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Zhou X, Xiao L, Meng F, Zuo F, Wu W, Li G, Han F, Peng G, Shen H. GAS6-AS1 drives bladder cancer progression by increasing MMP7 expression in a ceRNA- and RBP-dependent manner. Transl Oncol 2024; 48:102065. [PMID: 39053343 PMCID: PMC11326496 DOI: 10.1016/j.tranon.2024.102065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024] Open
Abstract
Numerous recent studies have underscored the indispensable roles of long non-coding RNAs (lncRNAs) in various diseases. However, their precise mechanisms in urinary bladder cancer (UBC) remain to be further elucidated. To delve into this inquiry, online databases were analyzed to identify differentially expressed lncRNAs in UBC, followed by the functional experiments in vivo and in vitro functional experiments. GAS6-AS1 exhibited high expression levels in UBC tissues and was shown to regulate the proliferation, migration, invasion, and cell cycle progression of UBC cells in vitro and in vivo. Then, a series of molecular biology experiments, including RNA pull-down, dual-luciferase reporter gene assays, RNA immunoprecipitation (RIP) assays, fluorescent in situ hybridization (FISH), and the triplex-capture assay demonstrated its interaction with miR-367-3p and PRC1. Mechanistically, GAS6-AS1 was found to enhance MMP7 expression by sequestering miR-367-3p. Moreover, GAS6-AS1 inhibited APC transcription by binding with PRC1, thereby activating several oncogenes downstream of the WNT pathway. To sum up, GAS6-AS1 promotes UBC progression through two distinct axes: the GAS6-AS1/miR-367-3p/MMP7 axis and the GAS6-AS1/PRC1/APC/Wnt/MMP7 axis, respectively. As a potential biomarker for UBC, GAS6-AS1 holds promising prospects for the diagnosis, treatment, and prognosis of UBC.
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Affiliation(s)
- Xinyi Zhou
- Department of General Surgery, Affiliated Hospital of Jiangnan University, 1000 Hefeng Road, Wuxi, 214000, China
| | - Linmei Xiao
- Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu 210029, China
| | - Fanyu Meng
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China
| | - Fei Zuo
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China
| | - Weili Wu
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China
| | - Gongyu Li
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China
| | - Fei Han
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China
| | - Guohui Peng
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China.
| | - Hua Shen
- BenQ Medical Center, The Affiliated BenQ Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210019, China.
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2
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Lin Y, Zhao W, Pu R, Lv Z, Xie H, Li Y, Zhang Z. Long non‑coding RNAs as diagnostic and prognostic biomarkers for colorectal cancer (Review). Oncol Lett 2024; 28:486. [PMID: 39185489 PMCID: PMC11342420 DOI: 10.3892/ol.2024.14619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the 3rd most common cancer globally and is the 2nd leading cause of cancer-related death. Owing to the lack of specific early symptoms and the limitations of existing early diagnostic methods, most patients with CRC are diagnosed at advanced stages. To overcome these challenges, researchers have increasingly focused on molecular biomarkers, with particular interest in long non-coding RNAs (lncRNAs). These non-protein-coding RNAs, which exceed 200 nucleotides in length, play critical roles in the development and progression of CRC. The stability and detectability of lncRNAs in the circulatory system make them promising candidate biomarkers. The analysis of circulating lncRNAs in peripheral blood represents a potential option for minimally invasive diagnostic tests based on liquid biopsy samples. The present review aimed to evaluate the efficacy of lncRNAs with altered expression levels in peripheral blood as diagnostic markers for CRC. Additionally, the clinical significance of lncRNAs as prognostic markers for this disease were summarized.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ruonan Pu
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ying Li
- Department of Ultrasonography, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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3
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Poliseno L, Lanza M, Pandolfi PP. Coding, or non-coding, that is the question. Cell Res 2024; 34:609-629. [PMID: 39054345 DOI: 10.1038/s41422-024-00975-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/30/2024] [Indexed: 07/27/2024] Open
Abstract
The advent of high-throughput sequencing uncovered that our genome is pervasively transcribed into RNAs that are seemingly not translated into proteins. It was also found that non-coding RNA transcripts outnumber canonical protein-coding genes. This mindboggling discovery prompted a surge in non-coding RNA research that started unraveling the functional relevance of these new genetic units, shaking the classic definition of "gene". While the non-coding RNA revolution was still taking place, polysome/ribosome profiling and mass spectrometry analyses revealed that peptides can be translated from non-canonical open reading frames. Therefore, it is becoming evident that the coding vs non-coding dichotomy is way blurrier than anticipated. In this review, we focus on several examples in which the binary classification of coding vs non-coding genes is outdated, since the same bifunctional gene expresses both coding and non-coding products. We discuss the implications of this intricate usage of transcripts in terms of molecular mechanisms of gene expression and biological outputs, which are often concordant, but can also surprisingly be discordant. Finally, we discuss the methodological caveats that are associated with the study of bifunctional genes, and we highlight the opportunities and challenges of therapeutic exploitation of this intricacy towards the development of anticancer therapies.
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Affiliation(s)
- Laura Poliseno
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy.
- Institute of Clinical Physiology, CNR, Pisa, Italy.
| | - Martina Lanza
- Oncogenomics Unit, Core Research Laboratory, ISPRO, Pisa, Italy
- Institute of Clinical Physiology, CNR, Pisa, Italy
- University of Siena, Siena, Italy
| | - Pier Paolo Pandolfi
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Torino, Italy.
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA.
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4
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Camilleri-Robles C, Amador R, Tiebe M, Teleman A, Serras F, Guigó R, Corominas M. Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genom Bioinform 2024; 6:lqae091. [PMID: 39157585 PMCID: PMC11327875 DOI: 10.1093/nargab/lqae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.
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Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
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5
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Peng X, Li S, Zeng A, Song L. Regulatory function of glycolysis-related lncRNAs in tumor progression: Mechanism, facts, and perspectives. Biochem Pharmacol 2024; 229:116511. [PMID: 39222714 DOI: 10.1016/j.bcp.2024.116511] [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: 05/27/2024] [Revised: 08/22/2024] [Accepted: 08/29/2024] [Indexed: 09/04/2024]
Abstract
Altered metabolism is a hallmark of cancer, and reprogramming of energy metabolism, known as the "Warburg effect", has long been associated with cancer. Cancer cells use the process of glycolysis to quickly manufacture energy from glucose, pyruvic acid, and lactate, which in turn accelerates the growth of cancer and glycolysis becomes a key target for anti-cancer therapies. Recent groundbreaking discoveries regarding long noncoding RNAs (lncRNAs) have opened a new chapter in the mechanism of cancer occurrence. It is widely recognized that lncRNAs regulate energy metabolism through glycolysis in cancer cells. LncRNAs have been demonstrated to engage in several cancer processes such as proliferation, apoptosis, migration, invasion, and chemoresistance, whereas glycolysis is enhanced or inhibited by the dysregulation of lncRNAs. As a result, cancer survival and development are influenced by different signaling pathways. In this review, we summarize the roles of lncRNAs in a variety of cancers and describe the mechanisms underlying their role in glycolysis. Additionally, the predictive potential of glycolysis and lncRNAs in cancer therapy is discussed.
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Affiliation(s)
- Xinyi Peng
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China
| | - Shuhao Li
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China
| | - Anqi Zeng
- Translational Chinese Medicine Key Laboratory of Sichuan Province, Sichuan Academy of Chinese Medicine Sciences, Sichuan Institute for Translational Chinese Medicine, Chengdu, Sichuan 610041, P.R. China.
| | - Linjiang Song
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan Province 611137, PR China.
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6
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Wang M, Tang W, Wu C, Chen Y, Li H, Wu P, Qian H, Guo X, Zhang Z. Linc20486 promotes BmCPV replication through inhibiting the transcription of AGO2 and Dicers. J Invertebr Pathol 2024; 206:108170. [PMID: 39173824 DOI: 10.1016/j.jip.2024.108170] [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: 01/29/2024] [Revised: 04/02/2024] [Accepted: 07/25/2024] [Indexed: 08/24/2024]
Abstract
The silkworm holds pivotal economic importance, serving not only as a primary source of silk but also as a prominent model organism in scientific research. Nonetheless, silkworm farming remains vulnerable to diverse factors, with viral infections posing the gravest threat to the sericulture industry. Among these, the Bombyx mori cytoplasmic polyhedrosis virus (BmCPV), a member of the Reoviridae family and the cytoplasmic polyhedrosis virus genus, emerges as a significant pathogen in silkworm production. BmCPV infection primarily induces midgut sepsis in silkworms, spreads rapidly, and can inflict substantial economic losses on sericulture production. Presently, effective strategies for preventing and treating BmCPV infections are lacking. Long non-coding RNA (lncRNA) constitutes a class of RNA molecules with transcripts exceeding 200 nt, playing a crucial role in mediating the interplay between pathogens and host cells. Investigation through high-throughput technology has unveiled that BmCPV infection markedly upregulates the expression of Linc20486. This observation suggests potential involvement of Linc20486 in regulating virus replication. Indeed, as anticipated, knockdown of Linc20486 in cells profoundly impedes BmCPV replication, whereas overexpression significantly enhances virus propagation. To probe into the mechanism underlying Linc20486's impact on virus replication, its effects on autophagy, innate immunity, and RNAi-related pathways were scrutinized. The findings revealed that Linc20486 exerts significant influence on the expression of RNAi pathway-related genes, such as Dicer1, Dicer2 and AGO2. This discovery holds promise for unveiling novel avenues to comprehend and combat BmCPV infections in silkworms.
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Affiliation(s)
- Mengdong Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Weiming Tang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Chengyue Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Yeping Chen
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Hao Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Ping Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Heying Qian
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Xijie Guo
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China
| | - Zhendong Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212100, China.
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7
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Afsar S, Syed RU, Khojali WMA, Masood N, Osman ME, Jyothi JS, Hadi MA, Khalifa AAS, Aboshouk NAM, Alsaikhan HA, Alafnan AS, Alrashidi BA. Non-coding RNAs in BRAF-mutant melanoma: targets, indicators, and therapeutic potential. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024:10.1007/s00210-024-03366-3. [PMID: 39167168 DOI: 10.1007/s00210-024-03366-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 08/07/2024] [Indexed: 08/23/2024]
Abstract
Melanoma, a highly aggressive skin cancer, is often driven by BRAF mutations, such as the V600E mutation, which promotes cancer growth through the MAPK pathway and contributes to treatment resistance. Understanding the role of non-coding RNAs (ncRNAs) in these processes is crucial for developing new therapeutic strategies. This review aims to elucidate the relationship between ncRNAs and BRAF mutations in melanoma, focusing on their regulatory roles and impact on treatment resistance. We comprehensively reviewed current literature to synthesize evidence on ncRNA-mediated regulation of BRAF-mutant melanoma and their influence on therapeutic responses. Key ncRNAs, including microRNAs and long ncRNAs, were identified as significant regulators of melanoma development and therapy resistance. MicroRNAs such as miR-15/16 and miR-200 families modulate critical pathways like Wnt signaling and melanogenesis. Long ncRNAs like ANRIL and SAMMSON play roles in cell growth, invasion, and drug susceptibility. Specific ncRNAs, such as BANCR and RMEL3, intersect with the MAPK pathway, highlighting their potential as therapeutic targets or biomarkers in BRAF-mutant melanoma. Additionally, ncRNAs involved in drug resistance, such as miR-579-3p and miR-1246, target processes like autophagy and immune checkpoint regulation. This review highlights the pivotal roles of ncRNAs in regulating BRAF-mutant melanoma and their contribution to drug resistance. These findings underscore the potential of ncRNAs as biomarkers and therapeutic targets, paving the way for innovative treatments to improve outcomes for melanoma patients.
