discovery of protein or DNA-based biomarkers while only recently the class of long non-coding RNA (lncRNA) has emerged as a new category of biomarker. The mammalian genome is pervasively transcribed yielding a vast amount of non-protein-coding RNAs including lncRNAs. Hence, these transcripts represent a rich source of information that has the potential to significantly contribute to precision medicine in the future. Importantly, many lncRNAs are differentially expressed in carcinomas and they are emerging as potent regulators of tumor progression and metastasis. Here, we will highlight prime examples of lncRNAs that serve as marker for cancer progression or therapy response and which might represent promising therapeutic targets. Furthermore, we will introduce lncRNA targeting tools and strategies, and we will discuss potential pitfalls in translating these into clinical trials.
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41
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Adamopoulos PG, Mavrogiannis AV, Kontos CK, Scorilas A. Novel alternative splice variants of the human protein arginine methyltransferase 1 (PRMT1) gene, discovered using next-generation sequencing. Gene 2019; 699:135-144. [PMID: 30849541 DOI: 10.1016/j.gene.2019.02.072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 01/24/2019] [Accepted: 02/17/2019] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) technology is highly expected to help researchers disclose the complexity of alternative splicing and understand its association with carcinogenesis. Alternative splicing alterations are firmly associated with multiple malignancies, in terms of functional roles in malignant transformation, motility, and/or metastasis of cancer cells. One perfect example illustrating the connection between alternative splicing and cancer is the human protein arginine methyltransferase 1 (PRMT1) gene, previously cloned from members of our research group and involved in a variety of processes including transcription, DNA repair, and signal transduction. Two splice variants of PRMT1 (variants v.1 and v.2) are downregulated in breast cancer. In addition, PRMT1 v.2 promotes the survival and invasiveness of breast cancer cells, while it could serve as a biomarker of unfavorable prognosis in colon cancer patients. The aim of this study was the molecular cloning of novel alternative splice variants of PRMT1 with the use of 3' RACE coupled with NGS technology. Extensive bioinformatics and computational analysis revealed a significant number of 19 novel alternative splicing events between annotated exons of PRMT1 as well as one novel exon, resulting in the discovery of multiple PRMT1 transcripts. In order to validate the full sequence of the novel transcripts, RT-PCR was carried out with the use of variant-specific primers. As a result, 58 novel PRMT1 transcripts were identified, 34 of which are mRNAs encoding new protein isoforms, whereas the rest 24 transcripts are candidates for nonsense-mediated mRNA decay (NMD).
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Adamantios V Mavrogiannis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece.
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42
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Turner AW, Wong D, Khan MD, Dreisbach CN, Palmore M, Miller CL. Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis. Front Cardiovasc Med 2019; 6:9. [PMID: 30838214 PMCID: PMC6389617 DOI: 10.3389/fcvm.2019.00009] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/30/2019] [Indexed: 12/15/2022] Open
Abstract
Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors.
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Affiliation(s)
- Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Doris Wong
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Mohammad Daud Khan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Caitlin N. Dreisbach
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- School of Nursing, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
| | - Meredith Palmore
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Data Science Institute, University of Virginia, Charlottesville, VA, United States
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, United States
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, United States
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43
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Cao H, Wahlestedt C, Kapranov P. Strategies to Annotate and Characterize Long Noncoding RNAs: Advantages and Pitfalls. Trends Genet 2018; 34:704-721. [DOI: 10.1016/j.tig.2018.06.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/30/2018] [Accepted: 06/12/2018] [Indexed: 12/21/2022]
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44
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Abstract
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets. The ideal approach toward resolving these remaining issues would involve the direct amplification-free sequencing of full-length RNA molecules. This has recently become practical with the advent of nanopore sequencing, which raises the possibility of yet another revolution in transcriptomics. I discuss the design considerations to be taken into account, the technical challenges that need to be addressed and the biological questions these advances can be expected to resolve.
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45
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Bijnsdorp IV, van Royen ME, Verhaegh GW, Martens-Uzunova ES. The Non-Coding Transcriptome of Prostate Cancer: Implications for Clinical Practice. Mol Diagn Ther 2018; 21:385-400. [PMID: 28299719 PMCID: PMC5511609 DOI: 10.1007/s40291-017-0271-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Prostate cancer (PCa) is the most common type of cancer and the second leading cause of cancer-related death in men. Despite extensive research, the molecular mechanisms underlying PCa initiation and progression remain unclear, and there is increasing need of better biomarkers that can distinguish indolent from aggressive and life-threatening disease. With the advent of advanced genomic technologies in the last decade, it became apparent that the human genome encodes tens of thousands non-protein-coding RNAs (ncRNAs) with yet to be discovered function. It is clear now that the majority of ncRNAs exhibit highly specific expression patterns restricted to certain tissues and organs or developmental stages and that the expression of many ncRNAs is altered in disease and cancer, including cancer of the prostate. Such ncRNAs can serve as important biomarkers for PCa diagnosis, prognosis, or prediction of therapy response. In this review, we give an overview of the different types of ncRNAs and their function, describe ncRNAs relevant for the diagnosis and prognosis of PCa, and present emerging new aspects of ncRNA research that may contribute to the future utilization of ncRNAs as clinically useful therapeutic targets.
