1
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Nickerson JA, Momen-Heravi F. Long non-coding RNAs: roles in cellular stress responses and epigenetic mechanisms regulating chromatin. Nucleus 2024; 15:2350180. [PMID: 38773934 PMCID: PMC11123517 DOI: 10.1080/19491034.2024.2350180] [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: 01/18/2024] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Most of the genome is transcribed into RNA but only 2% of the sequence codes for proteins. Non-coding RNA transcripts include a very large number of long noncoding RNAs (lncRNAs). A growing number of identified lncRNAs operate in cellular stress responses, for example in response to hypoxia, genotoxic stress, and oxidative stress. Additionally, lncRNA plays important roles in epigenetic mechanisms operating at chromatin and in maintaining chromatin architecture. Here, we address three lncRNA topics that have had significant recent advances. The first is an emerging role for many lncRNAs in cellular stress responses. The second is the development of high throughput screening assays to develop causal relationships between lncRNAs across the genome with cellular functions. Finally, we turn to recent advances in understanding the role of lncRNAs in regulating chromatin architecture and epigenetics, advances that build on some of the earliest work linking RNA to chromatin architecture.
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Affiliation(s)
- Jeffrey A Nickerson
- Division of Genes & Development, Department of Pediatrics, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Fatemeh Momen-Heravi
- College of Dental Medicine, Columbia University Medical Center, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
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2
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Gu L, Yue X, Niu S, Ma J, Liu S, Pan M, Song L, Su Q, Tan Y, Li Y, Chang J. Systematical identification of key genes and regulatory genetic variants associated with prognosis of esophageal squamous cell carcinoma. Mol Carcinog 2024; 63:1013-1023. [PMID: 38380955 DOI: 10.1002/mc.23704] [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: 12/20/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) stands as a highly lethal malignancy characterized by pronounced recurrence and metastasis, resulting in a bleak 5-year survival rate. Despite extensive investigations, encompassing genome-wide association studies, the identification of robust prognostic markers has remained elusive. In this study, leveraging four independent data sets comprising 404 ESCC patients, we conducted a systematic analysis to unveil pivotal genes influencing overall survival. our meta-analysis identified 278 genes significantly associated with ESCC prognosis. Further exploration of the prognostic landscape involved an examination of expression quantitative trait loci for these genes, leading to the identification of six tag single nucleotide polymorphisms predictive of overall survival in a cohort of 904 ESCC patients. Notably, functional annotation spotlighted rs11227223, residing in the enhancer region of nuclear paraspeckle assembly transcript 1 (NEAT1), as a crucial variant likely exerting a substantive biological role. Through a series of biochemistry experiments, we conclusively demonstrated that the rs11227223-T allele, indicative of a poorer prognosis, augmented NEAT1 expression. Our results underscore the substantive role of NEAT1 and its regulatory variant in prognostic predictions for ESCC. This comprehensive analysis not only advances our comprehension of ESCC prognosis but also unveils a potential avenue for targeted interventions, offering promise for enhanced clinical outcomes.
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Affiliation(s)
- Linglong Gu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xinying Yue
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Niu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jialing Ma
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shasha Liu
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Miaoxin Pan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lina Song
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qianqian Su
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuqian Tan
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yueping Li
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory for Environment and Health, Department of Health Toxicology, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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3
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Liu C, Li K, Ding W, Tang X, Wu Z, Zhu X, Gong W, Zhao H. LINC01535 promotes hepatocellular carcinoma proliferation and metastasis by regulating the miR-214-3p/VASP axis. J Cancer 2024; 15:3809-3824. [PMID: 38911365 PMCID: PMC11190762 DOI: 10.7150/jca.91756] [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: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/25/2024] Open
Abstract
Background: Emerging evidence has indicated that long noncoding RNAs (lncRNAs) are associated with the development and progression of several carcinomas, including hepatocellular carcinoma (HCC). However, the role of LINC01535 in HCC is still unknown. Materials and methods: In this study, RNA-seq, CCK-8, colony formation, wound healing, Transwell and tumor xenograft assays were used to explore the function of LINC01535 in the proliferation and metastasis of HCC in vitro and in vivo. Fluorescence in situ hybridization (FISH) assay, bioinformatics analysis, dual-luciferase assay, quantitative real-time polymerase chain reaction (qRT-PCR), and western blot analysis were used to reveal the interactions of LINC01535, miR-214-3p and VASP. Results: LINC01535 was overexpressed in HCC tissues and HCC cell lines. Gain- and loss-of-function studies revealed that LINC01535 could promote HCC cell proliferation, migration and invasion both in vitro and in vivo. In addition, upregulation of LINC01535 significantly decreased the expression of microRNA-214-3p (miR-214-3p), which was found closely associated with suppressing tumor progression. Moreover, VASP was identified as a direct downstream target gene of miR-214-3p. LINC01535 positively regulated VASP expression by sponging miR-214-3p, and VASP overexpression activated the PI3K/AKT signaling pathway and stimulated epithelial-to-mesenchymal transition (EMT) in HCC. Conclusions: Our study first found that LINC01535 promoted HCC progression by regulating its downstream target, the miR-214-3p/VASP axis, via the PI3K/AKT signaling pathway. The function and novel regulatory mechanism of LINC01535 may provide a valuable target for the diagnosis and treatment of HCC patients.
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Affiliation(s)
- Chunjiang Liu
- Department of General Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Kuan Li
- Department of Hepatobiliary Surgery, Kunshan Hospital of Traditional Chinese Medicine, Suzhou, 215000, China
| | - Wenzhou Ding
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Xiaoqi Tang
- Department of General Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Zhifeng Wu
- Department of General Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Xin Zhu
- Department of General Surgery, Shaoxing People's Hospital, Shaoxing, 312000, China
| | - Wanwan Gong
- Department of Hepatopancreatobiliary Surgery, Jiangnan University Medical Center, Wuxi, 214002, China
| | - Hui Zhao
- Department of Hepatopancreatobiliary Surgery, Jiangnan University Medical Center, Wuxi, 214002, China
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4
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Janas T, Sapoń K, Janas T. Selection of bifunctional RNAs with specificity for arginine and lipid membranes. FEBS Lett 2024; 598:1061-1079. [PMID: 38649155 DOI: 10.1002/1873-3468.14880] [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: 12/05/2023] [Revised: 02/23/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
The molecular mechanisms of selective RNA loading into exosomes and other extracellular vesicles are not yet completely understood. In order to show that a pool of RNA sequences binds both the amino acid arginine and lipid membranes, we constructed a bifunctional RNA 10Arg aptamer specific for arginine and lipid vesicles. The preference of RNA 10Arg for lipid rafts was visualized and confirmed using FRET microscopy in neuroblastoma cells. The selection-amplification (SELEX) method using a doped (with the other three nucleotides) pool of RNA 10Arg sequences yielded several RNA 10Arg(D) sequences, and the affinities of these RNAs both to arginine and liposomes are improved in comparison to pre-doped RNA. Generation of these bispecific aptamers supports the hypothesis that an RNA molecule can bind both to RNA-binding proteins (RBPs) through arginine within the RBP-binding site and to membrane lipid rafts, thus facilitating RNA loading into exosomes and other extracellular vesicles.
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Affiliation(s)
- Teresa Janas
- Institute of Biology, University of Opole, Poland
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5
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Liao B, Wang J, Xie Y, Luo H, Min J. LINK-A: unveiling its functional role and clinical significance in human tumors. Front Cell Dev Biol 2024; 12:1354726. [PMID: 38645412 PMCID: PMC11032015 DOI: 10.3389/fcell.2024.1354726] [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: 12/12/2023] [Accepted: 03/20/2024] [Indexed: 04/23/2024] Open
Abstract
LINK-A, also recognized as LINC01139, has emerged as a key oncological lncRNA in cancer. LINK-A is upregulated in solid and liquid tumor samples, including breast cancer, ovarian cancer, glioma, non-small-cell lung cancer, and mantle cell lymphoma. Notably, LINK-A is involved in regulating critical cancer-related pathways, such as AKT and HIF1α signaling, and is implicated in a range of oncogenic activities, including cell proliferation, apoptosis, epithelial-mesenchymal transition (EMT), cell invasion and migration, and glycolysis reprogramming. LINK-A's differential expression and its correlation with clinical features enable it to be a promising biomarker for cancer diagnosis, prognosis, and the stratification of tumor progression. Additionally, LINK-A's contribution to the development of resistance to cancer therapies, including AKT inhibitors and immunotherapy, underscores its potential as a therapeutic target. This review provides a comprehensive overview of the available data on LINK-A, focusing on its molecular regulatory pathways and clinical significance. By exploring the multifaceted nature of LINK-A in cancer, the review aims to offer a valuable resource for future research directions, potentially guiding the development of novel therapeutic strategies targeting this lncRNA in cancer treatment.
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Affiliation(s)
- Bing Liao
- Department of Otorhinolaryngology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Yilin Xie
- Second School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
| | - Jun Min
- Department of Neurology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China
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6
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Saeinasab M, Atlasi Y, M Matin M. Functional role of lncRNAs in gastrointestinal malignancies: the peculiar case of small nucleolar RNA host gene family. FEBS J 2024; 291:1353-1385. [PMID: 36282516 DOI: 10.1111/febs.16668] [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: 07/13/2022] [Revised: 09/18/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in normal physiology and are often de-regulated in disease states such as cancer. Recently, a class of lncRNAs referred to as the small nucleolar RNA host gene (SNHG) family have emerged as important players in tumourigenesis. Here, we discuss new findings describing the role of SNHGs in gastrointestinal tumours and summarize the three main functions by which these lncRNAs promote carcinogenesis, namely: competing with endogenous RNAs, modulating protein function, and regulating epigenetic marking. Furthermore, we discuss how SNHGs participate in different hallmarks of cancer, and how this class of lncRNAs may serve as potential biomarkers in cancer diagnosis and therapy.
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Affiliation(s)
- Morvarid Saeinasab
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
| | - Yaser Atlasi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Iran
- Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Iran
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7
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Kundu R, Kumar S, Chandra A, Datta A. Cell-Permeable Fluorescent Sensors Enable Rapid Live Cell Visualization of Plasma Membrane and Nuclear PIP3 Pools. JACS AU 2024; 4:1004-1017. [PMID: 38559732 PMCID: PMC10976597 DOI: 10.1021/jacsau.3c00738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024]
Abstract
Phosphoinositides, phospholipids that are key cell-signal mediators, are present at very low levels in cellular membranes and within nuclei. Phosphatidylinositol-(3,4,5)-trisphosphate (PIP3), a phosphoinositide barely present in resting cell membranes, is produced when cells receive either growth, proliferation, or movement signals. Aberrant PIP3 levels are associated with the formation of cancers. PIP3 pools are also present in the nucleus, specifically in the nucleolus. However, questions related to the organization and function of this lipid in such membraneless intranuclear structures remain unanswered. Therefore, chemical sensors for tracking cellular PIP3 are invaluable not only for timing signal initiation in membranes but also for identifying the organization and function of membraneless nuclear PIP3 pools. Because PIP3 is present in the inner leaflet of cell membranes and in the nucleus, cell-permeable, rapid-response fluorescent sensors would be ideal. We have designed two peptide-based, water-soluble, cell-permeable, ratiometric PIP3 sensors named as MFR-K17H and DAN-NG-H12G. MFR-K17H rapidly entered into the cell cytoplasm, distinctly reporting rapid (<1 min) time scales of growth factor-stimulated PIP3 generation and depletion within cell membranes in living cells. Importantly, MFR-K17H lighted up inherently high levels of PIP3 in triple-negative breast cancer cell membranes, implying future applications in the detection of enhanced PIP3 levels in cancerous cells. On the other hand, DAN-NG-H12G targeted intranuclear PIP3 pools, revealing that within membraneless structures, PIP3 resided in a hydrophobic environment. Together, both probes form a unique orthogonally targeted combination of cell-permeable, ratiometric probes that, unlike previous cell-impermeable protein-based sensors, are easy to apply and provide an unprecedented handle into PIP3-mediated cellular processes.