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Affiliation(s)
- S Afsar
- Department of Virology, Sri Venkateswara University, Tirupathi, Andhra Pradesh, 517502, India.
| | - Rahamat Unissa Syed
- Department of Pharmaceutics, College of Pharmacy, University of Ha'il, 81442, Hail, Saudi Arabia.
| | - Weam M A Khojali
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, 81442, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Omdurman Islamic University, Omdurman, 14415, Sudan
| | - Najat Masood
- Chemistry Department, Faculty of Science, University of Ha'il, P.O. Box 2440, 81451, Ha'il,, Saudi Arabia
| | - Mhdia Elhadi Osman
- Department of Clinical Pharmacy, Faculty of Pharmacy, University of Hail, Hail, Saudi Arabia
| | - J Siva Jyothi
- Department of Pharmaceutics, Hindu College of Pharmacy, Andhra Pradesh, India
| | - Mohd Abdul Hadi
- Department of Pharmaceutics, Bhaskar Pharmacy College, Moinabad, R.R.District, Hyderabad, 500075, Telangana, India
| | - Amna Abakar Suleiman Khalifa
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, 81442, Hail, Saudi Arabia
| | - Nayla Ahmed Mohammed Aboshouk
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hail, 81442, Hail, Saudi Arabia
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8
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Ladurner M, Lindner AK, Rehder P, Tulchiner G. The influence of sex hormones on renal cell carcinoma. Ther Adv Med Oncol 2024; 16:17588359241269664. [PMID: 39175990 PMCID: PMC11339752 DOI: 10.1177/17588359241269664] [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: 01/21/2024] [Accepted: 06/25/2024] [Indexed: 08/24/2024] Open
Abstract
Kidney cancer is a common malignancy that constitutes around 5% of all cancer cases. Males are twice as likely to acquire renal cell carcinoma (RCC) compared to females and experience a higher rate of mortality. These disparities indicate that sex hormone (SH)-dependent pathways may have an impact on the aetiology and pathophysiology of RCC. Examination of SH involvement in conventional signalling pathways, as well as genetics and genomics, especially the involvement of ribonucleic acid, reveal further insights into sex-related differences. An understanding of SHs and their influence on kidney cancer is essential to offer patients individualized medicine that would better meet their needs in terms of prevention, diagnosis and treatment. This review presents the understanding of sex-related differences in the clinical manifestation of kidney cancer patients and the underlying biological processes.
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Affiliation(s)
- Michael Ladurner
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Peter Rehder
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Gennadi Tulchiner
- Department of Urology, Medical University of Innsbruck, Anichstrasse 35, Innsbruck 6020, Austria
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9
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Yokoyama S, Muto H, Honda T, Kurokawa Y, Ogawa H, Nakajima R, Kawashima H, Tani H. Identification of Two Long Noncoding RNAs, Kcnq1ot1 and Rmst, as Biomarkers in Chronic Liver Diseases in Mice. Int J Mol Sci 2024; 25:8927. [PMID: 39201613 PMCID: PMC11354866 DOI: 10.3390/ijms25168927] [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: 07/21/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 09/02/2024] Open
Abstract
This study investigates novel short-lived long noncoding RNAs (lncRNAs) in mice with altered expression in metabolic dysfunction-associated steatotic liver (MASH) and liver fibrosis. LncRNAs share similarities with mRNAs in their transcription by RNA polymerase II, possession of a 5' cap structure, and presence of a polyA tail. We identified two lncRNAs, Kcnq1ot1 and Rmst, significantly decreased in both conditions. These lncRNAs showed dramatic expression changes in MASH livers induced by Western diets and CCl4, and in fibrotic livers induced by CCl4 alone. The decrease was more pronounced in liver fibrosis, suggesting their potential as biomarkers for disease progression. Our findings are consistent across different fibrosis models, indicating a crucial role for these lncRNAs in MASH and liver fibrosis in mice. With MASH becoming a global health issue and its progression to fibrosis associated with hepatocarcinogenesis and poor prognosis, understanding the underlying mechanisms is critical. This research contributes to elucidating lncRNA functions in murine liver diseases and provides a foundation for developing novel therapeutic strategies targeting lncRNAs in MASH and liver fibrosis, offering new avenues for potential therapeutic interventions.
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Affiliation(s)
- Shinya Yokoyama
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan; (S.Y.); (H.M.); (T.H.); (H.K.)
| | - Hisanori Muto
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan; (S.Y.); (H.M.); (T.H.); (H.K.)
- Department of Gastroenterology and Hepatology, Fujita Health University Bantane Hospital, 3-6-10, Otoubashi, Nakagawa-ku, Nagoya 454-8509, Japan
| | - Takashi Honda
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan; (S.Y.); (H.M.); (T.H.); (H.K.)
| | - Yoichi Kurokawa
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Eiheiji-cho, Fukui 910-1195, Japan;
| | - Hirotaka Ogawa
- Nagoya Industrial Science Research Institute, Nagoya 460-0008, Japan;
| | - Riku Nakajima
- Department of Health Pharmacy, Yokohama University of Pharmacy, 601 Matano, Totsuka, Yokohama 245-0066, Japan;
| | - Hiroki Kawashima
- Department of Gastroenterology and Hepatology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya 466-8560, Japan; (S.Y.); (H.M.); (T.H.); (H.K.)
| | - Hidenori Tani
- Department of Health Pharmacy, Yokohama University of Pharmacy, 601 Matano, Totsuka, Yokohama 245-0066, Japan;
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Abida, Eltaib L, Alhazmi BH, Alzahrani AR, Asdaq SMB, Ali A, Aldhafiri FJ, Alruwaili WT, Al-Hajeili M, Abdulkhaliq AA, Rabaan AA, Imran M. Long non-coding RNA HOTAIR: A biomarker and therapeutic target in urological tumors. Pathol Res Pract 2024; 262:155549. [PMID: 39173467 DOI: 10.1016/j.prp.2024.155549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/12/2024] [Accepted: 08/14/2024] [Indexed: 08/24/2024]
Abstract
Long non-coding RNAs (lncRNAs) significantly influence gene regulation across epigenetic, transcriptional, and post-transcriptional levels through their interactions with DNA, RNA, and proteins. There is growing evidence of lncRNAs' critical roles in the emergence and progression of various diseases, including urological tumors (UTs), such as cancers of the kidney, bladder, and prostate. Research increasingly links lncRNA dysregulation to diverse cellular processes like invasion, metastasis, apoptosis, and chromatin remodeling. Among these, HOTAIR stands out for its pivotal role in oncogenesis, impacting treatment resistance, cell migration, proliferation, survival, and genomic integrity. This review provides an overview of HOTAIR's functions, its identification, and its biological significance. Furthermore, it delves into HOTAIR's involvement in UTs, underlining its potential as a therapeutic target and biomarker for innovative approaches to treating these cancers.
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Affiliation(s)
- Abida
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Lina Eltaib
- Department of Pharmaceutics, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Bshayer Hmdan Alhazmi
- Department of Pharmacy, Northern Area Armed Forces Hospital, Hafer Al-batin 39745, Saudi Arabia
| | - Abdullah R Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | | | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | | | - Wafaa T Alruwaili
- College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Marwan Al-Hajeili
- Department of Medicine, King Abdulaziz University, Jeddah 23624, Saudi Arabia
| | - Altaf A Abdulkhaliq
- Department of Biochemistry, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia; Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia; Center for Health Research, Northern Border University, Arar, Saudi Arabia.
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11
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Yang Y, Huang J, Wang Q, Li J, Yu L, Xie X. Clinicopathologic and prognostic implications of HOXA gene and its associated long-noncoding RNAs expression in non-small cell carcinoma: A meta-analysis. Medicine (Baltimore) 2024; 103:e38087. [PMID: 39121297 PMCID: PMC11315518 DOI: 10.1097/md.0000000000038087] [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: 07/04/2023] [Accepted: 04/11/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND We conducted an investigation into the correlation between HOXA and associated long-noncoding RNAs, along with their clinicopathologic and prognostic features in non-small cell lung cancer (NSCLC). METHODS A comprehensive search across multiple electronic databases, including PubMed and the Web of Science, was conducted to identify relevant studies. The association between HOXA, clinicopathologic parameters, and prognosis was assessed using relative risk (RR) and hazard ratio (HR) with a 95% confidence interval (CI). Data compilation was performed using STATA 12.0 software. RESULTS A total of 11 trials involving 2058 patients with NSCLC were included in our study. Significant correlations were observed between HOXA-AS2 and TNM stage (III-IV) (RR=2.173, 95% CI: 1.386-5.437, P< 0.05) and HOTTIP and age (≥60-year-old) (RR=2.628, 95% CI: 1.185-5.829, P< 0.05) and non-smoking (RR=0.387, 95% CI: 0.156-0.959, P< 0.05). The combined results indicated a significant association between HOXA5 and increased overall survival (HR = 0.69, 95% CI = 0.57-0.84, P < .001). Additionally, HOXA-AS2, HOXA11 and HOTTIP were identified as potential independent predictors for poorer OS (HOXA-AS2: HR =3.48, 95% CI = 1.95 to 6.21, P < 0.05; HOXA11: HR=1.39, 95%CI = 1.08 to 1.79, P < 0.05; HOTTIP: HR=2.44, 95%CI = 1.10 to 5.42, P < 0.05). The prognostic significance of HOXA1, HOXA3 and HOXA4 was uncertain (HOXA1: HR=1.40, 95% CI =0.28 to 7.06, P > 0.05; HOXA3: HR=1.20, 95% CI = 0.96 to 1.50, P > 0.05; HOXA4: HR=0.97, 95% CI = 0.77 to 1.23, P > 0.05). CONCLUSIONS The HOXA gene family has some potential to emerge as a novel prognostic factor for NSCLC and is correlated with some clinicopathological parameters such as the TNM stage, age and smoking. However, further meticulously designed prospective studies are warranted to substantiate these findings.
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Affiliation(s)
- Yanhui Yang
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - JinYang Huang
- Department of Cardiothoracic Surgery, Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, P.R. China
| | - Qi Wang
- Department of Cardiothoracic Surgery, Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, P.R. China
| | - Ji Li
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - Lei Yu
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - Xiaoyang Xie
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
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12
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Cohen AB, Nikmehr B, Abdelaal OA, Escott M, Walker SJ, Atala A, Sadri-Ardekani H. MicroRNA Analysis of In Vitro Differentiation of Spermatogonial Stem Cells Using a 3D Human Testis Organoid System. Biomedicines 2024; 12:1774. [PMID: 39200238 PMCID: PMC11351903 DOI: 10.3390/biomedicines12081774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/20/2024] [Accepted: 07/25/2024] [Indexed: 09/02/2024] Open
Abstract
Spermatogenesis produces male gametes from spermatogonial stem cells (SSC), beginning at puberty. Modern-day laboratory techniques allow for the long-term culture of SSC and in vitro spermatogenesis. The specific biochemical processes that occur during spermatogenesis remain poorly understood. One particular element of spermatogenesis that has yet to be characterized is the role of microRNAs (miRNA), short, non-transcribed RNAs that act as post-translational regulators of gene activity. In this study, we seek to describe the presence of miRNA in a two-dimensional (2D) SSC culture and a 3D human testis organoid (HTO) system. Testicular cells were isolated from the frozen tissue of three brain-dead subjects, propagated in cultures for four to five weeks, and used to form 3D HTOs. Following organoid formation, differentiation of testicular cells was induced. RNA was isolated from the whole testis tissue (WT) showing in vivo conditions, HTO Day Zero (2D SSC culture), Day 2 HTOs, and Day 23 differentiated HTOs, then analyzed for changes in miRNA expression using the Nanostring nCounter miRNA panel. One hundred ninety-five miRNAs met the criteria for expression in WT, 186 in 2D culture, 190 in Day 2 HTOs, and 187 in differentiated HTOs. One hundred thirty-three miRNAs were common across all conditions, and 41, 17, 6, and 11 miRNAs were unique for WT, 2D culture, Day 2 HTOs, and differentiated HTOs, respectively. Twenty-two miRNAs were similar between WT and differentiated HTOS. We evaluated the miRNA expression profiles of progressively complex stages of testicular cell culture, culminating in a 3D organoid model capable of meiotic differentiation, and compared these to WT. We identified a great variance between the native tissue and the culture system; however, some miRNAs are preserved. These data may provide avenues for deeper understanding of spermatogenesis and the ability to improve this process in the laboratory. Research on miRNA continues to be an essential avenue for understanding human spermatogenesis.