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MESH Headings
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/metabolism
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/urine
- Early Detection of Cancer/methods
- Gene Expression Regulation, Neoplastic
- High-Throughput Nucleotide Sequencing
- Humans
- Male
- Molecular Targeted Therapy
- Precision Medicine
- Prognosis
- Prostatic Neoplasms/diagnosis
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- RNA, Untranslated/blood
- RNA, Untranslated/classification
- RNA, Untranslated/genetics
- RNA, Untranslated/urine
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Affiliation(s)
- Irene V Bijnsdorp
- Department of Urology, VU University Medical Center, Amsterdam, The Netherlands
| | - Martin E van Royen
- Department of Pathology and Erasmus Optical Imaging Centre (OIC), Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gerald W Verhaegh
- Department of Urology, Radboud university medical center, Nijmegen, The Netherlands
| | - Elena S Martens-Uzunova
- Department of Urology, Erasmus Medical Center, Erasmus Cancer Institute, Room Be-362b, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
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46
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Peng Z, Liu C, Wu M. New insights into long noncoding RNAs and their roles in glioma. Mol Cancer 2018; 17:61. [PMID: 29458374 PMCID: PMC5817731 DOI: 10.1186/s12943-018-0812-2] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/08/2018] [Indexed: 01/07/2023] Open
Abstract
Glioma is one of the most prevalent types of primary intracranial carcinoma with varying malignancy grades I–IV and histological subtypes, including astrocytomas, glioblastoma multiform (GBM), oligodendrogliomas and mixed tumors. Glioma is characterized by rapid cell proliferation and angiogenesis, and the WHO grade IV glioblastoma, which is highly malignant with poor prognosis because GBM stem-like cells (GSCs) are resistant to conventional therapy and easily recrudescent, accounts for the majority of gliomas. Consequently, investigations exploring the accurate molecular mechanisms and reliable therapeutic targets for gliomas have drawn extensive attention. Based on the increasing amount of functional lncRNAs aberrantly expressed in glioma tissues and cell lines, lncRNAs might be critical for glioma initiation, progression and other malignant phenotypes. This review summarizes the latest insights into the lncRNA field and their functional roles in glioma, therefore evaluating the potential clinical applications of lncRNAs as prospective novel biomarkers and therapeutic targets.
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Affiliation(s)
- Zixuan Peng
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410006, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, Hunan, 410078, China
| | - Changhong Liu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, Hunan, 410078, China
| | - Minghua Wu
- Hunan Provincial Tumor Hospital and the Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, Hunan, 410006, China. .,Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha, Hunan, 410078, China.
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47
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Adamopoulos PG, Kontos CK, Scorilas A. Molecular cloning of novel transcripts of human kallikrein-related peptidases 5, 6, 7, 8 and 9 (KLK5 - KLK9), using Next-generation sequencing. Sci Rep 2017; 7:17299. [PMID: 29229980 PMCID: PMC5725587 DOI: 10.1038/s41598-017-16269-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/04/2017] [Indexed: 11/26/2022] Open
Abstract
Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts of the human KLK5, KLK6, KLK7, KLK8 and KLK9 genes, using 3′ rapid amplification of cDNA ends (3′ RACE) and NGS technology, as well as their expression analysis in many established cell lines, originating from several distinct cancerous and normal tissues. Extensive bioinformatic analysis revealed novel splice variants of these five members of the KLK family, comprising entirely new exons, previously unknown boundaries of the already annotated exons (extensions and truncations) as well as alternative splicing events between these exons. Nested RT-PCR in a panel of human cell lines originating from seventeen cancerous and two normal tissues with the use of variant-specific pairs of primers was carried out for expression analysis of these novel splice variants, and Sanger sequencing of the respective amplicons confirmed our NGS results. Given that some splice variants of KLK family members possess clinical value, novel alternatively spliced transcripts appear as new candidate biomarkers for diagnostic and/or prognostic purposes and as targets for therapeutic strategies.
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Affiliation(s)
- Panagiotis G Adamopoulos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Athens, 15701, Greece.
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48
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Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R. High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet 2017; 49:1731-1740. [PMID: 29106417 PMCID: PMC5709232 DOI: 10.1038/ng.3988] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/11/2017] [Indexed: 12/20/2022]
Abstract
Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines targeted RNA capture with third-generation long-read sequencing. Here we present an experimental reannotation of the GENCODE intergenic lncRNA populations in matched human and mouse tissues that resulted in novel transcript models for 3,574 and 561 gene loci, respectively. CLS approximately doubled the annotated complexity of targeted loci, outperforming existing short-read techniques. Full-length transcript models produced by CLS enabled us to definitively characterize the genomic features of lncRNAs, including promoter and gene structure, and protein-coding potential. Thus, CLS removes a long-standing bottleneck in transcriptome annotation and generates manual-quality full-length transcript models at high-throughput scales.