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Affiliation(s)
- Rajasree Kundu
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400005, India
| | - Sahil Kumar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400005, India
| | - Amitava Chandra
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400005, India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, 1 Homi Bhabha Road, Mumbai 400005, India
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8
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Chen Y, Chen H, Wang Y, Liu F, Fan X, Shi C, Su X, Tan M, Yang Y, Lin B, Lei K, Qu L, Yang J, Zhu Z, Yuan Z, Xie S, Sun Q, Neculai D, Liu W, Yan Q, Wang X, Shao J, Liu J, Lin A. LncRNA LINK-A Remodels Tissue Inflammatory Microenvironments to Promote Obesity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2303341. [PMID: 38145352 PMCID: PMC10933663 DOI: 10.1002/advs.202303341] [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: 05/23/2023] [Revised: 11/09/2023] [Indexed: 12/26/2023]
Abstract
High-fat diet (HFD)-induced obesity is a crucial risk factor for metabolic syndrome, mainly due to adipose tissue dysfunctions associated with it. However, the underlying mechanism remains unclear. This study has used genetic screening to identify an obesity-associated human lncRNA LINK-A as a critical molecule bridging the metabolic microenvironment and energy expenditure in vivo by establishing the HFD-induced obesity knock-in (KI) mouse model. Mechanistically, HFD LINK-A KI mice induce the infiltration of inflammatory factors, including IL-1β and CXCL16, through the LINK-A/HB-EGF/HIF1α feedback loop axis in a self-amplified manner, thereby promoting the adipose tissue microenvironment remodeling and adaptive thermogenesis disorder, ultimately leading to obesity and insulin resistance. Notably, LINK-A expression is positively correlated with inflammatory factor expression in individuals who are overweight. Of note, targeting LINK-A via nucleic acid drug antisense oligonucleotides (ASO) attenuate HFD-induced obesity and metabolic syndrome, pointing out LINK-A as a valuable and effective therapeutic target for treating HFD-induced obesity. Briefly, the results reveale the roles of lncRNAs (such as LINK-A) in remodeling tissue inflammatory microenvironments to promote HFD-induced obesity.
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Affiliation(s)
- Yu Chen
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Hui Chen
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Ying Wang
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiao Fan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xinwan Su
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Manman Tan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Yebin Yang
- The Fourth School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouZhejiang310053China
| | - Bangxing Lin
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiang310006China
| | - Kai Lei
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jiecheng Yang
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Zhipeng Zhu
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Zengzhuang Yuan
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute)University School of MedicineInternational CampusZhejiang UniversityHainingZhejiang314400China
| | - Shanshan Xie
- The Children's HospitalNational Clinical Research Center for Child HealthZhejiang University School of MedicineHangzhouZhejiang310003China
- Department of Cell BiologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Qinming Sun
- Department of BiochemistryDepartment of Cardiology of Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang313000China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
| | - Dante Neculai
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
- Department of Cell BiologyDepartment of General Surgery of Sir Run Run Shaw HospitalZhejiang University School of MedicineHangzhouZhejiang310016China
| | - Wei Liu
- Department of BiochemistryDepartment of Cardiology of Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang313000China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Xiang Wang
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceAffiliated Hangzhou First People's HospitalZhejiang University School of MedicineHangzhouZhejiang310006China
- Department of Central LaboratoryThe First People's Hospital of HuzhouHuzhouZhejiang313000China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
| | - Jian Liu
- Zhejiang University‐University of Edinburgh Institute (ZJU‐UoE Institute)University School of MedicineInternational CampusZhejiang UniversityHainingZhejiang314400China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- Hangzhou Cancer InstitutionAffiliated Hangzhou Cancer HospitalZhejiang University School of MedicineZhejiang UniversityHangzhouZhejiang310002China
- College of Medicine and Veterinary MedicineThe University of EdinburghEdinburghEH16 4SBUK
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and ProtectionCollege of Life SciencesZhejiang UniversityHangzhouZhejiang310058China
- International School of MedicineInternational Institutes of MedicineThe 4th Affiliated Hospital of Zhejiang University School of MedicineYiwuZhejiang322000China
- Cancer CenterZhejiang UniversityHangzhouZhejiang310058China
- Key Laboratory for Cell and Gene Engineering of Zhejiang ProvinceHangzhouZhejiang310058China
- Future Health LaboratoryInnovation Center of Yangtze River DeltaZhejiang UniversityJiaxingZhejiang314100China
- Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationHangzhouZhejiang310009China
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9
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA 'T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. Mol Cancer 2024; 23:40. [PMID: 38383439 PMCID: PMC10882889 DOI: 10.1186/s12943-024-01955-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impact on normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
- Valentin Feichtenschlager
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA.
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria.
| | - Linan Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Yixuan James Zheng
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wilson Ho
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Martina Sanlorenzo
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Igor Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
| | - Eleanor Fewings
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Albert Lee
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Christopher Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Ciara Callanan
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Kevin Lin
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Tiange Qu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Dasha Hohlova
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Biology, University of San Francisco, San Francisco, CA, USA
| | - Marin Vujic
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Yeonjoo Hwang
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Kevin Lai
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Stephanie Chen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Thuan Nguyen
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Denise P Muñoz
- Department of Hematology-Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Yoshinori Kohwi
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Christian Posch
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
- Faculty of Medicine, Sigmund Freud Private University, Vienna, Austria
- Department of Dermatology and Allergy, School of Medicine, German Cancer Consortium (DKTK), Technical University of Munich, Munich, Germany
| | - Adil Daud
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
| | - Klemens Rappersberger
- Department of Dermatology, Academic Teaching Hospital, Clinic Landstrasse Vienna, Medical University Vienna, Vienna, Austria
| | - Terumi Kohwi-Shigematsu
- Department of Orofacial Science, Health Science West, University of California San Francisco School of Dentistry, San Francisco, CA, USA
| | - Jean-Philippe Coppé
- Department of Radiation Oncology, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Susana Ortiz-Urda
- Department of Dermatology, Mt Zion Cancer Research Center, University of California San Francisco, 2340 Sutter Street, Room N461, San Francisco, CA, 94115, USA
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10
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Jasim SA, Majeed AA, Uinarni H, Alshuhri M, Alzahrani AA, Ibrahim AA, Alawadi A, Abed Al-Abadi NK, Mustafa YF, Ahmed BA. Long non-coding RNA (lncRNA) PVT1 in drug resistance of cancers: Focus on pathological mechanisms. Pathol Res Pract 2024; 254:155119. [PMID: 38309019 DOI: 10.1016/j.prp.2024.155119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/05/2024]
Abstract
According to estimates, cancer will be the leading cause of death globally in 2022, accounting for 9.6 million deaths. At present, the three main therapeutic modalities utilized to treat cancer are radiation therapy, chemotherapy, and surgery. However, during treatment, tumor cells resistant to chemotherapy may arise. Drug resistance remains a major oppose since it often leads to therapeutic failure. Furthermore, the term "acquired drug resistance" describes the situation where tumor cells already display drug resistance before undergoing chemotherapy. However, little is still known about the basic mechanisms underlying chemotherapy-induced drug resistance. The development of new technologies and bioinformatics has led to the discovery of additional genes associated with drug resistance. Long noncoding RNA plasmacytoma variant translocation 1 (PVT1) has been linked to an increased risk of cancer, according to a growing body of research. Apart from biological functions associated with cell division, development, pluripotency, and cell cycle, lncRNA PVT1 contributes significantly to the regulation of various aspects of genome function, such as transcription, splicing, and epigenetics. The article will address the mechanism by which lncRNA PVT1 influences drug resistance in cancer cells.
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Affiliation(s)
- Saade Abdalkareem Jasim
- Medical Laboratory Techniques Department, Al-maarif University College, Anbar, Iraq; Biotechnology department, College of Applied Science, Fallujah University, Anbar, Iraq
| | - Ali A Majeed
- Department of Pathological Analyses, Faculty of Science, University of Kufa, Najaf, Iraq.
| | - Herlina Uinarni
- Department of Anatomy, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Indonesia; Radiology Department of Pantai Indah Kapuk Hospital, Jakarta, Indonesia.
| | - Mohammed Alshuhri
- Radiology and Medical Imaging Department, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Kharj, Sauadi Arabia
| | | | - Abeer A Ibrahim
- Inorganic Chemistry Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Iraq
| | - Ahmed Alawadi
- College of Technical Engineering, the Islamic University, Najaf, Iraq; College of Technical Engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of Technical Engineering, the Islamic University of Babylon, Babylon, Iraq
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul 41001, Iraq
| | - Batool Ali Ahmed
- Department of Medical Engineering, Al-Nisour University College, Baghdad, Iraq
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11
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Li H, Zhang Y, Feng Y, Hu X, Bi L, Zhu H, Wang Y. Predictors based on cuproptosis closely related to angiogenesis predict colorectal cancer recurrence. Front Oncol 2024; 13:1322421. [PMID: 38264748 PMCID: PMC10805227 DOI: 10.3389/fonc.2023.1322421] [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: 10/26/2023] [Accepted: 12/05/2023] [Indexed: 01/25/2024] Open
Abstract
Up to one-third of colorectal cancer (CRC) patients experience recurrence after radical surgery, and it is still very difficult to assess and predict the risk of recurrence. Angiogenesis is the key factor of recurrence as metastasis of CRC is closely related to copper metabolism. Expression profiling by microarray from two datasets in Gene Expression Omnibus (GEO) was selected for quality control, genome annotation, normalization, etc. The identified angiogenesis-derived and cuproptosis-related Long non-coding RNAs (lncRNAs) and clinical data were screened and used as predictors to construct a Cox regression model. The stability of the model was evaluated, and a nomogram was drawn. The samples were divided into high-risk and low-risk groups according to the linear prediction of the model, and a Kaplan-Meier survival analysis was performed. In this study, a model was established to predict the postoperative recurrence of colon cancer, which exhibits a high prediction accuracy. Furthermore, the negative correlation between cuproptosis and angiogenesis was validated in colorectal cancer cell lines and the expression of lncRNAs in vitro was examined.