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Affiliation(s)
- Adam B. Cohen
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Department of Urology, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27157, USA
| | - Banafsheh Nikmehr
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Carolinas Fertility Institute, Winston-Salem, NC 27103, USA
| | - Omar A. Abdelaal
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Department of Urology, Faculty of Medicine, Zagazig University, Zagazig 7120001, Egypt
| | - Megan Escott
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Department of Urology, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27157, USA
| | - Stephen J. Walker
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
| | - Anthony Atala
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Department of Urology, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27157, USA
| | - Hooman Sadri-Ardekani
- Wake Forest Institute of Regenerative Medicine, Winston-Salem, NC 27101, USA; (B.N.); (O.A.A.); (M.E.); (S.J.W.); (H.S.-A.)
- Department of Urology, Atrium Health Wake Forest Baptist, Winston-Salem, NC 27157, USA
- Carolinas Fertility Institute, Winston-Salem, NC 27103, USA
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13
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Saadh MJ, Hussain QM, Alazzawi TS, Fahdil AA, Athab ZH, Yarmukhamedov B, Al-Nuaimi AMA, Alsaikhan F, Farhood B. MicroRNA as Key Players in Hepatocellular Carcinoma: Insights into Their Role in Metastasis. Biochem Genet 2024:10.1007/s10528-024-10897-0. [PMID: 39103713 DOI: 10.1007/s10528-024-10897-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/29/2024] [Indexed: 08/07/2024]
Abstract
Liver cancer or hepatocellular carcinoma (HCC) remains the most common cancer in global epidemiology. Both the frequency and fatality of this malignancy have shown an upward trend over recent decades. Liver cancer is a significant concern due to its propensity for both intrahepatic and extrahepatic metastasis. Liver cancer metastasis is a multifaceted process characterized by cell detachment from the bulk tumor, modulation of cellular motility and invasiveness, enhanced proliferation, avoidance of the immune system, and spread either via lymphatic or blood vessels. MicroRNAs (miRNAs) are small non-coding ribonucleic acids (RNAs) playing a crucial function in the intricate mechanisms of tumor metastasis. A number of miRNAs can either increase or reduce metastasis via several mechanisms, such as control of motility, proliferation, attack by the immune system, cancer stem cell properties, altering the microenvironment, and the epithelial-mesenchymal transition (EMT). Besides, two other types of non-coding RNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) can competitively bind to endogenous miRNAs. This competition results in the impaired ability of the miRNAs to inhibit the expression of the specific messenger RNAs (mRNAs) that are targeted. Increasing evidence has shown that the regulatory axis comprising circRNA/lncRNA-miRNA-mRNA is correlated with the regulation of HCC metastasis. This review seeks to present a thorough summary of recent research on miRNAs in HCC, and their roles in the cellular processes of EMT, invasion and migration, as well as the metastasis of malignant cells. Finally, we discuss the function of the lncRNA/circRNA-miRNA-mRNA network as a crucial modulator of carcinogenesis and the regulation of signaling pathways or genes that are relevant to the metastasis of HCC. These findings have the potential to offer valuable insight into the discovery of novel therapeutic approaches for management of liver cancer metastasis.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | | | - Tuqa S Alazzawi
- College of Dentist, National University of Science and Technology, Nasiriyah, Dhi Qar, Iraq
| | - Ali A Fahdil
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
| | - Zainab H Athab
- Department of Pharmacy, Al-Zahrawi University College, Karbala, Iraq
| | - Bekhzod Yarmukhamedov
- Department of Public Health and Healthcare management, Samarkand State Medical University, 18 Amir Temur Street, Samarkand, Uzbekistan
| | | | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia.
- School of Pharmacy, Ibn Sina National College for Medical Studies, Jeddah, Saudi Arabia.
| | - Bagher Farhood
- Department of Medical Physics and Radiology, Faculty of Paramedical Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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14
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Fan L, Sun W, Lyu Y, Ju F, Sun W, Chen J, Ma H, Yang S, Zhou X, Wu N, Yi W, Chen E, Villaseñor R, Baubec T, Yan J. Chrom-seq identifies RNAs at chromatin marks. SCIENCE ADVANCES 2024; 10:eadn1397. [PMID: 39083617 PMCID: PMC11290522 DOI: 10.1126/sciadv.adn1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Chromatin marks are associated with transcriptional regulatory activities. However, very few lncRNAs have been characterized with the role in regulating epigenetic marks, largely due to the technical difficulty in identifying chromatin-associating RNA. Current methods are largely limited by the availability of ChIP-grade antibody and the crosslinking, which generates high noise. Here, we developed a method termed Chrom-seq to efficiently capture RNAs associated with various chromatin marks in living cells. Chrom-seq jointly applies highly specific chromatin mark reader with APEX2, which catalyzes the oxidation of biotin-aniline to label the adjacent RNAs for isolation by streptavidin-coated beads. Using the readers of mCBX7/dPC, mCBX1, and mTAF3, we detected RNA species significantly associated with H3K27me3, H3K9me3, and H3K4me3, respectively. We demonstrated that Chrom-seq outperformed other equivalent methods in terms of sensitivity, efficiency, and cost of practice. It provides an antibody-free approach to systematically map RNAs at chromatin marks with potential regulatory roles in epigenetic events.
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Affiliation(s)
- Ligang Fan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | | | - Yitong Lyu
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Furong Ju
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Wenju Sun
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Jie Chen
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Haiqian Ma
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Shifei Yang
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Xiaomin Zhou
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Nan Wu
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Wenkai Yi
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
| | - Erfei Chen
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
| | - Rodrigo Villaseñor
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tuncay Baubec
- Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Jian Yan
- Ministry of Education Key Laboratory of Resource Biology and Biotechnology in Western China; Shaanxi Provincial Key Laboratory of Biotechnology; School of Medicine, Northwest University, Xi’an, China
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences; The Tung Biomedical Sciences Centre, City University of Hong Kong, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, The City University of Hong Kong Shenzhen Futian Research Institute, Shenzhen, China
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15
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Wang Y, Cao L, Liu M, Yan P, Niu F, Dong S, Ma F, Lan D, Zhang X, Hu J, Xin X, Yang J, Luo X. Alternative splicing of lncRNA LAIR fine-tunes the regulation of neighboring yield-related gene LRK1 expression in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1751-1766. [PMID: 38943483 DOI: 10.1111/tpj.16882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/01/2024]
Abstract
The diversity in alternative splicing of long noncoding RNAs (lncRNAs) poses a challenge for functional annotation of lncRNAs. Moreover, little is known on the effects of alternatively spliced lncRNAs on crop yield. In this study, we cloned nine isoforms resulting from the alternative splicing of the lncRNA LAIR in rice. The LAIR isoforms are generated via alternative 5'/3' splice sites and different combinations of specific introns. All LAIR isoforms activate the expression of the neighboring LRK1 gene and enhance yield-related rice traits. In addition, there are slight differences in the binding ability of LAIR isoforms to the epigenetic modification-related proteins OsMOF and OsWDR5, which affect the enrichment of H4K16ac and H3K4me3 at the LRK1 locus, and consequently fine-tune the regulation of LRK1 expression and yield-related traits. These differences in binding may be caused by polymorphic changes to the RNA secondary structure resulting from alternative splicing. It was also observed that the composition of LAIR isoforms was sensitive to abiotic stress. These findings suggest that the alternative splicing of LAIR leads to the formation of a functional transcript population that precisely regulates yield-related gene expression, which may be relevant for phenotypic polymorphism-based crop breeding under changing environmental conditions.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Research Center for Ecological Science and Technology, Fudan Zhangjiang Institute, Shanghai, 201203, China
- National Science Park of Fudan University, Shanghai, 200433, China
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Mingyu Liu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Peiwen Yan
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fuan Niu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Shiqing Dong
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, 223300, China
| | - Fuying Ma
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dengyong Lan
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xinwei Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jian Hu
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaoyun Xin
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jinshui Yang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Department of Ecology and Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
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16
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Chen HF, Wu KJ. LncRNAs and asymmetric cell division: the epigenetic mechanisms. Biomed J 2024:100774. [PMID: 39059582 DOI: 10.1016/j.bj.2024.100774] [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: 04/23/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024] Open
Abstract
Asymmetric cell division (ACD) plays a pivotal role in development, tissue homeostasis, and stem cell maintenance. Emerging evidence suggests that long non-coding RNAs (lncRNAs) are key regulators of ACD, orchestrating the intricate molecular machinery that governs cell fate determination. This review summarizes current literature to elucidate the diverse roles of lncRNAs in modulating ACD across various biological contexts. The regulatory mechanisms of asymmetric cell division mediated by lncRNAs, including their interactions with protein effectors, epigenetic regulation, and subcellular localization are explored. Additionally, we discuss the implications of dysregulated lncRNAs in mediating ACD that lead to tumorigenesis. By integrating findings from diverse experimental models and cell types, this review provides insights into the multifaceted roles of lncRNAs in governing asymmetric cell division, shedding light on fundamental biological processes. Further research in this area may lead to the development of novel therapies targeting dysregulated lncRNAs to restore proper cell division and function. The knowledge of lncRNAs regulating ACD could potentially revolutionize the field of regenerative medicine and cancer therapy by targeting specific lncRNAs involved in ACD. By unraveling the complex interactions between lncRNAs and cellular processes, the potential novel opportunities for precision medicine approaches may be uncovered.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institutes of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; Graduate Institutes of Cell Biology, China Medical University, Taichung 404, Taiwan.
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan Dist., Taoyuan 333, Taiwan.
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17
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Moral-Turón C, Asencio-Cortés G, Rodriguez-Diaz F, Rubio A, Navarro AG, Brokate-Llanos AM, Garzón A, Muñoz MJ, Pérez-Pulido AJ. ASACO: Automatic and Serial Analysis of CO-expression to discover gene modifiers with potential use in drug repurposing. Brief Funct Genomics 2024; 23:484-494. [PMID: 38422352 DOI: 10.1093/bfgp/elae006] [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: 09/07/2023] [Revised: 01/21/2024] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Massive gene expression analyses are widely used to find differentially expressed genes under specific conditions. The results of these experiments are often available in public databases that are undergoing a growth similar to that of molecular sequence databases in the past. This now allows novel secondary computational tools to emerge that use such information to gain new knowledge. If several genes have a similar expression profile across heterogeneous transcriptomics experiments, they could be functionally related. These associations are usually useful for the annotation of uncharacterized genes. In addition, the search for genes with opposite expression profiles is useful for finding negative regulators and proposing inhibitory compounds in drug repurposing projects. Here we present a new web application, Automatic and Serial Analysis of CO-expression (ASACO), which has the potential to discover positive and negative correlator genes to a given query gene, based on thousands of public transcriptomics experiments. In addition, examples of use are presented, comparing with previous contrasted knowledge. The results obtained propose ASACO as a useful tool to improve knowledge about genes associated with human diseases and noncoding genes. ASACO is available at http://www.bioinfocabd.upo.es/asaco/.