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Affiliation(s)
- Julien Lagarde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Barbara Uszczynska-Ratajczak
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Silvia Carbonell
- R&D Department, Quantitative Genomic Medicine Laboratories (qGenomics), Barcelona, Spain
| | - Sílvia Pérez-Lluch
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Amaya Abad
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carrie Davis
- Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Thomas R. Gingeras
- Functional Genomics Group, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK CB10 1HH
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK CB10 1HH
| | - Roderic Guigo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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49
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Wang Q, Li ZX, Liu BW, He ZG, Liu C, Chen M, Liu SG, Wu WZ, Xiang HB. Altered expression of differential gene and lncRNA in the lower thoracic spinal cord on different time courses of experimental obstructive jaundice model accompanied with altered peripheral nociception in rats. Oncotarget 2017; 8:106098-106112. [PMID: 29285317 PMCID: PMC5739704 DOI: 10.18632/oncotarget.22532] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 10/28/2017] [Indexed: 12/17/2022] Open
Abstract
The spinal origin of jaundice-induced altered peripheral nociceptive response poorly understood. In the current study, we aimed to first validate rats with bile duct ligation (BDL) as a jaundice model accompanied by altered peripheral nociceptive response, and then to analyze differential gene and lncRNA expression patterns in the lower thoracic spinal cord on different time courses after BDL operation by using high-throughput RNA sequencing. The differentially expressed genes (DEGs) identified using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, followed by clustering analysis, Gene Ontology analysis and pathway analysis. As a result, a total of 2033 lncRNAs were differentially expressed 28d after BDL, in which 1545 probe sets were up-regulated and 488 probe sets were down-regulated, whereas a total of 2800 mRNAs were differentially expressed, in which 1548 probe sets were up-regulated and 1252 probe sets were down-regulated. The RNAseq data of select mRNAs and lncRNAs was validated by RT-qPCR. 28d after BDL, the expressions of lncRNA NONRATT002335 and NONRATT018085 were significantly up-regulated whereas the expression of lncRNA NONRATT025415, NONRATT025388 and NONRATT025409 was significantly down-regulated. 14d after BDL, the expressions of lncRNA NONRATT002335 and NONRATT018085 were significantly up-regulated; the expression of lncRNA NONRATT025415, NONRATT025388 and NONRATT025409 was significantly down-regulated. In conclusion, the present study showed that jaundice accompanied with decreased peripheral nociception involved in the changes of gene and lncRNA expression profiles in spinal cord. These findings extend current understanding of spinal mechanism for obstructive jaundice accompanied by decreased peripheral nociception.
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Affiliation(s)
- Qian Wang
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhi-Xiao Li
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Bao-Wen Liu
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhi-Gang He
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Cheng Liu
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Min Chen
- Department of Anesthesiology, Hubei Maternal and Child Health Hospital, Wuhan, P.R. China
| | - San-Guang Liu
- Department of Hepatobiliary Surgery, The Second Hospital, Hebei Medical University, Shijiazhuang, P.R. China
| | - Wei-Zhong Wu
- Department of General Surgery, The Second Hospital, Hebei Medical University, Shijiazhuang, P.R. China
| | - Hong-Bing Xiang
- Department of Anesthesiology and Pain Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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50
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Catsper1 promoter is bidirectional and regulates the expression of a novel lncRNA. Sci Rep 2017; 7:13351. [PMID: 29042633 PMCID: PMC5645346 DOI: 10.1038/s41598-017-13867-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 10/03/2017] [Indexed: 11/10/2022] Open
Abstract
The Catsper1 gene, whose expression is restricted to male germ cells, has great importance in reproductive biology because of its function in sperm motility and fertilization. We previously reported that the promoter of this gene has transcriptional activity in either direction in a heterologous system. In the present study, we found that the Catsper1 promoter has in vitro transcriptional activity in either orientation in GC-1 spg mouse spermatogonial cells. The results also showed that this promoter regulates the expression of a new divergent Catsper1 gene named Catsper1au (Catsper1 antisense upstream transcript). Catsper1au is expressed in adult male mouse testis and liver tissues but not in female mouse liver or ovary tissues. In the testis, Catsper1au is expressed in embryos at 11.5 days post-coitum and from newborns to adults. This gene is also expressed in 1- to 3-week postnatal hearts and in 1-week to adult stage livers. The analysis of the 1402 bp whole genome sequence revealed that Catsper1au is an intronless and polyadenylated lncRNA, located in the nuclei of Sertoli and spermatogenic cells from adult testis. These data indicate that Catsper1au is divergently expressed from the Catsper1 promoter and could regulate gene expression during spermatogenesis.
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