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Affiliation(s)
- Haoran Li
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yingru Zhang
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanyuan Feng
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xueqing Hu
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling Bi
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huirong Zhu
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Wang
- Oncology Institute, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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12
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Feichtenschlager V, Chen L, Zheng YJ, Ho W, Sanlorenzo M, Vujic I, Fewings E, Lee A, Chen C, Callanan C, Lin K, Qu T, Hohlova D, Vujic M, Hwang Y, Lai K, Chen S, Nguyen T, Muñoz DP, Kohwi Y, Posch C, Daud A, Rappersberger K, Kohwi-Shigematsu T, Coppé JP, Ortiz-Urda S. The therapeutically actionable long non-coding RNA ' T-RECS' is essential to cancer cells' survival in NRAS/MAPK-driven melanoma. RESEARCH SQUARE 2023:rs.3.rs-1297358. [PMID: 38077055 PMCID: PMC10705697 DOI: 10.21203/rs.3.rs-1297358/v3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Finding effective therapeutic targets to treat NRAS-mutated melanoma remains a challenge. Long non-coding RNAs (lncRNAs) recently emerged as essential regulators of tumorigenesis. Using a discovery approach combining experimental models and unbiased computational analysis complemented by validation in patient biospecimens, we identified a nuclear-enriched lncRNA (AC004540.4) that is upregulated in NRAS/MAPK-dependent melanoma, and that we named T-RECS. Considering potential innovative treatment strategies, we designed antisense oligonucleotides (ASOs) to target T-RECS. T-RECS ASOs reduced the growth of melanoma cells and induced apoptotic cell death, while having minimal impacton normal primary melanocytes. Mechanistically, treatment with T-RECS ASOs downregulated the activity of pro-survival kinases and reduced the protein stability of hnRNPA2/B1, a pro-oncogenic regulator of MAPK signaling. Using patient- and cell line- derived tumor xenograft mouse models, we demonstrated that systemic treatment with T-RECS ASOs significantly suppressed the growth of melanoma tumors, with no noticeable toxicity. ASO-mediated T-RECS inhibition represents a promising RNA-targeting approach to improve the outcome of MAPK pathway-activated melanoma.
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Affiliation(s)
| | | | | | - Wilson Ho
- University of California San Francisco
| | | | - Igor Vujic
- Department of Dermatology and Venerology, Medical Institution Rudolfstiftung, Vienna, Austria
| | | | | | | | | | - Kevin Lin
- University of California San Francisco
| | - Tiange Qu
- University of California San Francisco
| | | | | | | | - Kevin Lai
- University of California San Francisco
| | | | | | | | | | | | - Adil Daud
- University of California at San Francisco
| | - Klemens Rappersberger
- Department of Dermatology, Clinic Landstrasse Vienna, Academic Teaching Hospital, Medical University Vienna, Vienna, Austria
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13
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Bin Wang, Yuan C, Qie Y, Dang S. Long non-coding RNAs and pancreatic cancer: A multifaceted view. Biomed Pharmacother 2023; 167:115601. [PMID: 37774671 DOI: 10.1016/j.biopha.2023.115601] [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: 07/20/2023] [Revised: 09/17/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023] Open
Abstract
Pancreatic cancer (PC) is a highly malignant disease with a 5-year survival rate of only 10%. Families with PC are at greater risk, as are type 2 diabetes, pancreatitis, and other factors. Insufficient early detection methods make this cancer have a poor prognosis. Additionally, the molecular mechanisms underlying PC development remain unclear. Increasing evidence suggests that long non-coding RNAs (lncRNAs) contribute to PC pathology,which may control gene expression by recruiting histone modification complexes to chromatin and interacting with proteins and RNAs. In recent studies, abnormal regulation of lncRNAs has been implicated in PC proliferation, metastasis, invasion, angiogenesis, apoptosis, and chemotherapy resistance suggesting potential clinical implications. The paper reviews the progress of lncRNA research in PC about diabetes mellitus, pancreatitis, cancer metastasis, tumor microenvironment regulation, and chemoresistance. Furthermore, lncRNAs may serve as potential therapeutic targets and biomarkers for PC diagnosis and prognosis. This will help improve PC patients' survival rate from a lncRNA perspective.
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Affiliation(s)
- Bin Wang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Chang Yuan
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China
| | - Yinyin Qie
- General Surgery Department, Yixing People's Hospital, Wuxi, Jiangsu 214200, China
| | - Shengchun Dang
- General Surgery Department, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu 212000, China; Siyang Hospital, Suqian, Jiangsu 223700, China.
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14
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Nan Y, Liu S, Luo Q, Wu X, Zhao P, Chang W, Zhang R, Li Y, Liu Z. m 6A demethylase FTO stabilizes LINK-A to exert oncogenic roles via MCM3-mediated cell-cycle progression and HIF-1α activation. Cell Rep 2023; 42:113273. [PMID: 37858471 DOI: 10.1016/j.celrep.2023.113273] [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: 04/28/2023] [Revised: 08/28/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
RNA N6-methyladenosine (m6A) modification is implicated in cancer progression, yet its role in regulating long noncoding RNAs during cancer progression remains unclear. Here, we report that the m6A demethylase fat mass and obesity-associated protein (FTO) stabilizes long intergenic noncoding RNA for kinase activation (LINK-A) to promote cell proliferation and chemoresistance in esophageal squamous cell carcinoma (ESCC). Mechanistically, LINK-A promotes the interaction between minichromosome maintenance complex component 3 (MCM3) and cyclin-dependent kinase 1 (CDK1), increasing MCM3 phosphorylation. This phosphorylation facilitates the loading of the MCM complex onto chromatin, which promotes cell-cycle progression and subsequent cell proliferation. Moreover, LINK-A disrupts the interaction between MCM3 and hypoxia-inducible factor 1α (HIF-1α), abrogating MCM3-mediated HIF-1α transcriptional repression and promoting glycolysis and chemoresistance. These results elucidate the mechanism by which FTO-stabilized LINK-A plays oncogenic roles and identify the FTO/LINK-A/MCM3/HIF-1α axis as a promising therapeutic target for ESCC.
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Affiliation(s)
- Yabing Nan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shi Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qingyu Luo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaowei Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Pengfei Zhao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Wan Chang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Ruixiang Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yin Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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15
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Yang Z, Zhu J, Yang T, Tang W, Zheng X, Ji S, Ren Z, Lu F. Comprehensive analysis of the lncRNAs-related immune gene signatures and their correlation with immunotherapy in lung adenocarcinoma. Br J Cancer 2023; 129:1397-1408. [PMID: 37543671 PMCID: PMC10628174 DOI: 10.1038/s41416-023-02379-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 07/06/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs)-related immune genes (lrRIGs) play a crucial role in the development and progression of lung adenocarcinoma (LUAD). However, reliable prognostic signatures based on lrRIGs have not yet been identified. METHODS We screened lrRIGs associated with the prognosis of LUAD using The Cancer Genome Atlas (TCGA) database and then established a novel prognostic nine-gene signature composed of CD79A, INHA, SHC3, LIFR, TNFRSF11A, GPI, F2RL1, SEMA7A and WFDC2 through bioinformatic approaches. A risk score derived from this gene signature was used to divide LUAD patients into the low- and high-risk groups. The latter was confirmed to have markedly worse overall survival (O.S.). A nomogram was developed using the risk score and other independent prognostic elements, demonstrating excellent performance in predicting the O.S. rate of LUAD patients. RESULTS We observed that the infiltration of diverse immune cell subtypes and response to immunotherapy and chemotherapy significantly differed between the low- and high-risk groups. CONCLUSIONS Overall, stratification based on this gene signature could be used to guide better therapeutic management and improve outcomes for LUAD patients.
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Affiliation(s)
- Zhengyan Yang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Jianling Zhu
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Tiantian Yang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Wenjun Tang
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Xiaowei Zheng
- Department of Clinical Laboratory, Puyang Hospital of Traditional Chinese Medicine, Puyang, China
| | - Shaoping Ji
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhiguang Ren
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Institute of Traditional Chinese Medicine, Henan University, Kaifeng, China.
| | - Feng Lu
- Joint National Laboratory for Antibody Drug Engineering, the First Affiliated Hospital, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Department of Immunology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
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16
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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17
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Wang Y, Wang Y, Chen Y, Yan Q, Lin A. Research progress in mitochondrial gene editing technology. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:460-472. [PMID: 37643980 PMCID: PMC10495247 DOI: 10.3724/zdxbyxb-2023-0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations result in a variety of genetic diseases. As an emerging therapeutic method, mtDNA editing technology recognizes targets more based on the protein and less on the nucleic acid. Although the protein recognition type mtDNA editing technology represented by zinc finger nuclease technology, transcription activator like effector nuclease technology and base editing technology has made some progress, the disadvantages of complex recognition sequence design hinder further popularization. Gene editing based on nucleic acid recognition by the CRISPR system shows superiority due to the simple structure, easy design and modification. However, the lack of effective means to deliver nucleic acids into mitochondria limits application in the field of mtDNA editing. With the advances in the study of endogenous and exogenous import pathways and the deepening understanding of DNA repair mechanisms, growing evidence shows the feasibility of nucleic acid delivery and the broad application prospects of nucleic acid recognition type mtDNA editing technology. Based on the classification of recognition elements, this article summarizes the current principles and development of mitochondrial gene editing technology, and discusses its application prospects.
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Affiliation(s)
- Yichen Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
| | - Ying Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Yu Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Cancer Center, Hangzhou 310058, China
| | - Qingfeng Yan
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Aifu Lin
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
- Zhejiang University Cancer Center, Hangzhou 310058, China.
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Center for RNA Medicine, International Institutes of Medicine, Zhejiang University, Jinhua 322000, Zhejiang Province, China.
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18
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Wang Y, Wang M, Chen J, Li Y, Kuang Z, Dende C, Raj P, Quinn G, Hu Z, Srinivasan T, Hassell B, Ruhn K, Behrendt CL, Liang T, Dou X, Song Z, Hooper LV. The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9. Science 2023; 381:851-857. [PMID: 37616368 PMCID: PMC10688608 DOI: 10.1126/science.ade0522] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
The intestinal microbiota regulates mammalian lipid absorption, metabolism, and storage. We report that the microbiota reprograms intestinal lipid metabolism in mice by repressing the expression of long noncoding RNA (lncRNA) Snhg9 (small nucleolar RNA host gene 9) in small intestinal epithelial cells. Snhg9 suppressed the activity of peroxisome proliferator-activated receptor γ (PPARγ)-a central regulator of lipid metabolism-by dissociating the PPARγ inhibitor sirtuin 1 from cell cycle and apoptosis protein 2 (CCAR2). Forced expression of Snhg9 in the intestinal epithelium of conventional mice impaired lipid absorption, reduced body fat, and protected against diet-induced obesity. The microbiota repressed Snhg9 expression through an immune relay encompassing myeloid cells and group 3 innate lymphoid cells. Our findings thus identify an unanticipated role for a lncRNA in microbial control of host metabolism.
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Affiliation(s)
- Yuhao Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease of The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Meng Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease of The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
| | - Jiaxin Chen
- Department of Breast Surgery and Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310009, China
| | - Yun Li
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zheng Kuang
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Chaitanya Dende
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Prithvi Raj
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Gabriella Quinn
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Zehan Hu
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tarun Srinivasan
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Brian Hassell
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Kelly Ruhn
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Cassie L. Behrendt
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease of The First Affiliated Hospital, Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310029, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310029, China
| | - Xiaobing Dou
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Zhangfa Song
- Department of Colorectal Surgery and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang 310016, China
| | - Lora V. Hooper
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX 75390
- The Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390
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19
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Chai P, Lebedenko CG, Flynn RA. RNA Crossing Membranes: Systems and Mechanisms Contextualizing Extracellular RNA and Cell Surface GlycoRNAs. Annu Rev Genomics Hum Genet 2023; 24:85-107. [PMID: 37068783 DOI: 10.1146/annurev-genom-101722-101224] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The subcellular localization of a biopolymer often informs its function. RNA is traditionally confined to the cytosolic and nuclear spaces, where it plays critical and conserved roles across nearly all biochemical processes. Our recent observation of cell surface glycoRNAs may further explain the extracellular role of RNA. While cellular membranes are efficient gatekeepers of charged polymers such as RNAs, a large body of research has demonstrated the accumulation of specific RNA species outside of the cell, termed extracellular RNAs (exRNAs). Across various species and forms of life, protein pores have evolved to transport RNA across membranes, thus providing a mechanistic path for exRNAs to achieve their extracellular topology. Here, we review types of exRNAs and the pores capable of RNA transport to provide a logical and testable path toward understanding the biogenesis and regulation of cell surface glycoRNAs.