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Affiliation(s)
- Cristina Moral-Turón
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | | | | | - Alejandro Rubio
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Alberto G Navarro
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Ana M Brokate-Llanos
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Andrés Garzón
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Manuel J Muñoz
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
| | - Antonio J Pérez-Pulido
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA). Faculty of Experimental Sciences (Genetics Dept.), University Pablo de Olavide, 41013, Seville, Spain
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18
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Davis WJH, Drummond CJ, Diermeier S, Reid G. The Potential Links between lncRNAs and Drug Tolerance in Lung Adenocarcinoma. Genes (Basel) 2024; 15:906. [PMID: 39062685 PMCID: PMC11276205 DOI: 10.3390/genes15070906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/09/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Lung cancer patients treated with targeted therapies frequently respond well but invariably relapse due to the development of drug resistance. Drug resistance is in part mediated by a subset of cancer cells termed "drug-tolerant persisters" (DTPs), which enter a dormant, slow-cycling state that enables them to survive drug exposure. DTPs also exhibit stem cell-like characteristics, broad epigenetic reprogramming, altered metabolism, and a mutagenic phenotype mediated by adaptive mutability. While several studies have characterised the transcriptional changes that lead to the altered phenotypes exhibited in DTPs, these studies have focused predominantly on protein coding changes. As long non-coding RNAs (lncRNAs) are also implicated in the phenotypes altered in DTPs, it is likely that they play a role in the biology of drug tolerance. In this review, we outline how lncRNAs may contribute to the key characteristics of DTPs, their potential roles in tolerance to targeted therapies, and the emergence of genetic resistance in lung adenocarcinoma.
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Affiliation(s)
- William J. H. Davis
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
| | - Catherine J. Drummond
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
| | - Sarah Diermeier
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand;
- Amaroq Therapeutics, Auckland 1010, New Zealand
| | - Glen Reid
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; (W.J.H.D.); (C.J.D.)
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Private Bag, Auckland 1023, New Zealand
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Xie X, Macknight HP, Lu AL, Chalfant CE. RNA splicing variants of the novel long non-coding RNA, CyKILR, possess divergent biological functions in non-small cell lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.08.602494. [PMID: 39026815 PMCID: PMC11257467 DOI: 10.1101/2024.07.08.602494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The CDKN2A gene, responsible for encoding the tumor suppressors p16(INK4A) and p14(ARF), is frequently inactivated in non-small cell lung cancer (NSCLC). In this study, an uncharacterized long non-coding RNA (lncRNA) (ENSG00000267053) on chromosome 19p13.12 was found to be overexpressed in NSCLC cells with an active CDKN2A gene. This lncRNA, named Cy clin-Dependent K inase I nhibitor 2A-regulated l nc R NA (CyKILR), also correlated with the STK11 gene-coded tumor suppressor Liver kinase B1 (LKB1). CyKILR displayed two splice variants, CyKILRa (with exon 3) and CyKILRb (without exon 3), which are synergistically regulated by CDKN2A and STK11 as knockdown of both tumor suppressor genes led to a significant loss of exon 3 inclusion in mature CyKILR RNA. CyKILRa localized to the nucleus, and its downregulation using antisense RNA oligonucleotides enhanced cellular proliferation, migration, clonogenic survival, and tumor incidence. In contrast, CyKILRb localized to the cytoplasm, and downregulation of CyKILRb using siRNA reduced cell proliferation, migration, clonogenic survival, and tumor incidence. Transcriptomics analyses revealed enhancement of apoptotic pathways with concomitant suppression of key cell cycle pathways by CyKILRa demonstrating its tumor-suppressive role, while CyKILRb inhibited tumor suppressor microRNAs, indicating an oncogenic nature. These findings elucidate the intricate roles of lncRNAs in cell signaling and tumorigenesis.
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20
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Zhang L, Yu F, Zhang Y, Li P. Implications of lncRNAs in Helicobacter pylori-associated gastrointestinal cancers: underlying mechanisms and future perspectives. Front Cell Infect Microbiol 2024; 14:1392129. [PMID: 39035354 PMCID: PMC11257847 DOI: 10.3389/fcimb.2024.1392129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024] Open
Abstract
Helicobacter pylori (H. pylori) is a harmful bacterium that is difficult to conveniently diagnose and effectively eradicate. Chronic H. pylori infection increases the risk of gastrointestinal diseases, even cancers. Despite the known findings, more underlying mechanisms are to be deeply explored to facilitate the development of novel prevention and treatment strategies of H. pylori infection. Long noncoding RNAs (lncRNAs) are RNAs with more than 200 nucleotides. They may be implicated in cell proliferation, inflammation and many other signaling pathways of gastrointestinal cancer progression. The dynamic expression of lncRNAs indicates their potential to be diagnostic or prognostic biomarkers. In this paper, we comprehensively summarize the processes of H. pylori infection and the treatment methods, review the known findings of lncRNA classification and functional mechanisms, elucidate the roles of lncRNAs in H. pylori-related gastrointestinal cancer, and discuss the clinical perspectives of lncRNAs.
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Affiliation(s)
- Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | | | | | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
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21
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Lin Y, Zhao W, Lv Z, Xie H, Li Y, Zhang Z. The functions and mechanisms of long non-coding RNA in colorectal cancer. Front Oncol 2024; 14:1419972. [PMID: 39026978 PMCID: PMC11254705 DOI: 10.3389/fonc.2024.1419972] [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: 04/19/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
CRC poses a significant challenge in the global health domain, with a high number of deaths attributed to this disease annually. If CRC is detected only in its advanced stages, the difficulty of treatment increases significantly. Therefore, biomarkers for the early detection of CRC play a crucial role in improving patient outcomes and increasing survival rates. The development of a reliable biomarker for early detection of CRC is particularly important for timely diagnosis and treatment. However, current methods for CRC detection, such as endoscopic examination, blood, and stool tests, have certain limitations and often only detect cases in the late stages. To overcome these constraints, researchers have turned their attention to molecular biomarkers, which are considered a promising approach to improving CRC detection. Non-invasive methods using biomarkers such as mRNA, circulating cell-free DNA, microRNA, LncRNA, and proteins can provide more reliable diagnostic information. These biomarkers can be found in blood, tissue, stool, and volatile organic compounds. Identifying molecular biomarkers with high sensitivity and specificity for the early and safe, economic, and easily measurable detection of CRC remains a significant challenge for researchers.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Ying Li
- Ultrasonography Department, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
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22
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Song B, Luo T, Fan Y, Li M, Qiu Z, Tian Y, Shang Y, Ma C, Liu C, Cao Q, Peng Y, Xu P, Krishnan HB, Wang Z, Zhang S, Liu S. Generation of New β-Conglycinin-Deficient Soybean Lines by Editing the lincRNA lincCG1 Using the CRISPR/Cas9 System. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15013-15026. [PMID: 38907729 DOI: 10.1021/acs.jafc.4c02269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
Soybean β-conglycinin is a major allergen that adversely affects the nutritional properties of soybean. Soybean deficient in β-conglycinin is associated with low allergenicity and high nutritional value. Long intergenic noncoding RNAs (lincRNAs) regulate gene expression and are considered important regulators of essential biological processes. Despite increasing knowledge of the functions of lincRNAs, relatively little is known about the effects of lincRNAs on the accumulation of soybean β-conglycinin. The current study presents the identification of a lincRNA lincCG1 that was mapped to the intergenic noncoding region of the β-conglycinin α-subunit locus. The full-length lincCG1 sequence was cloned and found to regulate the expression of soybean seed storage protein (SSP) genes via both cis- and trans-acting regulatory mechanisms. Loss-of-function lincCG1 mutations generated using the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) system led to the deficiency of the allergenic α'-, α-, and β-subunits of soybean β-conglycinin as well as higher content of proteins, sulfur-containing amino acids, and free arginine. The dominant null allele LincCG1, and consequently, the β-conglycinin-deficient phenotype associated with the lincCG1-gene-edited line was stably inherited by the progenies in a Mendelian fashion. The dominant null allele LincCG1 may therefore be exploited for engineering/developing novel hypoallergenic soybean varieties. Furthermore, Cas9-free and β-conglycinin-deficient homozygous mutant lines were obtained in the T1 generation. This study is the first to employ the CRISPR/Cas9 technology for editing a lincRNA gene associated with the soybean allergenic protein β-conglycinin. Moreover, this study reveals that lincCG1 plays a crucial role in regulating the expression of the β-conglycinin subunit gene cluster, besides highlighting the efficiency of employing the CRISPR/Cas9 system for modulating lincRNAs, and thereby regulating soybean seed components.
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Affiliation(s)
- Bo Song
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
- Key Laboratory of Molecular and Cytogenetics, College of Life Sciences and Technology, Harbin Normal University, Harbin 150025, China
| | - Tingting Luo
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuanhang Fan
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Ming Li
- Keshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161000, China
| | - Zhendong Qiu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yusu Tian
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuzhuo Shang
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Chongxuan Ma
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Chang Liu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Qingqian Cao
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Yuhan Peng
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Pengfei Xu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Hari B Krishnan
- Plant Genetics Research, USDA Agricultural Research Service, Columbia, Missouri 65211, United States
- Plant Science Division, University of Missouri, Columbia, Missouri 65201, United States
| | - Zhenhui Wang
- Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Shuzhen Zhang
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
| | - Shanshan Liu
- Soybean Research Institute, Northeast Agricultural University/Key Laboratory of Soybean Biology of the Chinese Education Ministry, Harbin 150030, China
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23
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Campos FG, Ibelli AMG, Cantão ME, Oliveira HC, Peixoto JO, Ledur MC, Guimarães SEF. Long Non-Coding RNAs Differentially Expressed in Swine Fetuses. Animals (Basel) 2024; 14:1897. [PMID: 38998009 PMCID: PMC11240794 DOI: 10.3390/ani14131897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding transcripts involved in various biological processes. The Y chromosome is known for determining the male sex in mammals. LncRNAs on the Y chromosome may play important regulatory roles. However, knowledge about their action mechanisms is still limited, especially during early fetal development. Therefore, we conducted this exploratory study aiming to identify, characterize, and investigate the differential expression of lncRNAs between male and female swine fetuses at 35 days of gestation. RNA-Seq libraries from 10 fetuses were prepared and sequenced using the Illumina platform. After sequencing, a data quality control was performed using Trimmomatic, alignment with HISAT2, and transcript assembly with StringTie. The differentially expressed lncRNAs were identified using the limma package of the R software (4.3.1). A total of 871 potentially novel lncRNAs were identified and characterized. Considering differential expression, eight lncRNAs were upregulated in male fetuses. One was mapped onto SSC12 and seven were located on the Y chromosome; among them, one lncRNA is potentially novel. These lncRNAs are involved in diverse functions, including the regulation of gene expression and the modulation of chromosomal structure. These discoveries enable future studies on lncRNAs in the fetal stage in pigs.