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Affiliation(s)
- Peiyuan Chai
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Charlotta G Lebedenko
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA;
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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20
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Lv J, Liu Y, Tang J, Xiao H, Hu R, Wang G, Niu D, Shao PL, Yang J, Jin Z, Xu Z, Zhang B. A Novel Cell Membrane-Associated RNA Extraction Method and Its Application in the Discovery of Breast Cancer Markers. Anal Chem 2023; 95:11706-11713. [PMID: 37459193 DOI: 10.1021/acs.analchem.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Cell membrane-associated RNA (mem-RNA) has been demonstrated to be cell-specific and disease-related and are considered as potential biomarkers for disease diagnostics, drug delivery, and cell screening. However, there is still a lack of methods specifically designed to extract mem-RNA from cells, limiting the discovery and applications of mem-RNA. In this study, we propose the first all-in-one solution for high-purity mem-RNA isolation based on two types of magnetic nanoparticles, named MREMB (Membrane-associated RNA Extraction based on Magnetic Beads), which achieved ten times enrichment of cell membrane components and over 90% recovery rate of RNA extraction. To demonstrate MREMB's potential in clinical research, we extracted and sequenced mem-RNA of typical breast cancer MCF-7, MDA-MB-231, and SKBR-3 cell lines and non-neoplastic breast epithelial cell MCF-10A. Compared to total RNA, sequencing results revealed that membrane/secreted protein-encoding mRNAs and long noncoding RNAs (lncRNAs) were enriched in the mem-RNA, some of which were significantly overexpressed in the three cancer cell lines, including extracellular matrix-related genes COL5A1 and lncRNA TALAM1. The results indicated that MREMB could enrich membrane/secreted protein-coding RNA and amplify the expression differences of related RNAs between cancer and non-neoplastic cells, promising for cancer biomarker discovery.
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Affiliation(s)
- Jiahui Lv
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahu Tang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hongjun Xiao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruibin Hu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guanghui Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dan Niu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Pan-Lin Shao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jingkai Yang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziqi Jin
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ziyi Xu
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
| | - Bo Zhang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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21
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Bayona-Hernandez A, Guerra S, Jiménez-Ramirez IA, Sztacho M, Hozak P, Rodriguez-Zapata LC, Pereira-Santana A, Castaño E. LIPRNAseq: a method to discover lipid interacting RNAs by sequencing. Mol Biol Rep 2023; 50:6619-6626. [PMID: 37349607 DOI: 10.1007/s11033-023-08548-5] [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: 02/27/2023] [Accepted: 05/24/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Current biological research extensively describes the interactions of molecules such as RNA with other nucleic acids or proteins. However, the relatively recent discovery of nuclear phospholipids playing biologically relevant processes outside membranes, as well as, RNA-lipid interactions shows the need for new methods to explore the identity of these RNAs. METHODS AND RESULTS In this study, we describe the method for LIPID-RNA isolation followed by sequencing and analysis of the RNA that has the ability to interact with the selected lipids. Here we utilized specific phospholipid coated beads for selective RNA binding. We tested RNA from organisms belonging to different realms (human, plant, and yeast), and tested their ability to bind a specific lipid. CONCLUSIONS The results show several RNAs differentially enriched in the pull-down of phosphatidyl Inositol 4,5 bisphosphate coated beads. This method is helpful to screen lipid-binding RNA, which may have relevant biological functions. The method can be used with different lipids and comparison of pull-downs and can narrow the selection of RNAs that interact with a particular lipid for further studies.
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Affiliation(s)
- Andrea Bayona-Hernandez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Susana Guerra
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Irma Angélica Jiménez-Ramirez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, Prague, 1083, 142 20, Czech Republic
| | - Pavel Hozak
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská, Prague, 1083, 142 20, Czech Republic
| | - Luis Carlos Rodriguez-Zapata
- Unidad de Biotecnologia, Centro de Investigación Científica de Yucatán, Chuburná de Hidalgo, Calle 43, Número 130, Mérida, Yucatán, CP 97205, México
| | - Alejandro Pereira-Santana
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. Subsede Sureste, Parque Científico Tecnológico de Yucatán, Km 5.5 Carretera Sierra Papacal-Chuburná-Puerto, Mérida, 97302, Yucatán, México
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, 03940, México
| | - Enrique Castaño
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Calle 43, Número 130, Chuburná de Hidalgo, Mérida, Yucatán, CP 97205, México.
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22
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Han L, Huang D, Wu S, Liu S, Wang C, Sheng Y, Lu X, Broxmeyer HE, Wan J, Yang L. Lipid droplet-associated lncRNA LIPTER preserves cardiac lipid metabolism. Nat Cell Biol 2023; 25:1033-1046. [PMID: 37264180 PMCID: PMC10344779 DOI: 10.1038/s41556-023-01162-4] [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: 02/23/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023]
Abstract
Lipid droplets (LDs) are cellular organelles critical for lipid homeostasis, with intramyocyte LD accumulation implicated in metabolic disorder-associated heart diseases. Here we identify a human long non-coding RNA, Lipid-Droplet Transporter (LIPTER), essential for LD transport in human cardiomyocytes. LIPTER binds phosphatidic acid and phosphatidylinositol 4-phosphate on LD surface membranes and the MYH10 protein, connecting LDs to the MYH10-ACTIN cytoskeleton and facilitating LD transport. LIPTER and MYH10 deficiencies impair LD trafficking, mitochondrial function and survival of human induced pluripotent stem cell-derived cardiomyocytes. Conditional Myh10 deletion in mouse cardiomyocytes leads to LD accumulation, reduced fatty acid oxidation and compromised cardiac function. We identify NKX2.5 as the primary regulator of cardiomyocyte-specific LIPTER transcription. Notably, LIPTER transgenic expression mitigates cardiac lipotoxicity, preserves cardiac function and alleviates cardiomyopathies in high-fat-diet-fed and Leprdb/db mice. Our findings unveil a molecular connector role of LIPTER in intramyocyte LD transport, crucial for lipid metabolism of the human heart, and hold significant clinical implications for treating metabolic syndrome-associated heart diseases.
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Affiliation(s)
- Lei Han
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dayang Huang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Shiyong Wu
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Cheng Wang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yi Sheng
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Lei Yang
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.
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23
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Huang LA, Lin C, Yang L. Plumbing mysterious RNAs in "dark genome" for the conquest of human diseases. Mol Ther 2023; 31:1577-1595. [PMID: 37165619 PMCID: PMC10278048 DOI: 10.1016/j.ymthe.2023.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/11/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023] Open
Abstract
Next-generation sequencing has revealed that less than 2% of transcribed genes are translated into proteins, with a large portion transcribed into noncoding RNAs (ncRNAs). Among these, long noncoding RNAs (lncRNAs) represent the largest group and are pervasively transcribed throughout the genome. Dysfunctions in lncRNAs have been found in various diseases, highlighting their potential as therapeutic, diagnostic, and prognostic targets. However, challenges, such as unknown molecular mechanisms and nonspecific immune responses, and issues of drug specificity and delivery present obstacles in translating lncRNAs into clinical applications. In this review, we summarize recent publications that have explored lncRNA functions in human diseases. We also discuss challenges and future directions for developing lncRNA treatments, aiming to bridge the gap between functional studies and clinical potential and inspire further exploration in the field.
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Affiliation(s)
- Lisa A Huang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunru Lin
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Liuqing Yang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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24
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 369] [Impact Index Per Article: 369.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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25
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He XY, Fan X, Qu L, Wang X, Jiang L, Sang LJ, Shi CY, Lin S, Yang JC, Yang ZZ, Lei K, Li JH, Ju HQ, Yan Q, Liu J, Wang F, Shao J, Xiong Y, Wang W, Lin A. LncRNA modulates Hippo-YAP signaling to reprogram iron metabolism. Nat Commun 2023; 14:2253. [PMID: 37080959 PMCID: PMC10119135 DOI: 10.1038/s41467-023-37871-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Iron metabolism dysregulation is tightly associated with cancer development. But the underlying mechanisms remain poorly understood. Increasing evidence has shown that long noncoding RNAs (lncRNAs) participate in various metabolic processes via integrating signaling pathway. In this study, we revealed one iron-triggered lncRNA, one target of YAP, LncRIM (LncRNA Related to Iron Metabolism, also named ZBED5-AS1 and Loc729013), which effectively links the Hippo pathway to iron metabolism and is largely independent on IRP2. Mechanically, LncRIM directly binds NF2 to inhibit NF2-LATS1 interaction, which causes YAP activation and increases intracellular iron level via DMT1 and TFR1. Additionally, LncRIM-NF2 axis mediates cellular iron metabolism dependent on the Hippo pathway. Clinically, high expression of LncRIM correlates with poor patient survival, suggesting its potential use as a biomarker and therapeutic target. Taken together, our study demonstrated a novel mechanism in which LncRIM-NF2 axis facilitates iron-mediated feedback loop to hyperactivate YAP and promote breast cancer development.
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Affiliation(s)
- Xin-Yu He
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, 310058, Hangzhou, Zhejiang, China
| | - Xiao Fan
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, 310058, Hangzhou, Zhejiang, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, 310058, Hangzhou, Zhejiang, China
| | - Xiang Wang
- Department of Central Laboratory, the First People's Hospital of Huzhou, 158 Guangchang Back Road, 313000, Huzhou, Zhejiang, P.R. China
| | - Li Jiang
- Department of Nutrition, Precision Nutrition Innovation Center, School of Public Health, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
| | - Ling-Jie Sang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Cheng-Yu Shi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Siyi Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jie-Cheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Zuo-Zhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Kai Lei
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jun-Hong Li
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Huai-Qiang Ju
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, Guangdong, China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Jian Liu
- Hangzhou Cancer Institution, Affiliated Hangzhou Cancer Hospital, Zhejiang University School of Medicine, Zhejiang University, 310002, Hangzhou, Zhejiang, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 314400, Haining, Zhejiang, China
| | - Fudi Wang
- Department of Nutrition, Precision Nutrition Innovation Center, School of Public Health, Zhejiang University School of Medicine, 310058, Hangzhou, Zhejiang, China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China
| | - Yan Xiong
- Department of Orthopedic Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, 88 Jiefang Road, 310000, Hangzhou, Zhejiang, China
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, 310058, Hangzhou, Zhejiang, China.
- International School of Medicine, International Institutes of Medicine, The 4th Affiliated Hospital of Zhejiang University School of Medicine, 322000, Yiwu, Zhejiang, China.
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, Zhejiang, China.
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26
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Arriaga-Canon C, Contreras-Espinosa L, Aguilar-Villanueva S, Bargalló-Rocha E, García-Gordillo JA, Cabrera-Galeana P, Castro-Hernández C, Jiménez-Trejo F, Herrera LA. The Clinical Utility of lncRNAs and Their Application as Molecular Biomarkers in Breast Cancer. Int J Mol Sci 2023; 24:ijms24087426. [PMID: 37108589 PMCID: PMC10138835 DOI: 10.3390/ijms24087426] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Given their tumor-specific and stage-specific gene expression, long non-coding RNAs (lncRNAs) have demonstrated to be potential molecular biomarkers for diagnosis, prognosis, and treatment response. Particularly, the lncRNAs DSCAM-AS1 and GATA3-AS1 serve as examples of this because of their high subtype-specific expression profile in luminal B-like breast cancer. This makes them candidates to use as molecular biomarkers in clinical practice. However, lncRNA studies in breast cancer are limited in sample size and are restricted to the determination of their biological function, which represents an obstacle for its inclusion as molecular biomarkers of clinical utility. Nevertheless, due to their expression specificity among diseases, such as cancer, and their stability in body fluids, lncRNAs are promising molecular biomarkers that could improve the reliability, sensitivity, and specificity of molecular techniques used in clinical diagnosis. The development of lncRNA-based diagnostics and lncRNA-based therapeutics will be useful in routine medical practice to improve patient clinical management and quality of life.
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Affiliation(s)
- Cristian Arriaga-Canon
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Laura Contreras-Espinosa
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio D, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, Mexico City C.P. 04510, Mexico
| | - Sergio Aguilar-Villanueva
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Enrique Bargalló-Rocha
- Departamento de Tumores Mamarios, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - José Antonio García-Gordillo
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Paula Cabrera-Galeana
- Departamento de Oncología Médica de Mama, Instituto Nacional de Cancerología, Tlalpan, Mexico City C.P. 14080, Mexico
| | - Clementina Castro-Hernández
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
| | | | - L A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, UNAM, Avenida San Fernando No. 22 Col. Sección XVI, Tlalpan, Mexico City C.P. 14080, Mexico
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey C.P. 64710, Mexico
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27
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Zhang Z, Lu YX, Liu F, Sang L, Shi C, Xie S, Bian W, Yang JC, Yang Z, Qu L, Chen SY, Li J, Yang L, Yan Q, Wang W, Fu P, Shao J, Li X, Lin A. lncRNA BREA2 promotes metastasis by disrupting the WWP2-mediated ubiquitination of Notch1. Proc Natl Acad Sci U S A 2023; 120:e2206694120. [PMID: 36795754 PMCID: PMC9974429 DOI: 10.1073/pnas.2206694120] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/12/2023] [Indexed: 02/17/2023] Open
Abstract
Notch has been implicated in human cancers and is a putative therapeutic target. However, the regulation of Notch activation in the nucleus remains largely uncharacterized. Therefore, characterizing the detailed mechanisms governing Notch degradation will identify attractive strategies for treating Notch-activated cancers. Here, we report that the long noncoding RNA (lncRNA) BREA2 drives breast cancer metastasis by stabilizing the Notch1 intracellular domain (NICD1). Moreover, we reveal WW domain containing E3 ubiquitin protein ligase 2 (WWP2) as an E3 ligase for NICD1 at K1821 and a suppressor of breast cancer metastasis. Mechanistically, BREA2 impairs WWP2-NICD1 complex formation and in turn stabilizes NICD1, leading to Notch signaling activation and lung metastasis. BREA2 loss sensitizes breast cancer cells to inhibition of Notch signaling and suppresses the growth of breast cancer patient-derived xenograft tumors, highlighting its therapeutic potential in breast cancer. Taken together, these results reveal the lncRNA BREA2 as a putative regulator of Notch signaling and an oncogenic player driving breast cancer metastasis.
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Affiliation(s)
- Zhen Zhang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang310058, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang310058, China
| | - Yun-xin Lu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong510060, China
| | - Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang310058, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang310058, China
| | - Lingjie Sang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Shaofang Xie
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang310024, China
| | - Weixiang Bian
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang310024, China
| | - Jie-cheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Zuozhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Shi-yi Chen
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Jun Li
- Department of Pathology School of Medicine, The First Affiliated Hospital Zhejiang University, Hangzhou, Zhejiang310003, China
| | - Lu Yang
- Department of Radiotherapy, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, School of Medicine South China University of Technology, Guangzhou510080, China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, CA92697
| | - Peifen Fu
- Department of Breast Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang310003, China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
| | - Xu Li
- Key Laboratory of Structural Biology of Zhejiang Province, Westlake Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou, Zhejiang310024, China
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang310058, China
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang310058, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang310058, China
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang310003, China
- International School of Medicine, International Institutes of Medicine, The 4th Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, Zhejiang322000, China
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28
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Singh DD, Lee HJ, Yadav DK. Recent Clinical Advances on Long Non-Coding RNAs in Triple-Negative Breast Cancer. Cells 2023; 12:cells12040674. [PMID: 36831341 PMCID: PMC9955037 DOI: 10.3390/cells12040674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a more aggressive type of breast cancer due to its heterogeneity and complex molecular mechanisms. TNBC has a high risk for metastasis, and it is difficult to manage clinical conditions of the patients. Various investigations are being conducted to overcome these challenges using RNA, DNA, and proteins for early diagnosis and treatment. Recently, long non-coding RNAs (lncRNAs) have emerged as a novel target to treat the multistep process of TNBC. LncRNAs regulate epigenetic expression levels, cell proliferation and apoptosis, and tumour invasiveness and metastasis. Thus, lncRNA-based early diagnosis and treatment options could be helpful, especially for patients with severe TNBC. lncRNAs are expressed in a highly specific manner in cells and tissues and are involved in TNBC progression and development. lncRNAs could be used as sensitive and specific targets for diagnosis, treatment, and monitoring of patients with TNBC. Therefore, the exploration of novel diagnostic and prognostic biomarkers is of extreme importance. Here, we discuss the molecular advances on lncRNA regulation of TNBC and lncRNA-based early diagnosis, treatment, and drug resistance.
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Affiliation(s)
- Desh Deepak Singh
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India
| | - Hae-Jeung Lee
- Department of Food and Nutrition, College of Bionano Technology, Gachon University, Seongnam-si 13120, Republic of Korea
- Correspondence: (H.-J.L.); (D.K.Y.)
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29
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Zhang K, Ni X, Ma X, Sun R, Qiu J, Luo C. LINC01012 upregulation promotes cervical cancer proliferation and migration via downregulation of CDKN2D. Oncol Lett 2023; 25:124. [PMID: 36844616 PMCID: PMC9950337 DOI: 10.3892/ol.2023.13710] [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: 08/21/2022] [Accepted: 01/12/2023] [Indexed: 02/10/2023] Open
Abstract
The incidence and mortality of cervical cancer (CC) rank fourth among those of all gynecological malignancies. Long noncoding RNAs (lncRNAs) serve important roles in the development of various types of cancer. The aim of the present study was to explore the role of lncRNAs in the pathogenesis of CC and to identify novel therapeutic targets. LINC01012 was identified to be associated with an unfavorable prognosis in patients with CC based on bioinformatics analyses. Upregulated LINC01012 expression was further verified in CC samples and in cervical intraepithelial neoplasia grade 3 tissues compared with healthy tissues using reverse transcription-quantitative PCR. Functionally, following transfection with LINC01012 short hairpin RNA (sh-LINC01012), the proliferation and migration of CC cell lines were examined using 5-ethynyl-2'-deoxyuridine staining, colony formation and Transwell assays, which demonstrated that knockdown of LINC01012 in CC cells suppressed cell proliferation and migration in vitro and tumor growth in an in vivo xenograft model. The potential mechanisms of LINC01012 were further explored. A negative association between LINC01012 and cyclin dependent kinase inhibitor 2D (CDKN2D) was also identified based on The Cancer Genome Atlas data and this was confirmed using western blotting and rescue experiments. Consistently, knockdown of LINC01012 in CC cells upregulated CDKN2D expression. The inhibition of proliferation and migration of CC cells following transfection with sh-LINC01012 was reversed following co-transfection of sh-LINC01012 and CDKN2D short hairpin RNA. These findings suggested that upregulated LINC01012 expression in CC may stimulate the proliferation and migration of cancer cells, thus promoting CC progression via downregulation of CDKN2D.
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Affiliation(s)
- Keyi Zhang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China
| | - Xiao Ni
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China
| | - Xiaoling Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China
| | - Rui Sun
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China
| | - Jiangnan Qiu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China
| | - Chengyan Luo
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu 210036, P.R. China,Correspondence to: Professor Chengyan Luo, Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, 368 North Jiangdong Road, Nanjing, Jiangsu 210036, P.R. China, E-mail:
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30
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Long noncoding RNA-mediated activation of PROTOR1/PRR5-AKT signaling shunt downstream of PI3K in triple-negative breast cancer. Proc Natl Acad Sci U S A 2022; 119:e2203180119. [PMID: 36269860 PMCID: PMC9618063 DOI: 10.1073/pnas.2203180119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phosphoinositide 3-kinase (PI3K) pathway represents the most hyperactivated oncogenic pathway in triple-negative breast cancer (TNBC), a highly aggressive tumor subtype encompassing ∼15% of breast cancers and which possesses no targeted therapeutics. Despite critical contributions of its signaling arms to disease pathogenesis, PI3K pathway inhibitors have not achieved expected clinical responses in TNBC, owing largely to a still-incomplete understanding of the compensatory cascades that operate downstream of PI3K. Here, we investigated the contributions of long noncoding RNAs (lncRNAs) to PI3K activities in clinical and experimental TNBC and discovered a prominent role for LINC01133 as a PI3K-AKT signaling effector. We found that LINC01133 exerted protumorigenic roles in TNBC and that it governed a previously undescribed mTOR Complex 2 (mTORC2)-dependent pathway that activated AKT in a PI3K-independent manner. Mechanistically, LINC01133 induced the expression of the mTORC2 component PROTOR1/PRR5 by competitively coupling away its negative messenger RNA (mRNA) regulator, the heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1). PROTOR1/PRR5 in turn was sufficient and necessary for LINC01133-triggered functions, casting previously unappreciated roles for this Rictor-binding protein in cellular signaling and growth. Notably, LINC01133 antagonism undermined cellular growth, and we show that the LINC01133-PROTOR1/PRR5 pathway was tightly associated with TNBC poor patient survival. Altogether, our findings uncovered a lncRNA-driven signaling shunt that acts as a critical determinant of malignancy downstream of the PI3K pathway and as a potential RNA therapeutic target in clinical TNBC management.
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31
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QU L, HE X, TANG Q, FAN X, LIU J, LIN A. Iron metabolism, ferroptosis, and lncRNA in cancer: knowns and unknowns. J Zhejiang Univ Sci B 2022; 23:844-862. [PMID: 36226538 PMCID: PMC9561407 DOI: 10.1631/jzus.b2200194] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Cancer cells undergo substantial metabolic alterations to sustain increased energy supply and uncontrolled proliferation. As an essential trace element, iron is vital for many biological processes. Evidence has revealed that cancer cells deploy various mechanisms to elevate the cellular iron concentration to accelerate proliferation. Ferroptosis, a form of cell death caused by iron-catalyzed excessive peroxidation of polyunsaturated fatty acids (PUFAs), is a promising therapeutic target for therapy-resistant cancers. Previous studies have reported that long noncoding RNA (lncRNA) is a group of critical regulators involved in modulating cell metabolism, proliferation, apoptosis, and ferroptosis. In this review, we summarize the associations among iron metabolism, ferroptosis, and ferroptosis-related lncRNA in tumorigenesis. This information will help deepen understanding of the role of lncRNA in iron metabolism and raise the possibility of targeting lncRNA and ferroptosis in cancer combination therapy.