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Affiliation(s)
- Francelly G Campos
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
| | - Adriana M G Ibelli
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro Oeste, Guarapuava 85040-167, PR, Brazil
| | | | - Haniel C Oliveira
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
| | - Jane O Peixoto
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro Oeste, Guarapuava 85040-167, PR, Brazil
| | - Mônica C Ledur
- Embrapa Suínos e Aves, Concordia 89715-899, SC, Brazil
- Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, Chapecó 89815-630, SC, Brazil
| | - Simone E F Guimarães
- Laboratory of Animal Biotecnology, Department of Animal Science, Universidade Federal de Viçosa, Viçosa 36570-000, MG, Brazil
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24
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Sun X, Yuan Y, Li S, Gan L, Xu M, Li Q, Liu M, Hu K, Nan K, Zhang J, Dong Y, Lin Y, Zhang X, Hou P, Liu T. Prostate cancer-associated transcript 6 (PCAT6) promotes epithelial-mesenchymal transition and stemness and worsens prognosis in patients with colorectal cancer. Acta Biochim Biophys Sin (Shanghai) 2024; 56:866-878. [PMID: 38606479 PMCID: PMC11214952 DOI: 10.3724/abbs.2024031] [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: 11/27/2023] [Accepted: 01/15/2024] [Indexed: 04/13/2024] Open
Abstract
Approximately 20% of colorectal cancer (CRC) patients are first diagnosed with metastatic colorectal cancer (mCRC) because they develop symptoms at an advanced stage. Despite advancements in treatment, patients with metastatic disease still experience inferior survival rates. Our objective is to investigate the association between long noncoding RNAs (lncRNAs) and prognosis and to explore their role in mCRC. In this study, we find that elevated expression of PCAT6 is independently linked to unfavourable survival outcomes in The Cancer Genome Atlas (TCGA) data, and this finding is further confirmed in CRC samples obtained from Fudan University Shanghai Cancer Center. Cell lines and xenograft mouse models are used to examine the impact of PCAT6 on tumor metastasis. Knockdown of PCAT6 is observed to impede the metastatic phenotype of CRC, as evidenced by functional assays, demonstrating the suppression of epithelial-mesenchymal transition (EMT) and stemness. Our findings show the significance of PCAT6 in mCRC and its potential use as a prognostic biomarker.
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Affiliation(s)
- Xun Sun
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yitao Yuan
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Suyao Li
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Lu Gan
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Cancer CenterZhongshan HospitalFudan UniversityShanghai200032China
- Fudan Zhangjiang InstituteShanghai201203China
| | - Midie Xu
- Department of Pathology and Tissue BankFudan University Shanghai Cancer CenterShanghai200032China
| | - Qingguo Li
- Department of Colorectal SurgeryFudan University Shanghai Cancer CenterShanghai200032China
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Mengling Liu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Keshu Hu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Ke Nan
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Jiayu Zhang
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yu Dong
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
| | - Yufu Lin
- Department of OncologyZhongshan Hospital (Xiamen)Fudan UniversityXiamen361015China
| | - Xiuping Zhang
- Xiamen Clinical Research Center for Cancer TherapyXiamen BranchZhongshan HospitalFudan UniversityXiamen361015China
| | - Pengcong Hou
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Shanghai Institute of Precision MedicineShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai200032China
| | - Tianshu Liu
- Department of Medical OncologyZhongshan HospitalFudan UniversityShanghai200032China
- Cancer CenterZhongshan HospitalFudan UniversityShanghai200032China
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25
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Rossi MN, Fiorucci C, Mariottini P, Cervelli M. Unveiling the hidden players: noncoding RNAs orchestrating polyamine metabolism in disease. Cell Biosci 2024; 14:84. [PMID: 38918813 PMCID: PMC11202255 DOI: 10.1186/s13578-024-01235-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/19/2024] [Indexed: 06/27/2024] Open
Abstract
Polyamines (PA) are polycations with pleiotropic functions in cellular physiology and pathology. In particular, PA have been involved in the regulation of cell homeostasis and proliferation participating in the control of fundamental processes like DNA transcription, RNA translation, protein hypusination, autophagy and modulation of ion channels. Indeed, their dysregulation has been associated to inflammation, oxidative stress, neurodegeneration and cancer progression. Accordingly, PA intracellular levels, derived from the balance between uptake, biosynthesis, and catabolism, need to be tightly regulated. Among the mechanisms that fine-tune PA metabolic enzymes, emerging findings highlight the importance of noncoding RNAs (ncRNAs). Among the ncRNAs, microRNA, long noncoding RNA and circRNA are the most studied as regulators of gene expression and mRNA metabolism and their alteration have been frequently reported in pathological conditions, such as cancer progression and brain diseases. In this review, we will discuss the role of ncRNAs in the regulation of PA genes, with a particular emphasis on the changes of this modulation observed in health disorders.
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Affiliation(s)
| | | | - Paolo Mariottini
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy
| | - Manuela Cervelli
- Department of Sciences, University of Roma Tre, 00146, Rome, Italy.
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26
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Cabané P, Correa C, Bode I, Aguilar R, Elorza AA. Biomarkers in Thyroid Cancer: Emerging Opportunities from Non-Coding RNAs and Mitochondrial Space. Int J Mol Sci 2024; 25:6719. [PMID: 38928426 PMCID: PMC11204084 DOI: 10.3390/ijms25126719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Thyroid cancer diagnosis primarily relies on imaging techniques and cytological analyses. In cases where the diagnosis is uncertain, the quantification of molecular markers has been incorporated after cytological examination. This approach helps physicians to make surgical decisions, estimate cancer aggressiveness, and monitor the response to treatments. Despite the availability of commercial molecular tests, their widespread use has been hindered in our experience due to cost constraints and variability between them. Thus, numerous groups are currently evaluating new molecular markers that ultimately will lead to improved diagnostic certainty, as well as better classification of prognosis and recurrence. In this review, we start reviewing the current preoperative testing methodologies, followed by a comprehensive review of emerging molecular markers. We focus on micro RNAs, long non-coding RNAs, and mitochondrial (mt) signatures, including mtDNA genes and circulating cell-free mtDNA. We envision that a robust set of molecular markers will complement the national and international clinical guides for proper assessment of the disease.
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Affiliation(s)
- Patricio Cabané
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago 8380453, Chile
| | - Claudio Correa
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
| | - Ignacio Bode
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Rodrigo Aguilar
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Alvaro A. Elorza
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
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27
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Larue AEM, Atlasi Y. The epigenetic landscape in intestinal stem cells and its deregulation in colorectal cancer. Stem Cells 2024; 42:509-525. [PMID: 38597726 PMCID: PMC11177158 DOI: 10.1093/stmcls/sxae027] [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: 10/08/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024]
Abstract
Epigenetic mechanisms play a pivotal role in controlling gene expression and cellular plasticity in both normal physiology and pathophysiological conditions. These mechanisms are particularly important in the regulation of stem cell self-renewal and differentiation, both in embryonic development and within adult tissues. A prime example of this finely tuned epigenetic control is observed in the gastrointestinal lining, where the small intestine undergoes renewal approximately every 3-5 days. How various epigenetic mechanisms modulate chromatin functions in intestinal stem cells (ISCs) is currently an active area of research. In this review, we discuss the main epigenetic mechanisms that control ISC differentiation under normal homeostasis. Furthermore, we explore the dysregulation of these mechanisms in the context of colorectal cancer (CRC) development. By outlining the main epigenetic mechanisms contributing to CRC, we highlight the recent therapeutics development and future directions for colorectal cancer research.
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Affiliation(s)
- Axelle E M Larue
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, United Kingdom
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28
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Yin G, Hu J, Huang X, Cai Y, Gao Z, Guo X, Feng X. The Identification and Function of Linc01615 on Influenza Virus Infection and Antiviral Response. Int J Mol Sci 2024; 25:6584. [PMID: 38928290 PMCID: PMC11203770 DOI: 10.3390/ijms25126584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Influenza virus infection poses a great threat to human health globally each year. Non-coding RNAs (ncRNAs) in the human genome have been reported to participate in the replication process of the influenza virus, among which there are still many unknowns about Long Intergenic Non-Coding RNAs (LincRNAs) in the cell cycle of viral infections. Here, we observed an increased expression of Linc01615 in A549 cells upon influenza virus PR8 infection, accompanied by the successful activation of the intracellular immune system. The knockdown of Linc01615 using the shRNAs promoted the proliferation of the influenza A virus, and the intracellular immune system was inhibited, in which the expressions of IFN-β, IL-28A, IL-29, ISG-15, MX1, and MX2 were decreased. Predictions from the catRAPID website suggested a potential interaction between Linc01615 and DHX9. Also, knocking down Linc01615 promoted influenza virus proliferation. The subsequent transcriptome sequencing results indicated a decrease in Linc01615 expression after influenza virus infection when DHX9 was knocked down. Further analysis through cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq) in HEK293 cells stably expressing DHX9 confirmed the interaction between DHX9 and Linc01615. We speculate that DHX9 may interact with Linc01615 to partake in influenza virus replication and that Linc01615 helps to activate the intracellular immune system. These findings suggest a deeper connection between DHX9 and Linc01615, which highlights the significant role of Linc01615 in the influenza virus replication process. This research provides valuable insights into understanding influenza virus replication and offers new targets for preventing influenza virus infections.
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Affiliation(s)
- Guihu Yin
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianing Hu
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangyu Huang
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqin Cai
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Zichen Gao
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Guo
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiuli Feng
- Key Laboratory of Animal Microbiology of China’s Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (G.Y.); (J.H.); (X.H.); (Y.C.); (Z.G.); (X.G.)
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [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: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Andrabi SBA, Kalim UU, Palani S, Khan MM, Khan MH, Fagersund J, Orpana J, Paulin N, Batkulwar K, Junttila S, Buchacher T, Grönroos T, Toikka L, Ammunet T, Sen P, Orešič M, Kumpulainen V, Tuomisto JEE, Sinha R, Marson A, Rasool O, Elo LL, Lahesmaa R. Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4 + regulatory T cells by regulating IL2RA. Proc Natl Acad Sci U S A 2024; 121:e2315363121. [PMID: 38805281 PMCID: PMC11161746 DOI: 10.1073/pnas.2315363121] [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: 09/08/2023] [Accepted: 04/24/2024] [Indexed: 05/30/2024] Open
Abstract
Regulatory T cells (Tregs) are central in controlling immune responses, and dysregulation of their function can lead to autoimmune disorders or cancer. Despite extensive studies on Tregs, the basis of epigenetic regulation of human Treg development and function is incompletely understood. Long intergenic noncoding RNAs (lincRNA)s are important for shaping and maintaining the epigenetic landscape in different cell types. In this study, we identified a gene on the chromosome 6p25.3 locus, encoding a lincRNA, that was up-regulated during early differentiation of human Tregs. The lincRNA regulated the expression of interleukin-2 receptor alpha (IL2RA), and we named it the lincRNA regulator of IL2RA (LIRIL2R). Through transcriptomics, epigenomics, and proteomics analysis of LIRIL2R-deficient Tregs, coupled with global profiling of LIRIL2R binding sites using chromatin isolation by RNA purification, followed by sequencing, we identified IL2RA as a target of LIRIL2R. This nuclear lincRNA binds upstream of the IL2RA locus and regulates its epigenetic landscape and transcription. CRISPR-mediated deletion of the LIRIL2R-bound region at the IL2RA locus resulted in reduced IL2RA expression. Notably, LIRIL2R deficiency led to reduced expression of Treg-signature genes (e.g., FOXP3, CTLA4, and PDCD1), upregulation of genes associated with effector T cells (e.g., SATB1 and GATA3), and loss of Treg-mediated suppression.
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Affiliation(s)
- Syed Bilal Ahmad Andrabi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Senthil Palani
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Mohd Moin Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Meraj Hasan Khan
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Jimmy Fagersund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Julius Orpana
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Niklas Paulin
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Kedar Batkulwar
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Tanja Buchacher
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Lea Toikka
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Tea Ammunet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- School of Medical Sciences, Örebro University, Örebro702 81, Sweden
| | - Venla Kumpulainen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Johanna E. E. Tuomisto
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA94305
| | - Alexander Marson
- Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA94158
| | - Omid Rasool
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Laura L. Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520Turku, Finland
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- InFLAMES – Innovation Ecosystem Based on the Immune System Flagship University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Institute of Biomedicine, University of Turku, 20520Turku, Finland
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Cantile M, Belli V, Scognamiglio G, Martorana A, De Pietro G, Tracey M, Budillon A. The role of HOTAIR in the modulation of resistance to anticancer therapy. Front Mol Biosci 2024; 11:1414651. [PMID: 38887279 PMCID: PMC11181001 DOI: 10.3389/fmolb.2024.1414651] [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: 04/09/2024] [Accepted: 05/10/2024] [Indexed: 06/20/2024] Open
Abstract
Leading anti-tumour therapeutic strategies typically involve surgery and radiotherapy for locally advanced (non-metastatic) cancers, while hormone therapy, chemotherapy, and molecular targeted therapy are the current treatment options for metastatic cancer. Despite the initially high sensitivity rate to anticancer therapies, a large number of patients develop resistance, leading to a poor prognosis. The mechanisms related to drug resistance are highly complex, and long non-coding RNAs appear to play a crucial role in these processes. Among these, the lncRNA homeobox transcript antisense intergenic RNA (HOTAIR), widely implicated in cancer initiation and progression, likewise plays a significant role in anticancer drug resistance. It can modulate cell activities such as proliferation, apoptosis, hypoxia, autophagy, as well as epithelial-mesenchymal transition, thereby contributing to the development of resistant tumour cells. In this manuscript, we describe different mechanisms of antitumor drug resistance in which HOTAIR is involved and suggest its potential as a therapeutic predictive biomarker for the management of cancer patients.
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Affiliation(s)
- Monica Cantile
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Valentina Belli
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Giosuè Scognamiglio
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Anna Martorana
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Giovanna De Pietro
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Maura Tracey
- Rehabilitation Medicine Unit, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Alfredo Budillon
- Scientific Directorate, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
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32
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Gail EH, Healy E, Flanigan SF, Jones N, Ng XH, Uckelmann M, Levina V, Zhang Q, Davidovich C. Inseparable RNA binding and chromatin modification activities of a nucleosome-interacting surface in EZH2. Nat Genet 2024; 56:1193-1202. [PMID: 38744974 PMCID: PMC11176075 DOI: 10.1038/s41588-024-01740-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 04/02/2024] [Indexed: 05/16/2024]
Abstract
Polycomb repressive complex 2 (PRC2) interacts with RNA in cells, but there is no consensus on how RNA regulates PRC2 canonical functions, including chromatin modification and the maintenance of transcription programs in lineage-committed cells. We assayed two separation-of-function mutants of the PRC2 catalytic subunit EZH2, defective in RNA binding but functional in methyltransferase activity. We find that part of the RNA-binding surface of EZH2 is required for chromatin modification, yet this activity is independent of RNA. Mechanistically, the RNA-binding surface within EZH2 is required for chromatin modification in vitro and in cells, through interactions with nucleosomal DNA. Contrarily, an RNA-binding-defective mutant exhibited normal chromatin modification activity in vitro and in lineage-committed cells, accompanied by normal gene repression activity. Collectively, we show that part of the RNA-binding surface of EZH2, rather than the RNA-binding activity per se, is required for the histone methylation in vitro and in cells, through interactions with the substrate nucleosome.
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Affiliation(s)
- Emma H Gail
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Evan Healy
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Sarena F Flanigan
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Natasha Jones
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Xiao Han Ng
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Vitalina Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- EMBL-Australia at SAiGENCI, Adelaide, South Australia, Australia.
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia.
- EMBL-Australia, Clayton, Victoria, Australia.
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Leisegang MS, Warwick T, Stötzel J, Brandes RP. RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends Biochem Sci 2024; 49:532-544. [PMID: 38582689 DOI: 10.1016/j.tibs.2024.03.009] [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: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.
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Affiliation(s)
- Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany.
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Julia Stötzel
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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34
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Kansara S, Sawant P, Kaur T, Garg M, Pandey AK. LncRNA-mediated orchestrations of alternative splicing in the landscape of breast cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195017. [PMID: 38341138 DOI: 10.1016/j.bbagrm.2024.195017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/19/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024]
Abstract
Alternative splicing (AS) is a fundamental post-transcriptional process in eukaryotes, enabling a single gene to generate diverse mRNA transcripts, thereby enhancing protein variability. This process involves the excision of introns and the joining of exons in pre-mRNA(s) to form mature mRNA. The resulting mature mRNAs exhibit various combinations of exons, contributing to functional diversity. Dysregulation of AS can substantially modulate protein functions, impacting the onset and progression of numerous diseases, including cancer. Non-coding RNAs (ncRNAs) are distinct from protein-coding RNAs and consist of short and long types. Long non-coding RNAs (lncRNAs) play an important role in regulating several cellular processes, particularly alternative splicing, according to new research. This review provides insight into the latest discoveries concerning how lncRNAs influence alternative splicing within the realm of breast cancer. Additionally, it explores potential therapeutic strategies focused on targeting lncRNAs.
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Affiliation(s)
- Samarth Kansara
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Prajwali Sawant
- Amity Institute of Biotechnology, Amity University Haryana, Panchgaon, Manesar, Haryana 122413, India
| | - Taranjeet Kaur
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Uttar Pradesh, Sector-125, Noida 201313, India
| | - Amit Kumar Pandey
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar, 382355, Gujarat, India.
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35
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Yazarlou F, Lipovich L, Loeb JA. Emerging roles of long non-coding RNAs in human epilepsy. Epilepsia 2024; 65:1491-1511. [PMID: 38687769 PMCID: PMC11166529 DOI: 10.1111/epi.17937] [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: 09/01/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 05/02/2024]
Abstract
Genome-scale biological studies conducted in the post-genomic era have revealed that two-thirds of human genes do not encode proteins. Most functional non-coding RNA transcripts in humans are products of long non-coding RNA (lncRNA) genes, an abundant but still poorly understood class of human genes. As a result of their fundamental and multitasking regulatory roles, lncRNAs are associated with a wide range of human diseases, including neurological disorders. Approximately 40% of lncRNAs are specifically expressed in the brain, and many of them exhibit distinct spatiotemporal patterns of expression. Comparative genomics approaches have determined that 65%-75% of human lncRNA genes are primate-specific and hence can be posited as a contributing potential cause of the higher-order complexity of primates, including human, brains relative to those of other mammals. Although lncRNAs present important mechanistic examples of epileptogenic functions, the human/primate specificity of lncRNAs questions their relevance in rodent models. Here, we present an in-depth review that supports the contention that human lncRNAs are direct contributors to the etiology and pathogenesis of human epilepsy, as a means to accelerate the integration of lncRNAs into clinical practice as potential diagnostic biomarkers and therapeutic targets. Meta-analytically, the major finding of our review is the commonality of lncRNAs in epilepsy and cancer pathogenesis through mitogen-activated protein kinase (MAPK)-related pathways. In addition, neuroinflammation may be a relevant part of the common pathophysiology of cancer and epilepsy. LncRNAs affect neuroinflammation-related signaling pathways such as nuclear factor kappa- light- chain- enhancer of activated B cells (NF-κB), Notch, and phosphatidylinositol 3- kinase/ protein kinase B (Akt) (PI3K/AKT), with the NF-κB pathway being the most common. Besides the controversy over lncRNA research in non-primate models, whether neuroinflammation is triggered by injury and/or central nervous system (CNS) toxicity during epilepsy modeling in animals or is a direct consequence of epilepsy pathophysiology needs to be considered meticulously in future studies.
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Affiliation(s)
- Fatemeh Yazarlou
- Center for Childhood Cancer, Abigail Wexner Research Institute, Nationwide Children’s Hospital, Columbus, OH, U.S.A
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co. Ltd., 601 Building C1, Guangming Science Park, Fenghuang Street, 518000, Shenzhen, Guangdong, People’s Republic of China
- College of Science, Mathematics, and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai District, 325060, Wenzhou, Zhejiang, People’s Republic of China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, 3222 Scott Hall, 540 E. Canfield St., Detroit, Michigan 48201, U.S.A
| | - Jeffrey A. Loeb
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
- University of Illinois NeuroRepository, University of Illinois at Chicago, Chicago, Illinois 60612, U.S.A
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36
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Kulakova MA, Maslakov GP, Poliushkevich LO. Irreducible Complexity of Hox Gene: Path to the Canonical Function of the Hox Cluster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:987-1001. [PMID: 38981695 DOI: 10.1134/s0006297924060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 07/11/2024]
Abstract
The evolution of major taxa is often associated with the emergence of new gene families. In all multicellular animals except sponges and comb jellies, the genomes contain Hox genes, which are crucial regulators of development. The canonical function of Hox genes involves colinear patterning of body parts in bilateral animals. This general function is implemented through complex, precisely coordinated mechanisms, not all of which are evolutionarily conserved and fully understood. We suggest that the emergence of this regulatory complexity was preceded by a stage of cooperation between more ancient morphogenetic programs or their individual elements. Footprints of these programs may be present in modern animals to execute non-canonical Hox functions. Non-canonical functions of Hox genes are involved in maintaining terminal nerve cell specificity, autophagy, oogenesis, pre-gastrulation embryogenesis, vertical signaling, and a number of general biological processes. These functions are realized by the basic properties of homeodomain protein and could have triggered the evolution of ParaHoxozoa and Nephrozoa subsequently. Some of these non-canonical Hox functions are discussed in our review.
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Affiliation(s)
- Milana A Kulakova
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia.
| | - Georgy P Maslakov
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
| | - Liudmila O Poliushkevich
- Department of Embryology, Faculty of Biology, St. Petersburg State University, St. Petersburg, 199034, Russia
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37
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Liu G, Kim J, Nguyen N, Zhou L, Dean A. Long noncoding RNA GATA2AS influences human erythropoiesis by transcription factor and chromatin landscape modulation. Blood 2024; 143:2300-2313. [PMID: 38447046 PMCID: PMC11181357 DOI: 10.1182/blood.2023021287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 03/08/2024] Open
Abstract
ABSTRACT Long noncoding RNAs (lncRNAs) are extensively expressed in eukaryotic cells and have been revealed to be important for regulating cell differentiation. Many lncRNAs have been found to regulate erythroid differentiation in the mouse. However, given the low sequence conservation of lncRNAs between mouse and human, our understanding of lncRNAs in human erythroid differentiation remains incomplete. lncRNAs are often transcribed opposite to protein coding genes and regulate their expression. Here, we characterized a human erythrocyte-expressed lncRNA, GATA2AS, which is transcribed opposite to erythroid transcription regulator GATA2. GATA2AS is a 2080-bp long, primarily nucleus-localized noncoding RNA that is expressed in erythroid progenitor cells and decreases during differentiation. Knockout of GATA2AS in human HUDEP2 erythroid progenitor cells using CRISPR-Cas9 genome editing to remove the transcription start site accelerated erythroid differentiation and dysregulated erythroblast gene expression. We identified GATA2AS as a novel GATA2 and HBG activator. Chromatin isolation by RNA purification showed that GATA2AS binds to thousands of genomic sites and colocalizes at a subset of sites with erythroid transcription factors including LRF and KLF1. RNA pulldown and RNA immunoprecipitation confirmed interaction between GATA2AS and LRF and KLF1. Chromatin immunoprecipitation sequencing (ChIP-seq) showed that knockout of GATA2AS reduces binding of these transcription factors genome wide. Assay for transposase-accessible chromatin sequencing (ATAC-seq) and H3K27ac ChIP-seq showed that GATA2AS is essential to maintain the chromatin regulatory landscape during erythroid differentiation. Knockdown of GATA2AS in human primary CD34+ cells mimicked results in HUDEP2 cells. Overall, our results implicate human-specific lncRNA GATA2AS as a regulator of erythroid differentiation by influencing erythroid transcription factor binding and the chromatin regulatory landscape.