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Affiliation(s)
- Lei QU
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Xinyu HE
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Qian TANG
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining314400, China,Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou310006, China,College of Medicine and Veterinary Medicine, the University of Edinburgh, EdinburghEH16 4SB, UK,Biomedical and Health Translational Research Center of Zhejiang Province, Haining314400, China
| | - Xiao FAN
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China
| | - Jian LIU
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining314400, China,Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People’s Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou310006, China,College of Medicine and Veterinary Medicine, the University of Edinburgh, EdinburghEH16 4SB, UK,Biomedical and Health Translational Research Center of Zhejiang Province, Haining314400, China,Jian LIU,
| | - Aifu LIN
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou310058, China,Cancer Center, Zhejiang University, Hangzhou310058, China,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Hangzhou310058, China,Breast Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310003, China,International School of Medicine, International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu322000, China,ZJU-QILU Joint Research Institute, Hangzhou310058, China,Aifu LIN,
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32
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Li R, Wang X, Zhu C, Wang K. lncRNA PVT1: a novel oncogene in multiple cancers. Cell Mol Biol Lett 2022; 27:84. [PMID: 36195846 PMCID: PMC9533616 DOI: 10.1186/s11658-022-00385-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 09/07/2022] [Indexed: 12/01/2022] Open
Abstract
Long noncoding RNAs are involved in epigenetic gene modification, including binding to the chromatin rearrangement complex in pre-transcriptional regulation and to gene promoters in gene expression regulation, as well as acting as microRNA sponges to control messenger RNA levels in post-transcriptional regulation. An increasing number of studies have found that long noncoding RNA plasmacytoma variant translocation 1 (PVT1) plays an important role in cancer development. In this review of a large number of studies on PVT1, we found that PVT1 is closely related to tumor onset, proliferation, invasion, epithelial–mesenchymal transformation, and apoptosis, as well as poor prognosis and radiotherapy and chemotherapy resistance in some cancers. This review comprehensively describes PVT1 expression in various cancers and presents novel approaches to the diagnosis and treatment of cancer.
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Affiliation(s)
- Ruiming Li
- Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Xia Wang
- Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China
| | - Chunming Zhu
- Department of Family Medicine, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
| | - Kefeng Wang
- Department of Urology, Shengjing Hospital of China Medical University, #36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, China.
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33
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Agostini M, Mancini M, Candi E. Long non-coding RNAs affecting cell metabolism in cancer. Biol Direct 2022; 17:26. [PMID: 36182907 PMCID: PMC9526990 DOI: 10.1186/s13062-022-00341-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 11/27/2021] [Indexed: 11/10/2022] Open
Abstract
Metabolic reprogramming is commonly recognized as one important hallmark of cancers. Cancer cells present significant alteration of glucose metabolism, oxidative phosphorylation, and lipid metabolism. Recent findings demonstrated that long non-coding RNAs control cancer development and progression by modulating cell metabolism. Here, we give an overview of breast cancer metabolic reprogramming and the role of long non-coding RNAs in driving cancer-specific metabolic alteration.
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Affiliation(s)
- Massimiliano Agostini
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy
| | - Mara Mancini
- IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy
| | - Eleonora Candi
- Department Experimental Medicine, University of Rome "Tor Vergata", TOR, Via Montpellier,1, 00133, Rome, Italy. .,IDI-IRCCS, Via Monti di Creta 104, 00166, Rome, Italy.
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34
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Liu F, Tian T, Zhang Z, Xie S, Yang J, Zhu L, Wang W, Shi C, Sang L, Guo K, Yang Z, Qu L, Liu X, Liu J, Yan Q, Ju HQ, Wang W, Piao HL, Shao J, Zhou T, Lin A. Long non-coding RNA SNHG6 couples cholesterol sensing with mTORC1 activation in hepatocellular carcinoma. Nat Metab 2022; 4:1022-1040. [PMID: 35995997 DOI: 10.1038/s42255-022-00616-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Cholesterol contributes to the structural basis of biological membranes and functions as a signaling molecule, whose dysregulation has been associated with various human diseases. Here, we report that the long non-coding RNA (lncRNA) SNHG6 increases progression from non-alcoholic fatty liver disease (NAFLD) to hepatocellular carcinoma (HCC) by modulating cholesterol-induced mTORC1 activation. Mechanistically, cholesterol binds ER-anchored FAF2 protein to promote the formation of a SNHG6-FAF2-mTOR complex. As a putative cholesterol effector, SNHG6 enhances cholesterol-dependent mTORC1 lysosomal recruitment and activation via enhancing FAF2-mTOR interaction at ER-lysosome contacts, thereby coordinating mTORC1 kinase cascade activation with cellular cholesterol biosynthesis in a self-amplified cycle to accelerate cholesterol-driven NAFLD-HCC development. Notably, loss of SNHG6 inhibits mTORC1 signaling and impairs growth of patient-derived xenograft liver cancer tumors, identifyifng SNHG6 as a potential target for liver cancer treatment. Together, our findings illustrate the crucial role of organelle-associated lncRNA in organelle communication, nutrient sensing, and kinase cascades.
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Affiliation(s)
- Fangzhou Liu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Tian Tian
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Zhen Zhang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, China
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jiecheng Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Linyu Zhu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wen Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Chengyu Shi
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lingjie Sang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Kaiqiang Guo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Zuozhen Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiangrui Liu
- Cancer Center, Zhejiang University, Hangzhou, China
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, China
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Haining, China
| | - Qingfeng Yan
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Huai-Qiang Ju
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
| | - Hai-Long Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jianzhong Shao
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, China.
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, China.
| | - Aifu Lin
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
- Cancer Center, Zhejiang University, Hangzhou, China.
- Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang, China.
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- International School of Medicine, International Institutes of Medicine, The 4th Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.
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35
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Kerr AG, Wang Z, Wang N, Kwok KHM, Jalkanen J, Ludzki A, Lecoutre S, Langin D, Bergo MO, Dahlman I, Mim C, Arner P, Gao H. The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase. Nat Commun 2022; 13:2958. [PMID: 35618718 PMCID: PMC9135762 DOI: 10.1038/s41467-022-30620-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 05/04/2022] [Indexed: 12/27/2022] Open
Abstract
The pleiotropic function of long noncoding RNAs is well recognized, but their direct role in governing metabolic homeostasis is less understood. Here, we describe a human adipocyte-specific lncRNA, ADIPINT, that regulates pyruvate carboxylase, a pivotal enzyme in energy metabolism. We developed an approach, Targeted RNA-protein identification using Orthogonal Organic Phase Separation, which identifies that ADIPINT binds to pyruvate carboxylase and validated the interaction with electron microscopy. ADIPINT knockdown alters the interactome and decreases the abundance and enzymatic activity of pyruvate carboxylase in the mitochondria. Reduced ADIPINT or pyruvate carboxylase expression lowers adipocyte lipid synthesis, breakdown, and lipid content. In human white adipose tissue, ADIPINT expression is increased in obesity and linked to fat cell size, adipose insulin resistance, and pyruvate carboxylase activity. Thus, we identify ADIPINT as a regulator of lipid metabolism in human white adipocytes, which at least in part is mediated through its interaction with pyruvate carboxylase. Adipocyte-expressed long non-coding RNAs (lncRNAs) have been shown to regulate the transcription of genes involved in lipid metabolism. Here the authors describe a human adipocyte-specific lncRNA, ADIPINT, which regulates lipid metabolism in white adipocytes in part through its interaction with the metabolic enzyme pyruvate carboxylase.
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Affiliation(s)
- Alastair G Kerr
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Zuoneng Wang
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute, Stockholm, Sweden
| | - Na Wang
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Kelvin H M Kwok
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
| | - Jutta Jalkanen
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Alison Ludzki
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Simon Lecoutre
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Dominique Langin
- Institute of Metabolic and Cardiovascular Diseases (I2MC), Institut National de la Santé et de la Recherche Médicale (Inserm), Université de Toulouse, UPS, UMR1297, Toulouse, France.,Department of Biochemistry, Toulouse University Hospitals, CHU Toulouse, Toulouse, France
| | - Martin O Bergo
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
| | - Ingrid Dahlman
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden
| | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute, Stockholm, Sweden
| | - Peter Arner
- Department of Medicine (H7), Karolinska Institutet, Karolinska University Hospital Huddinge, Huddinge, 141 86, Sweden.
| | - Hui Gao
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden.
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Zhuo Y, Li S, Hu W, Zhang Y, Shi Y, Zhang F, Zhang J, Wang J, Liao M, Chen J, Qian H, Li D, Sun C. Targeting SNORA38B attenuates tumorigenesis and sensitizes immune checkpoint blockade in non-small cell lung cancer by remodeling the tumor microenvironment via regulation of GAB2/AKT/mTOR signaling pathway. J Immunother Cancer 2022; 10:e004113. [PMID: 35577506 PMCID: PMC9115109 DOI: 10.1136/jitc-2021-004113] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2022] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Non-coding RNAs (ncRNAs), including small nucleolar RNAs (snoRNAs), are widely involved in the physiological and pathological processes of human beings. While up to date, although considerable progress has been achieved in ncRNA-related pathogenesis of non-small cell lung cancer (NSCLC), the underlying mechanisms and biological significance of snoRNAs in NSCLC still need to be further clarified. METHODS Quantitative real-time polymerase chain reaction or RNAscope was performed to verify the expression of Small Nucleolar RNA, H/ACA Box 38B (SNORA38B) in NSCLC cell lines or clinical samples. BALB/c nude mice xenograft model or C57BL/6J mice syngeneic tumor model were estimated to detect the effects of SNORA38B in tumor growth or tumor immune microenvironment in vivo. Cytometry by time of flight, enzyme-linked immunosorbent assay and flow cytometry assay were conducted to clarify the effects and mechanisms of SNORA38B-mediated tumor immunosuppressive microenvironment. The binding activity between SNORA38B and E2F transcription factor 1(E2F1) was detected by RNA immunoprecipitation and RNA pull-down assays. Then, bioinformatics analysis and chromatin immunoprecipitation were utilized to demonstrate the regulation of GRB2-associated-binding protein 2 (GAB2) by E2F1. Moreover, the combinatorial treatment of SNORA38B locked nucleic acid (LNA) and immune checkpoint blockade (ICB) was used to treat murine Lewis lung carcinoma-derived tumor burden C57BL/6J mice to clarify the effectiveness of targeting SNORA38B in NSCLC immunotherapy. RESULTS SNORA38B was found highly expressed in NSCLC tissues and cell lines, and associated with worse prognosis. Further results showed that SNORA38B functioned as an oncogene via facilitating cell proliferation, migration, invasion, and inhibiting cell apoptosis in vitro and promoting tumorigenesis of NSCLC cells in vivo. SNORA38B could also recruit the CD4+FOXP3+ regulatory T cells by triggering tumor cells to secrete interleukin 10, which in turn reduced the infiltration of CD3+CD8+ T cells in NSCLC tumor microenvironment (TME), favoring tumor progression and poorer immune efficacy. Mechanistically, SNORA38B mainly distributed in the nucleus, and promoted NSCLC progression by regulating GAB2 transcription to activate protein kinase B (AKT)/mammalian target of rapamycin (mTOR) pathway through directly binding with E2F1. Moreover, we found that SNORA38B LNAs were able to ameliorate CD3+CD8+ T cell infiltration in TME, which sensitized NSCLC to the treatment of ICB. CONCLUSIONS In conclusion, our data demonstrated that SNORA38B functioned as an oncogene in NSCLC both in vitro and in vivo at least in part by regulating the GAB2/AKT/mTOR pathway via directly binding to E2F1. SNORA38B could also sensitize NSCLC to immunotherapy, which may be a critical therapeutic target for NSCLC.
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Affiliation(s)
- Yue Zhuo
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Shujun Li
- Department of Physical Examination, Wuhan Hospital for the Prevention and Treatment of Occupational Diseases, Wuhan, Hubei, People's Republic of China
| | - Wei Hu
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, Shanghai, China
| | - Yu Zhang
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Yufan Shi
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Faxue Zhang
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Jian Zhang
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Juan Wang
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Meijuan Liao
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Jiahao Chen
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Huiling Qian
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Dejia Li
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Chengcao Sun
- Department of Occupational and Environmental Health, Wuhan University, Wuhan, Hubei, People's Republic of China
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Sang L, Yang L, Ge Q, Xie S, Zhou T, Lin A. Subcellular distribution, localization, and function of noncoding RNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1729. [PMID: 35413151 DOI: 10.1002/wrna.1729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/06/2022]
Abstract
Eukaryotic cells contain subcellular organelles with spatiotemporal regulation to coordinate various biochemical reactions. The various organelles perform their essential biological functions by employing specific biomolecules, including nucleic acids. Recent studies have revealed that noncoding RNAs (ncRNAs) are highly compartmentalized in cells and that their spatial distribution is intimately related to their functions. Dysregulation of subcellular ncRNAs can disrupt cellular homeostasis and cause human diseases. Mitochondria are responsible for energy generation to fuel cell growth and proliferation. Therefore, identifying mitochondria-associated ncRNAs helps to reveal new regulatory mechanisms and physiological functions of mitochondria. In this review, we summarize the latest advances in subcellular ncRNAs derived from either the nuclear or mitochondrial genome. We also discuss available biological approaches for investigating organelle-specific ncRNAs. Exploring the distribution and function of subcellular ncRNAs may facilitate the understanding of endomembrane dynamics and provide potential strategies for clinical transformation. This article is categorized under: RNA Export and Localization > RNA Localization Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Lingjie Sang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Luojia Yang
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qiwei Ge
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shanshan Xie
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tianhua Zhou
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Gastroenterology, The Second Affiliated Hospital, School of Medicine and Institute of Gastroenterology, Zhejiang University, Hangzhou, Zhejiang, China.,Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Aifu Lin
- International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,Key Laboratory for Cell and Gene Engineering of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China
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Veeraraghavan VP, Mony U, Renu K, Mohan SK, Ammar RB, AlZahrani AM, Ahmed EA, Rajendran P. Effects of Polyphenols on ncRNAs in cancer - An update. Clin Exp Pharmacol Physiol 2022; 49:613-623. [PMID: 35275419 DOI: 10.1111/1440-1681.13641] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/24/2022] [Accepted: 03/02/2022] [Indexed: 11/27/2022]
Abstract
In recent years, oncotherapy has received considerable attention concerning plant polyphenols. Increasing evidence suggests that due to the efficiency of polyphenols, they may have antitumor effects in various cancers. However, their regulatory structures remain elusive. Long non-coding RNAs (LncRNAs) have been identified in the regulation of various forms of tumorigenesis and tumor development. Long non-coding RNAs (LncRNAs) have recently emerged as regulatory eukaryotic transcripts and therapeutic targets with important and diverse functions in health and diseases. LncRNAs may be associated with the initiation, development, and progression of cancer. This review summarizes the research on the modulatory effects of LncRNAs and their roles in mediating cellular processes. The mechanisms of action of polyphenols underlying their therapeutic effects on cancers are also discussed. Based on our review, polyphenols might facilitate a significant epigenetic modification as part of their tissue-/cell-related biological effects. This finding may be attributed to their interaction with cellular signaling pathways involved in chronic diseases. Certain LncRNAs might be the target of specific polyphenols, and some critical signaling processes involved in the intervention of cancers might mediate the therapeutic roles of polyphenols. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Ullas Mony
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Kaviyarasi Renu
- Centre of Molecular Medicine and Diagnostics (COMManD), Department of Biochemistry, Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
| | - Surapaneni Krishna Mohan
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills& Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai, Tamil Nadu, India
| | - Rebai Ben Ammar
- College of Science, Department of Biological Sciences, King Faisal University, Al Ahsa, Saudi Arabia.,Laboratory of Aromatic and Medicinal Plants, Center of Biotechnology, Technopole of Borj-Cedria PBOX 901, 2050, Hammam-Lif, Tunisia
| | - Abdullah M AlZahrani
- College of Science, Department of Biological Sciences, King Faisal University, Al Ahsa, Saudi Arabia
| | - Emad A Ahmed
- College of Science, Department of Biological Sciences, King Faisal University, Al Ahsa, Saudi Arabia.,Molecular Physiology Laboratory, Zoology department, Faculty of Science, Assiut University, Egypt
| | - Peramaiyan Rajendran
- College of Science, Department of Biological Sciences, King Faisal University, Al Ahsa, Saudi Arabia
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Xue ST, Zheng B, Cao SQ, Ding JC, Hu GS, Liu W, Chen C. Long non-coding RNA LINC00680 functions as a ceRNA to promote esophageal squamous cell carcinoma progression through the miR-423-5p/PAK6 axis. Mol Cancer 2022; 21:69. [PMID: 35255921 PMCID: PMC8900330 DOI: 10.1186/s12943-022-01539-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 02/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is a common invasive malignancy worldwide with poor clinical outcomes. Increasing amount of long non-coding RNAs (lncRNAs) have been reported to be involved in cancer development. However, lncRNAs that are functional in ESCC and the underlying molecular mechanisms remain largely unknown. Methods Transcriptomic analysis was performed to identify dysregulated lncRNAs in ESCC tissue samples. The high expression of LINC00680 in ESCC was validated by RT-qPCR, and the oncogenic functions of LINC00680 was investigated by cell proliferation, colony formation, migration and invasion assays in ESCC cells in vitro and xenografts derived from ESCC cells in mice. RNA-seq, competitive endogenous RNA (ceRNA) network analysis, and luciferase reporter assays were carried out to identify LINC00680 target genes and the microRNAs (miRNAs) bound to LINC00680. Antisense oligonucleotides (ASOs) were used for in vivo treatment. Results Transcriptome profiling revealed that a large number of lncRNAs was dysregulated in ESCC tissues. Notably, LINC00680 was highly expressed, and upregulation of LINC00680 was associated with large tumor size, advanced tumor stage, and poor prognosis. Functionally, knockdown of LINC00680 restrained ESCC cell proliferation, colony formation, migration, and invasion in vitro and inhibited tumor growth in vivo. Mechanistically, LINC00680 was found to act as a ceRNA by sponging miR-423-5p to regulate PAK6 (p21-activated kinase 6) expression in ESCC cells. The cell viability and motility inhibition induced by LINC00680 knockdown was significantly reversed upon PAK6 restoration and miR-423-5p inhibition. Furthermore, ASO targeting LINC00680 substantially suppressed ESCC both in vitro and in vivo. Conclusions An oncogenic lncRNA, LINC00680, was identified in ESCC, which functions as a ceRNA by sponging miR-423-5p to promote PAK6 expression and ESCC. LINC00680/miR-423-5p/PAK6 axis may serve as promising diagnostic and prognostic biomarkers and therapeutic targets for ESCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01539-3.
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Arora S, Khan S, Zaki A, Tabassum G, Mohsin M, Bhutto HN, Ahmad T, Fatma T, Syed MA. Integration of chemokine signaling with non-coding RNAs in tumor microenvironment and heterogeneity in different cancers. Semin Cancer Biol 2022; 86:720-736. [DOI: 10.1016/j.semcancer.2022.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/15/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
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Micropeptides translated from putative long non-coding RNAs. Acta Biochim Biophys Sin (Shanghai) 2022; 54:292-300. [PMID: 35538037 PMCID: PMC9827906 DOI: 10.3724/abbs.2022010] [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] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) transcribed in mammals and eukaryotes were thought to have no protein coding capability. However, recent studies have suggested that plenty of lncRNAs are mis-annotated and virtually contain coding sequences which are translated into functional peptides by ribosomal machinery, and these functional peptides are called micropeptides or small peptides. Here we review the rapidly advancing field of micropeptides translated from putative lncRNAs, describe the strategies for their identification, and elucidate their critical roles in many fundamental biological processes. We also discuss the prospects of research in micropeptides and the potential applications of micropeptides.
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Tyagi W, Pandey V, Pokharel YR. Membrane linked RNA glycosylation as new trend to envision epi-transcriptome epoch. Cancer Gene Ther 2022; 30:641-646. [PMID: 35136215 DOI: 10.1038/s41417-022-00430-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/09/2022]
Abstract
RNAs play several prominent roles in the cellular environment ranging from structural, messengers, translators, and effector molecules. RNA molecules while performing these roles are associated with several chemical modifications occurring post-transcriptionally, responsible for these supporting vital functions. The recent documentation of surface RNA modification with sialic acid residues has sparked advancement to the framework of RNA modifications. Glycan modification of surface RNA which was previously known to modify only proteins and lipids has opened new vistas to explore how these surface RNA modifications affect the cellular responses and phenotype. This paradigm shift in RNA biology with a vision of "glycans being all over the cells" has posed the field with a repertoire of questions and has given headway to the RNA world hypothesis. The review provides a comprehensive overview of glycoRNA discovery with a conceptual understanding of its previous underlying discoveries and their biological consequences with possible insights into the dynamic influence of this modification on their molecular versatility deciding cancer-immunology fate with potential implications of these glycosylation in cellular interaction, signaling, immune regulation, cancer evasion and proliferation.
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Affiliation(s)
- Witty Tyagi
- Molecular Oncology Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vivek Pandey
- Faculty of Life Science and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India
| | - Yuba Raj Pokharel
- Faculty of Life Science and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India.
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Lin X, Luo ML, Song E. Long non-coding RNA and non-coding nucleic acids: Signaling players in the networks of the tumor ecosystem. CELL INSIGHT 2022; 1:100004. [PMID: 37192988 PMCID: PMC10120285 DOI: 10.1016/j.cellin.2022.100004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 05/18/2023]
Abstract
Recent findings have revealed that human genome encodes tens of thousands long noncoding RNAs (lncRNAs), which play essential roles in broad spectrum of cellular processes. Emerging evidence has uncovered a new archetype of lncRNAs which functions as key components of cell signaling pathways. In this review, we describe how lncRNAs interact with proteins to regulate cancer intracellular signaling and intercellular signaling in the tumor microenvironment (TME), which enable cancer cells to acquire malignant hallmarks. Moreover, besides lncRNAs, non-coding nucleic acids, such as neutrophil extracellular trap-DNA (NET-DNA), endogenous DNA and RNA, can act as signal molecules to connect cells from distant organs and trigger systemic responses in the macroenvironment of tumor-bearing hosts. Overall, the widely observed dysregulation of non-coding nucleic acids in cancer alters signaling networks in the tumor ecosystem, providing a rich resource for the identification of cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Xiaorong Lin
- Diagnosis and Treatment Center of Breast Diseases, Shantou Central Hospital, Shantou, 515031, People's Republic of China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, People's Republic of China
| | - Man-Li Luo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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Mechanism of Gegen Qinlian Decoction Regulating ABTB1 Expression in Colorectal Cancer Metastasis Based on PI3K/AKT/FOXO1 Pathway. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8131531. [PMID: 35111848 PMCID: PMC8803423 DOI: 10.1155/2022/8131531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022]
Abstract
It was to investigate the role of Gegen Qinlian decoction (GQD) in the regulation of ABTB1 gene based on PI3K/AKT/FOXO1 signaling pathway in colorectal cancer (CRC) metastasis. In this study, 10 cases of the CRC mouse model were established by inoculating CT26 cells into the spleen of mice, which were divided into the experimental group and the control group, 5 cases in each group; the control group was intragastrically administered with normal saline 0.3 mL/d, and the experimental group was intragastrically administered with GQD 0.2 mL/d at a ratio of 0.2 g medicinal materials/10 g for 10 days and sacrificed, and pathological sections were made. The expression density of signaling pathway PI3K/AKT/FOXO1 as well as gene ABTB1 was detected in the sections of the two groups, and the mechanism of action of this gene in the two groups of mice was studied. It was found that the densities of p-PI3K, p-AKT, and p-FOXO1 in the experimental group of mice were 26.55 g/cm3, 70.2 g/cm3, and 24.36 g/cm3, respectively, which were significantly increased compared with the control group, P < 0.05; the density of ABTB1 was 35.4 g/cm3, which was significantly increased compared with the control group, P < 0.05; the proliferation and migration ability of CRC cells in the experimental group were significantly decreased, P < 0.05. GQD can promote the expression of ABTB1 by activating the PI3K/AKT/FOXO1 signaling pathway, in order to inhibit the proliferation and growth ability of CRC cells.