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Affiliation(s)
- Guoyou Liu
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Nicole Nguyen
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Lecong Zhou
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
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Alammari F, Al-Hujaily EM, Alshareeda A, Albarakati N, Al-Sowayan BS. Hidden regulators: the emerging roles of lncRNAs in brain development and disease. Front Neurosci 2024; 18:1392688. [PMID: 38841098 PMCID: PMC11150811 DOI: 10.3389/fnins.2024.1392688] [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: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 06/07/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as critical players in brain development and disease. These non-coding transcripts, which once considered as "transcriptional junk," are now known for their regulatory roles in gene expression. In brain development, lncRNAs participate in many processes, including neurogenesis, neuronal differentiation, and synaptogenesis. They employ their effect through a wide variety of transcriptional and post-transcriptional regulatory mechanisms through interactions with chromatin modifiers, transcription factors, and other regulatory molecules. Dysregulation of lncRNAs has been associated with certain brain diseases, including Alzheimer's disease, Parkinson's disease, cancer, and neurodevelopmental disorders. Altered expression and function of specific lncRNAs have been implicated with disrupted neuronal connectivity, impaired synaptic plasticity, and aberrant gene expression pattern, highlighting the functional importance of this subclass of brain-enriched RNAs. Moreover, lncRNAs have been identified as potential biomarkers and therapeutic targets for neurological diseases. Here, we give a comprehensive review of the existing knowledge of lncRNAs. Our aim is to provide a better understanding of the diversity of lncRNA structure and functions in brain development and disease. This holds promise for unravelling the complexity of neurodevelopmental and neurodegenerative disorders, paving the way for the development of novel biomarkers and therapeutic targets for improved diagnosis and treatment.
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Affiliation(s)
- Farah Alammari
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ensaf M. Al-Hujaily
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Alaa Alshareeda
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Saudi Biobank Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Ministry of the National Guard-Health Affairs, Jeddah, Saudi Arabia
| | - Batla S. Al-Sowayan
- Department of Blood and Cancer Research, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
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Min Q, Zheng K, Liu T, Wang Z, Xue X, Li W, Liu Y, Zhang Y, Qiao F, Chen J, Su X, Han S. Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus. BIOLOGY 2024; 13:349. [PMID: 38785831 PMCID: PMC11118044 DOI: 10.3390/biology13050349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.
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Affiliation(s)
- Qinyue Min
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Tao Liu
- School of Ecology and Environmental Science, Qinghai University of Science and Technology, Xining 810016, China;
| | - Zitao Wang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xiuhua Xue
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Wanjie Li
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
| | - Yuping Liu
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Yanfen Zhang
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Feng Qiao
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Jinyuan Chen
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
| | - Xu Su
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, School of Life Sciences, Qinghai Normal University, Xining 810008, China; (Q.M.); (Z.W.); (Y.L.); (Y.Z.); (F.Q.); (J.C.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China; (K.Z.); (X.X.); (W.L.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810008, China
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Wen P, Qi X, Zheng R. Value of the HOTAIR expression assay in predicting therapy target in hepatocellular carcinoma: A meta-analysis and bioinformatics analysis. Int J Biol Markers 2024:3936155241252458. [PMID: 38748534 DOI: 10.1177/03936155241252458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
BACKGROUND Several studies show that the long non-coding RNA HOX transcript antisense RNA (HOTAIR) was upregulated in human cancer, which was associated with several clinical features and may have the potential to be prognostic markers. However, the significance of HOTAIR in hepatocellular carcinoma remains unclear. We performed a meta-analysis and bioanalysis to further investigate the association between HOTAIR and hepatocellular carcinoma. METHODS Eligible literature was systematically retrieved from PubMed, Embase, and Web of Science databases. The pooled hazard ratios with 95% confidence intervals were used to evaluate to the effect. Raw data on HOTAIR expression were obtained from The Cancer Genome Atlas data portals. All bioinformatics analyses were performed using R software (version 4.3.1). RESULTS We identified eight studies in this meta-analysis with a total of 399 patients. High-level HOTAIR expression was found to be significantly related to advanced tumor node metastasis stage, distant metastasis, poor tumor differentiation, and patients with hepatitis. Correspondingly, HOTAIR was also associated with poor overall survival and relapse-free survival. Subsequently, in bioanalysis, HOTAIR expression was higher in hepatocellular carcinoma as well as poor overall survival. High HOTAIR expression was strongly correlated with tumor node metastasis stage. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the differentially expressed genes related to HOTAIR may be involved in the cancer-associated signaling pathway. CONCLUSION HOTAIR may be a potential biomarker for HCC prediction and is expected to become a new choice for clinical HCC prediction..
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Affiliation(s)
- Ping Wen
- Department of Second Stationed Out-Patient, General Hospital of Northern Theatre Command, Wenhua Road 83, Shenyang, Liaoning 110068, P.R. China
| | - Xiyu Qi
- Department of Nutrition, General Hospital of Northern Theatre Command, Wenhua Road 83, Shenyang, Liaoning 110068, P.R. China
| | - Ruzhen Zheng
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Yanguan Lane34, Hangzhou, Zhejiang 310002, P.R. China
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Thi YVN, Vu TD, Huong NTL, Chu DT. Epigenetic contribution to the relationship between obesity and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:195-213. [PMID: 39179347 DOI: 10.1016/bs.ircmb.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
Obesity and cancer are two major health issues all around the world due to their elevated prevalence. Several experimental and epidemiological studies have demonstrated the relationship between obesity and cancer, in which obesity is considered a risk factor for cancer development. The ultimate goal of knowing the epigenetic contribution to the relationship between obesity and cancer is to find the method of intervention or treatment of obesity and cancer. Therefore, providing the most general perspective on epigenetic contribution to the relationship between obesity and cancer is necessary. Obesity is closely related to some common cancers that are currently encountered, including breast, esophagus, liver, kidney, uterus, colorectal, pancreatic, and gallbladder. Obesity has a significant impact that increases the risk of cancer deaths and thereby indirectly affects the choice of treatment. It is estimated that about 4-8% of cancer cases are caused by obesity. In particular, the basic mechanism to understand the relationship between cancer is very complicated and has not been fully understood. This work is aimed at summarizing the current knowledge of the role of epigenetic regulation in the relationship between obesity, and potential applications.
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Affiliation(s)
- Yen-Vy Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Thuy-Duong Vu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | | | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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Wu C, Yu X, Li X, An R, Li S, Liu X, Hu X, Li S, Zhou Q, Li L, Yu H, Zhao M, Chang A. Aberrant METTL14 gene expression contributes to malignant transformation of benzene-exposed myeloid cells. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 276:116302. [PMID: 38608381 DOI: 10.1016/j.ecoenv.2024.116302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/14/2024]
Abstract
Benzene is a known contributor to human leukaemia through its toxic effects on bone marrow cells, and epigenetic modification is believed to be a potential mechanism underlying benzene pathogenesis. However, the specific roles of N6-methyladenosine (m6A), a newly discovered RNA post-transcriptional modification, in benzene-induced hematotoxicity remain unclear. In this study, we identified self-renewing malignant proliferating cells in the bone marrow of benzene-exposed mice through in vivo bone marrow transplantation experiments and Competitive Repopulation Assay. Subsequent analysis using whole transcriptome sequencing and RNA m6A methylation sequencing revealed a significant upregulation of RNA m6A modification levels in the benzene-exposed group. Moreover, RNA methyltransferase METTL14, known as a pivotal player in m6A modification, was found to be aberrantly overexpressed in Lin-Sca-1+c-Kit+ (LSK) cells of benzene-exposed mice. Further analysis based on the GEO database showed a positive correlation between the expression of METTL14, mTOR, and GFI and benzene exposure dose. In vitro cellular experiments, employing experiments such as western blot, q-PCR, m6A RIP, and CLIP, validated the regulatory role of METTL14 on mTOR and GFI1. Mechanistically, continuous damage inflicted by benzene exposure on bone marrow cells led to the overexpression of METTL14 in LSK cells, which, in turn, increased m6A modification on the target genes' (mTOR and GFI1) RNA. This upregulation of target gene expression activated signalling pathways such as mTOR-AKT, ultimately resulting in malignant proliferation of bone marrow cells. In conclusion, this study offers insights into potential early targets for benzene-induced haematologic malignant diseases and provides novel perspectives for more targeted preventive and therapeutic strategies.
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Affiliation(s)
- Chao Wu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xin Yu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiaoling Li
- Department of Minimally Invasive Interventional, Peking University Cancer Hospital (Inner Mongolia Campus) & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Regio 010000, China
| | - Ran An
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, and Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Shengnan Li
- Cancer Center, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, China
| | - Xinyue Liu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xiangting Hu
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Shufei Li
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China
| | - Qinghong Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China
| | - Limei Li
- Department of Blood Cell Therapy, The Second Affiliated Hospital of Hainan Medical University, China
| | - Hai Yu
- Department of Minimally Invasive Interventional, Peking University Cancer Hospital (Inner Mongolia Campus) & Affiliated Cancer Hospital of Inner Mongolia Medical University, Hohhot, Inner Mongolia Autonomous Regio 010000, China.
| | - Miao Zhao
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin 300011, China.
| | - Antao Chang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.
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Chen X, Wang S, Jiang X, Zhang M, Ding Y. Long non-coding RNA HOTAIR: from pan-cancer analysis to colorectal cancer-related uridine metabolism. Aging (Albany NY) 2024; 16:7752-7773. [PMID: 38696320 PMCID: PMC11132002 DOI: 10.18632/aging.205781] [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: 09/26/2023] [Accepted: 03/29/2024] [Indexed: 05/04/2024]
Abstract
Long non-coding RNAs (lncRNAs) are involved significantly in the development of human cancers. lncRNA HOTAIR has been reported to play an oncogenic role in many human cancers. Its specific regulatory role is still elusive. And it might have enormous potential to interpret the malignant progression of tumors in a broader perspective, that is, in pan-cancer. We comprehensively investigated the effect of HOTAIR expression on tumor prognosis across human malignancies by analyzing multiple cancer-related databases like The Cancer Genome Atlas (TCGA) and Tumor Immune Estimation Resource (TIMER). Bioinformatics data indicated that HOTAIR was overexpressed in most of these human malignancies and was significantly associated with the prognosis of patients with cancer, especially in colorectal cancer (CRC). Subsequently, this study further clarified the utility of HOTAIR that downregulation of its expression could result in reduced proliferation and invasion of CRC cells. Mechanistically, HOTAIR upregulated the metabolic enzymes UPP1 by recruiting histone methyltransferase EZH2, thereby increasing the tumor progression. Our results highlight the essential role of HOTAIR in pan-cancer and uridine bypass, suggesting that the HOTAIR/EZH2/UPP1 axis might be a novel target for overcoming CRC. We anticipate that the role of HOTAIR in metabolism could be important in the context of CRC and even exploited for therapeutic purposes.