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Zhang Y, Lu P, Zhou Y, Zhang L. Inhibition of LINK-A lncRNA overcomes ibrutinib resistance in mantle cell lymphoma by regulating Akt/Bcl2 pathway. PeerJ 2021; 9:e12571. [PMID: 35003920 PMCID: PMC8686732 DOI: 10.7717/peerj.12571] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/08/2021] [Indexed: 12/15/2022] Open
Abstract
Ibrutinib, a bruton tyrosine kinase (BTK) inhibitor which suppresses B-cell receptor signaling, has remarkably improved the outcome of patients with mantle cell lymphoma (MCL). However, approximately 33% of MCL patients have primary Ibrutinib resistance, and acquired Ibrutinib resistance is nearly universal. Long intergenic non-coding RNA for kinase activation (LINK-A) exerts oncogenic role in different types of tumors, but the role of LINK-A in intrinsic ibrutinib resistance in MCL is still unclear. Here, LINK-A expression level was first assessed using quantitative Real-time PCR (qPCR) and immunofluorescence analysis in five MCL cell lines. The effect of LINK-A on regulating MCL cells viability and apoptosis was assayed using CCK-8 and TdT-mediated dUTP nick end labeling (TUNEL) assay, respectively. The association of LINK-A with AKT activation and B cell lymphoma 2 (Bcl2)expression was evaluated using qPCR and western blot analysis. We found that LINK-A level was elevated in Ibrutinib-resistant MCL cell lines (Mino, REC-1, MAVER-1, and Granta-519) compared to Ibrutinib-sensitive MCL cell lines (Jeko-1). Functionally, LINK-A overexpression in Jeko-1 cells enhanced cell viability and repressed Ibrutinib-induced cell apoptosis. LINK-A knockdown in MAVER-1 cells decreased cell viability and further accelerated Ibrutinib-induced cell apoptosis. LINK-A overexpression enhanced Bcl2 expression in Jeko-1 cells, and Bcl2 inhibition blocked the effect of LINK-A on increasing cell viability in the presence of Ibrutinib. On the contrary, LINK-A knockdown reduced Bcl2 expression in MAVER-1 cells, and Bcl2 overexpression damaged the role of LINK-A inhibition in regulating cell viability. Mechanistically, LINK-A positively regulated the activation of AKT signaling, and inhibition of AKT signaling destroyed LINK-A-induced increased of Bcl2 and resulted in a subsequent suppression of cell viability. Taken together, the current results demonstrate that LINK-A inhibition overcomes Ibrutinib resistance in MCL cells by regulating AKT/Bcl2 pathway.
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Affiliation(s)
- Ye Zhang
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Peng Lu
- Department of Neurosurgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Zhou
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lifei Zhang
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Han S, Li X, Wang K, Zhu D, Meng B, Liu J, Liang X, Jin Y, Liu X, Wen Q, Zhou L. PURPL represses autophagic cell death to promote cutaneous melanoma by modulating ULK1 phosphorylation. Cell Death Dis 2021; 12:1070. [PMID: 34759263 PMCID: PMC8581000 DOI: 10.1038/s41419-021-04362-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/18/2021] [Accepted: 10/27/2021] [Indexed: 01/26/2023]
Abstract
Uncontrolled overactivation of autophagy may lead to autophagic cell death, suppression of which is a pro-survival strategy for tumors. However, mechanisms involving key regulators in modulating autophagic cell death remain poorly defined. Here, we report a novel long noncoding RNA, p53 upregulated regulator of p53 levels (PURPL), functions as an oncogene to promote cell proliferation, colony formation, migration, invasiveness, and inhibits cell death in melanoma cells. Mechanistic studies showed that PURPL promoted mTOR-mediated ULK1 phosphorylation at Ser757 by physical interacting with mTOR and ULK1 to constrain autophagic response to avoid cell death. Loss of PURPL led to AMPK-mediated phosphorylation of ULK1 at Ser555 and Ser317 to over-activate autophagy and induce autophagic cell death. Our results identify PURPL as a key regulator to modulate the activity of autophagy initiation factor ULK1 to repress autophagic cell death in melanoma and may represent a potential intervention target for melanoma therapy.
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Affiliation(s)
- Shuo Han
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xue Li
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
- School of Clinical Medicine and Technology, Sichuan Vocational College of Health and Rehabilitation, Zigong, China
| | - Ke Wang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Dingheng Zhu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
| | - Bingyao Meng
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Jieyu Liu
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xiaoting Liang
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yi Jin
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Xingyuan Liu
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China
| | - Qian Wen
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, Guangdong, China.
| | - Liang Zhou
- Department of Toxicology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, China.
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The neurobiology of non-coding RNAs and Alzheimer's disease pathogenesis: Pathways, mechanisms and translational opportunities. Ageing Res Rev 2021; 71:101425. [PMID: 34384901 DOI: 10.1016/j.arr.2021.101425] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022]
Abstract
In the past two decades, advances in sequencing technology and analysis of the human and mouse genome have led to the discovery of many non-protein-coding RNAs (ncRNAs) including: microRNA, small-interfering RNAs, piwi-associated small RNAs, transfer RNA-derived small RNAs, long-non-coding RNAs and circular RNAs. Compared with healthy controls, levels of some ncRNAs are significantly altered in the central nervous system and blood of patients affected by neurodegenerative disorders like Alzheimer's disease (AD). Although the mechanisms are still not fully elucidated, studies have revealed that these highly conserved ncRNAs are important modulators of gene expression, amyloid-β production, tau phosphorylation, inflammation, synaptic plasticity and neuronal survival, all features considered central to AD pathogenesis. Despite considerable difficulties due to their large heterogeneity, and the complexity of their regulatory pathways, research in this rapidly growing field suggests that ncRNAs hold great potential as biomarkers and therapeutic targets against AD. Herein, we summarize the current knowledge regarding the neurobiology of ncRNA in the context of AD pathophysiology.
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Wang PS, Wang Z, Yang C. Dysregulations of long non-coding RNAs - The emerging "lnc" in environmental carcinogenesis. Semin Cancer Biol 2021; 76:163-172. [PMID: 33823237 PMCID: PMC8487435 DOI: 10.1016/j.semcancer.2021.03.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/26/2021] [Accepted: 03/28/2021] [Indexed: 02/09/2023]
Abstract
Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are more than 200 nucleotides in length and usually lack protein-coding capacity. LncRNAs play important roles in regulating gene expression as well as many aspects of normal physiological processes. Dysregulations of lncRNA expressions and functions are considered to be critically involved in the development and progression of many diseases especially cancer. The lncRNA research in the field of cancer biology over the past decade reveals that a large number of lncRNAs are dysregulated in various types of cancer and that dysregulated lncRNAs may play important roles in cancer initiation, metastasis and therapeutic responses. Metal carcinogens and other common environmental carcinogens such as polycyclic aromatic hydrocarbons, fine particular matters, cigarette smoke, ultraviolet and ionizing radiation are important cancer etiology factors. However, the mechanisms of how metal carcinogens and other common environmental carcinogen exposures initiate cancer and promote cancer progression remain largely unknown. Accumulating evidence show that exposure to metal carcinogens and other common environmental carcinogens dysregulate lncRNA expression in various model systems, which may offer novel mechanistic insights for environmental carcinogenesis. This review will first provide a brief introduction about lncRNA biology and the mechanisms of lncRNA functions, followed by summarizing and discussing recent studies about lncRNA dysregulation by metal carcinogen and other common environment carcinogen exposures and the potential roles of dysregulated lncRNAs in environmental carcinogenesis. A perspective for future studies in this emerging and important field is also presented.
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Affiliation(s)
- Po-Shun Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA
| | - Zhishan Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA
| | - Chengfeng Yang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, 44109, USA.
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Hudson QJ, Proestling K, Perricos A, Kuessel L, Husslein H, Wenzl R, Yotova I. The Role of Long Non-Coding RNAs in Endometriosis. Int J Mol Sci 2021; 22:11425. [PMID: 34768856 PMCID: PMC8583837 DOI: 10.3390/ijms222111425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 01/04/2023] Open
Abstract
Endometriosis is a chronic gynecological disorder affecting the quality of life and fertility of many women around the world. Heterogeneous and non-specific symptoms may lead to a delay in diagnosis, with treatment options limited to surgery and hormonal therapy. Hence, there is a need to better understand the pathogenesis of the disease to improve diagnosis and treatment. Long non-coding RNAs (lncRNAs) have been increasingly shown to be involved in gene regulation but remain relatively under investigated in endometriosis. Mutational and transcriptomic studies have implicated lncRNAs in the pathogenesis of endometriosis. Single-nucleotide polymorphisms (SNPs) in lncRNAs or their regulatory regions have been associated with endometriosis. Genome-wide transcriptomic studies have identified lncRNAs that show deregulated expression in endometriosis, some of which have been subjected to further experiments, which support a role in endometriosis. Mechanistic studies indicate that lncRNAs may regulate genes involved in endometriosis by acting as a molecular sponge for miRNAs, by directly targeting regulatory elements via interactions with chromatin or transcription factors or by affecting signaling pathways. Future studies should concentrate on determining the role of uncharacterized lncRNAs revealed by endometriosis transcriptome studies and the relevance of lncRNAs implicated in the disease by in vitro and animal model studies.
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Affiliation(s)
| | | | | | | | | | | | - Iveta Yotova
- Department of Obstetrics and Gynecology, Medical University of Vienna, Waehringer Guertel 18-20, A-1090 Vienna, Austria; (Q.J.H.); (K.P.); (A.P.); (L.K.); (H.H.); (R.W.)
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Wakatsuki S, Araki T. Novel Molecular Basis for Synapse Formation: Small Non-coding Vault RNA Functions as a Riboregulator of MEK1 to Modulate Synaptogenesis. Front Mol Neurosci 2021; 14:748721. [PMID: 34630040 PMCID: PMC8498202 DOI: 10.3389/fnmol.2021.748721] [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: 07/28/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Small non-coding vault RNAs (vtRNAs) have been described as a component of the vault complex, a hollow-and-barrel-shaped ribonucleoprotein complex found in most eukaryotes. It has been suggested that the function of vtRNAs might not be limited to simply maintaining the structure of the vault complex. Despite the increasing research on vtRNAs, little is known about their physiological functions. Recently, we have shown that murine vtRNA (mvtRNA) up-regulates synaptogenesis by activating the mitogen activated protein kinase (MAPK) signaling pathway. mvtRNA binds to and activates mitogen activated protein kinase 1 (MEK1), and thereby enhances MEK1-mediated extracellular signal-regulated kinase activation. Here, we introduce the regulatory mechanism of MAPK signaling in synaptogenesis by vtRNAs and discuss the possibility as a novel molecular basis for synapse formation.
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Affiliation(s)
- Shuji Wakatsuki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Toshiyuki Araki
- Department of Peripheral Nervous System Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
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