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Affiliation(s)
- Xuyu Chen
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Siying Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xin Jiang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Min Zhang
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yanbing Ding
- Department of Gastroenterology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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Wen H, Ni X, Qian S, Abdul S, Lv H, Chen Y. Construction of a gene signature associated with anoikis to evaluate the prognosis and immune infiltration in patients with colorectal cancer. Transl Cancer Res 2024; 13:1904-1923. [PMID: 38737694 PMCID: PMC11082817 DOI: 10.21037/tcr-23-1221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/08/2024] [Indexed: 05/14/2024]
Abstract
Background Colorectal cancer (CRC) is characterized by a high metastasis rate, leading to poor prognosis and increased mortality. Anoikis, a physiological process, serves as a crucial barrier against metastasis. The objective of this research is to construct a prognostic model for CRC based on genes associated with anoikis. Methods The study involved differential analysis and univariate Cox analysis of anoikis-related genes (ARGs), resulting in the selection of 47 genes closely associated with prognosis. Subsequently, unsupervised k-means clustering analysis was conducted on all patients to identify distinct clusters. Survival analysis, principal component analysis (PCA), and t-distributed stochastic neighbor embedding (t-SNE) analysis were performed on the different clusters to investigate associations within the clusters. Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were utilized to assess metabolic pathway enrichment between the identified clusters. Furthermore, single-sample GSEA (ssGSEA) was applied to explore variations in immune infiltration. Multivariable Cox regression and least absolute shrinkage and selection operator (LASSO) analyses were conducted to construct a risk model based on ten signatures, which enabled the grouping of all samples according to their risk scores. The prognostic value of the model was validated using receiver operating characteristic (ROC) curves, area under the curve (AUC) calculations, and survival curves. Additionally, the expression of candidate genes was validated using quantitative real-time polymerase chain reaction (qRT-PCR). Results Forty-seven survival-related ARGs were screened out. Somatic mutation analysis showed that these genes revealed a high mutation rate. Based on their expression, two clusters were identified. Cluster B patients exhibited a shortened overall survival and higher immune infiltration. A risk scoring model including ten genes was subsequently developed, which exhibited excellent prognostic predictive ability for CRC, as evidenced by the survival curve, ROC curve, and AUC curve. In addition, a nomogram was developed for predicting 3- and 5-year survival probabilities. The qRT-PCR results indicated the dissimilarities among the ten signatures in the tumor tissues and adjacent tissues of patients with CRC were fundamentally consistent with the analytical findings. Conclusions This study comprehensively evaluated the prognostic significance of ARGs in CRC. It identified two distinct anoikis-related clusters and examined their respective immune microenvironments. Furthermore, an ARGs signature was developed to effectively predict the prognosis of CRC, thereby establishing a solid foundation for investigating the clinical prognostic role of anoikis in CRC.
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Affiliation(s)
- Hang Wen
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xixian Ni
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sicheng Qian
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sammad Abdul
- International Education College, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hang Lv
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, China
| | - Yitao Chen
- School of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Ahmad F, Sudesh R, Ahmed AT, Arumugam M, Mathkor DM, Haque S. The multifaceted functions of long non-coding RNA HOTAIR in neuropathologies and its potential as a prognostic marker and therapeutic biotarget. Expert Rev Mol Med 2024; 26:e11. [PMID: 38682637 PMCID: PMC11140545 DOI: 10.1017/erm.2024.11] [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: 09/05/2023] [Revised: 12/21/2023] [Accepted: 03/08/2024] [Indexed: 05/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) are progressively being perceived as prominent molecular agents controlling multiple aspects of neuronal (patho)physiology. Amongst these is the HOX transcript antisense intergenic RNA, often abbreviated as HOTAIR. HOTAIR epigenetically regulates its target genes via its interaction with two different chromatin-modifying agents; histone methyltransferase polycomb-repressive complex 2 and histone demethylase lysine-specific demethylase 1. Parenthetically, HOTAIR elicits trans-acting sponging function against multiple micro-RNA species. Oncological research studies have confirmed the pathogenic functions of HOTAIR in multiple cancer types, such as gliomas and proposed it as a pro-oncological lncRNA. In fact, its expression has been suggested to be a predictor of the severity/grade of gliomas, and as a prognostic biomarker. Moreover, a propound influence of HOTAIR in other aspects of brain heath and disease states is just beginning to be unravelled. The objective of this review is to recapitulate all the relevant data pertaining to the regulatory roles of HOTAIR in neuronal (patho)physiology. To this end, we discuss the pathogenic mechanisms of HOTAIR in multiple neuronal diseases, such as neurodegeneration, traumatic brain injury and neuropsychiatric disorders. Finally, we also summarize the results from the studies incriminating HOTAIR in the pathogeneses of gliomas and other brain cancers. Implications of HOTAIR serving as a suitable therapeutic target in neuropathologies are also discussed.
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Affiliation(s)
- Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Ravi Sudesh
- Department of Biomedical Sciences, School of Bio Sciences (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Atheeq Toufeeq Ahmed
- Department of Biotechnology, School of Bio Sciences (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Bio Sciences (SBST), Vellore Institute of Technology (VIT), Vellore 632014, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
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47
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Lu J, Xu L, Wang Y, Guan B. lncRNAs regulate cell stemness in physiology and pathology during differentiation and development. AMERICAN JOURNAL OF STEM CELLS 2024; 13:59-74. [PMID: 38765805 PMCID: PMC11101988 DOI: 10.62347/vhvu7361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/06/2024] [Indexed: 05/22/2024]
Abstract
Long non-coding RNA (lncRNA) are an important class of ubiquitous genes involved in diverse biological functions. lncRNAs, defined as noncoding RNAs with a length exceeding 200 nucleotides, are abundantly expressed throughout cells; however, their precise functions remain largely elusive. From embryonic stem cell proliferation and differentiation to cancer cell proliferation and invasion, lncRNAs play multifaceted regulatory roles across various cellular stages. Moreover, lncRNAs participate in the regulation of differentiation and regeneration during cellular development processes while also playing a pivotal role in maintaining and regulating cell stemness. In this article, we comprehensively review the current knowledge regarding lncRNAs in this field, discussing their biological functions and mechanisms underlying stemness regulation along with the factors implicated in these processes. We emphasize the growing evidence supporting the significance of lncRNAs in governing cell stemness while indicating that disruptions or mutations within them may serve as fundamental causes for certain developmental disorders.
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Affiliation(s)
- Jie Lu
- Department of Otolaryngology Head and Neck Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University Yangzhou, Jiangsu, China
| | - Li Xu
- Department of Otolaryngology Head and Neck Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University Yangzhou, Jiangsu, China
| | - Ying Wang
- Department of Otolaryngology Head and Neck Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University Yangzhou, Jiangsu, China
| | - Bing Guan
- Department of Otolaryngology Head and Neck Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University Yangzhou, Jiangsu, China
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48
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Wang Y, Pattarayan D, Huang H, Zhao Y, Li S, Wang Y, Zhang M, Li S, Yang D. Systematic investigation of chemo-immunotherapy synergism to shift anti-PD-1 resistance in cancer. Nat Commun 2024; 15:3178. [PMID: 38609378 PMCID: PMC11015024 DOI: 10.1038/s41467-024-47433-y] [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: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Chemo-immunotherapy combinations have been regarded as one of the most practical ways to improve immunotherapy response in cancer patients. In this study, we integrate the transcriptomics data from anti-PD-1-treated tumors and compound-treated cancer cell lines to systematically screen for chemo-immunotherapy synergisms in silico. Through analyzing anti-PD-1 induced expression changes in patient tumors, we develop a shift ability score to measure if a chemotherapy or a small molecule inhibitor treatment can shift anti-PD-1 resistance in tumor cells. By applying shift ability analysis to 41,321 compounds and 16,853 shRNA treated cancer cell lines transcriptomic data, we characterize the landscape of chemo-immunotherapy synergism and experimentally validated a mitochondrial RNA-dependent mechanism for drug-induced immune activation in tumor. Our study represents an effort to mechanistically characterize chemo-immunotherapy synergism and will facilitate future pre-clinical and clinical studies.
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Affiliation(s)
- Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Dhamotharan Pattarayan
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Haozhe Huang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yueshan Zhao
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Sihan Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yifei Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA.
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49
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Guo JK, Blanco MR, Walkup WG, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M. Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. Mol Cell 2024; 84:1271-1289.e12. [PMID: 38387462 PMCID: PMC10997485 DOI: 10.1016/j.molcel.2024.01.026] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 01/30/2024] [Indexed: 02/24/2024]
Abstract
Polycomb repressive complex 2 (PRC2) is reported to bind to many RNAs and has become a central player in reports of how long non-coding RNAs (lncRNAs) regulate gene expression. Yet, there is a growing discrepancy between the biochemical evidence supporting specific lncRNA-PRC2 interactions and functional evidence demonstrating that PRC2 is often dispensable for lncRNA function. Here, we revisit the evidence supporting RNA binding by PRC2 and show that many reported interactions may not occur in vivo. Using denaturing purification of in vivo crosslinked RNA-protein complexes in human and mouse cell lines, we observe a loss of detectable RNA binding to PRC2 and chromatin-associated proteins previously reported to bind RNA (CTCF, YY1, and others), despite accurately mapping bona fide RNA-binding sites across others (SPEN, TET2, and others). Taken together, these results argue for a critical re-evaluation of the broad role of RNA binding to orchestrate various chromatin regulatory mechanisms.
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Affiliation(s)
- Jimmy K Guo
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Mario R Blanco
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ward G Walkup
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant Bonesteele
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Carl R Urbinati
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Biology, Loyola Marymount University, Los Angeles, CA 90045, USA
| | - Abhik K Banerjee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Amy Chow
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Olivia Ettlin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mackenzie Strehle
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Parham Peyda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Enrique Amaya
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Vickie Trinh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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50
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Khalafizadeh A, Hashemizadegan SD, Shokri F, Bakhshinejad B, Jabbari K, Motavaf M, Babashah S. Competitive endogenous RNA networks: Decoding the role of long non-coding RNAs and circular RNAs in colorectal cancer chemoresistance. J Cell Mol Med 2024; 28:e18197. [PMID: 38506091 PMCID: PMC10951891 DOI: 10.1111/jcmm.18197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 02/04/2024] [Indexed: 03/21/2024] Open
Abstract
Colorectal cancer (CRC) is recognized as one of the most common gastrointestinal malignancies across the globe. Despite significant progress in designing novel treatments for CRC, there is a pressing need for more effective therapeutic approaches. Unfortunately, many patients undergoing chemotherapy develop drug resistance, posing a significant challenge for cancer treatment. Non-coding RNAs (ncRNAs) have been found to play crucial roles in CRC development and its response to chemotherapy. However, there are still gaps in our understanding of interactions among various ncRNAs, such as long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) and microRNAs (miRNAs). These ncRNAs can act as either oncogenes or tumour suppressors, affecting numerous biological functions in different cancers including CRC. A class of ncRNA molecules known as competitive endogenous RNAs (ceRNAs) has emerged as a key player in various cellular processes. These molecules form networks through lncRNA/miRNA/mRNA and circRNA/miRNA/mRNA interactions. In CRC, dysregulation of ceRNA networks has been observed across various cellular processes, including proliferation, apoptosis and angiogenesis. These dysregulations are believed to play a significant role in the progression of CRC and, in certain instances, may contribute to the development of chemoresistance. Enriching our knowledge of these dysregulations holds promise for advancing the field of diagnostic and therapeutic modalities for CRC. In this review, we discuss lncRNA- and circRNA-associated ceRNA networks implicated in the emergence and advancement of drug resistance in colorectal carcinogenesis.
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Affiliation(s)
- Ali Khalafizadeh
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | | | - Fatemeh Shokri
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
| | - Babak Bakhshinejad
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Keyvan Jabbari
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Mahsa Motavaf
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological SciencesTarbiat Modares UniversityTehranIran
- Research and Development Center of BiotechnologyTarbiat Modares UniversityTehranIran
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