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Diao LT, Xie SJ, Xu WY, Zhang HH, Hou YR, Hu YX, Liang XX, Liang JB, Zhang Q, Xiao ZD. CRISPR/Cas13 sgRNA-Mediated RNA-RNA Interaction Mapping in Live Cells with APOBEC RNA Editing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2409004. [PMID: 39392366 DOI: 10.1002/advs.202409004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 09/18/2024] [Indexed: 10/12/2024]
Abstract
Current research on long non-coding RNA (lncRNA) has predominantly focused on identifying their protein partners and genomic binding sites, leaving their RNA partners largely unknown. To address this gap, the study has developed a method called sarID (sgRNA scaffold assisted RNA-RNA interaction detection), which integrates Cas13-based RNA targeting, sgRNA engineering, and proximity RNA editing to investigate lncRNA-RNA interactomes. By applying sarID to the lncRNA NEAT1, over one thousand previously unidentified binding transcripts are discovered. sarID is further expanded to investigate binders of XIST, MALAT1, NBR2, and DANCR, demonstrating its broad applicability in identifying lncRNA-RNA interactions. The findings suggest that lncRNAs may regulate gene expression by interacting with mRNAs, expanding their roles beyond known functions as protein scaffolds, miRNA sponges, or guides for epigenetic modulators. sarID has the potential to be adapted for studying other specific RNAs, providing a novel immunoprecipitation-free method for uncovering RNA partners and facilitating the exploration of the RNA-RNA interactome.
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Affiliation(s)
- Li-Ting Diao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | - Shu-Juan Xie
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | - Wan-Yi Xu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | | | - Ya-Rui Hou
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | - Yan-Xia Hu
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | | | | | - Qi Zhang
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
- Institute of Vaccine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
| | - Zhen-Dong Xiao
- Biotherapy Center, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
- Guangdong Provincial Key Laboratory of Liver Disease Research, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, P. R. China
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2
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Luo H, Chong H, Wang Y, Gao Y, Xie W, Wang D. Screening lncRNAs essential for cardiomyocyte proliferation by integrative profiling of lncRNAs and mRNAs associated with heart development. Exp Cell Res 2024; 442:114277. [PMID: 39383929 DOI: 10.1016/j.yexcr.2024.114277] [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: 07/23/2024] [Revised: 09/28/2024] [Accepted: 10/05/2024] [Indexed: 10/11/2024]
Abstract
BACKGROUND The proliferation potential of mammalian cardiomyocytes declines markedly shortly after birth. Both long non-coding RNAs (lncRNAs) and mRNAs demonstrate altered expression patterns during cardiac development. However, the role of lncRNAs in the cell cycle arrest of cardiomyocytes remains inadequately understood. METHOD The expression pattern of lncRNAs and mRNAs was analyzed in mouse hearts exhibiting varying regenerative potentials on postnatal days (P) 1, 7, and 28. Weighted correlation network analysis (WGCNA) was employed to elucidate the co-expression relationship between lncRNAs and mRNAs. Protein-protein interaction (PPI) network was built using the STRING database, and hub lncRNAs were identified by CytoHubba. Molecular Complex Detection (MCODE) was used to screen core modules of the PPI network in Cytoscape. Upstream lncRNAs and miRNAs which may regulate mRNAs were predicted using miRTarBase and AnnoLnc2, respectively. Myocardial infarction (MI) was induced by ligation of the left anterior descending coronary artery. RESULTS Compared with the P1 heart, 618 mRNAs and 414 lncRNAs displayed. transcriptional changes in the P7 heart, while 2358 mRNAs and 1290 lncRNAs showed from P7 to P28. Gene Ontology (GO) analysis revealed that module 1 in the both comparisons was enriched in the mitotic cell cycle process. 2810408I11Rik and 2010110K18Rik were identified as hub lncRNAs and their effects on the proliferation of cardiomyocytes were verified in vitro. Additionally, four lncRNA-miRNA-mRNA regulatory axes were predicted to explain the mechanism by which 2810408I11Rik and 2010110K18Rik regulate cardiomyocyte proliferation. Notably, the overexpression of 2810408I11Rik enhances cardiomyocyte proliferation and heart regeneration in the adult heart following MI. CONCLUSION This study systematically analyzed the landscape of lncRNAs and mRNAs at P1, P7, and P28. These findings may enhance our understanding of the framework for heart development and could have significant implications for heart regeneration.
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Affiliation(s)
- Hanqing Luo
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Hoshun Chong
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Yapeng Wang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Chinese Academy of Medical Science & Peking Union Medical College, China
| | - Yaxuan Gao
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Wei Xie
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Dongjin Wang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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Ranjan G, Scaria V, Sivasubbu S. Syntenic lncRNA locus exhibits DNA regulatory functions with sequence evolution. Gene 2024; 933:148988. [PMID: 39378975 DOI: 10.1016/j.gene.2024.148988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/12/2024] [Accepted: 10/04/2024] [Indexed: 10/10/2024]
Abstract
Syntenic long non-coding RNAs (lncRNAs) often show limited sequence conservation across species, prompting concern in the field. This study delves into functional signatures of syntenic lncRNAs between humans and zebrafish. Syntenic lncRNAs are highly expressed in zebrafish, with ∼90 % located near protein-coding genes, either in sense or antisense orientation. During early zebrafish development and in human embryonic stem cells (H1-hESC), syntenic lncRNA loci are enriched with cis-regulatory repressor signatures, influencing the expression of development-associated genes. In later zebrafish developmental stages and specific human cell lines, these syntenic lncRNA loci function as enhancers or transcription start sites (TSS) for protein-coding genes. Analysis of transposable elements (TEs) in syntenic lncRNA sequences revealed intriguing patterns: human lncRNAs are enriched in simple repeat elements, while their zebrafish counterparts show enrichment in LTR elements. This sequence evolution likely arises from post-rearrangement mutations that enhance DNA elements or cis-regulatory functions. It may also contribute to vertebrate innovation by creating novel transcription factor binding sites within the locus. This study highlights the conserved functionality of syntenic lncRNA loci through DNA elements, emphasizing their conserved roles across species despite sequence divergence.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi 110024, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Vishwanath Cancer Care Foundation, Mumbai, India.; Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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4
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Henninger JE, Young RA. An RNA-centric view of transcription and genome organization. Mol Cell 2024; 84:3627-3643. [PMID: 39366351 DOI: 10.1016/j.molcel.2024.08.021] [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: 05/07/2024] [Revised: 08/13/2024] [Accepted: 08/16/2024] [Indexed: 10/06/2024]
Abstract
Foundational models of transcriptional regulation involve the assembly of protein complexes at DNA elements associated with specific genes. These assemblies, which can include transcription factors, cofactors, RNA polymerase, and various chromatin regulators, form dynamic spatial compartments that contribute to both gene regulation and local genome architecture. This DNA-protein-centric view has been modified with recent evidence that RNA molecules have important roles to play in gene regulation and genome structure. Here, we discuss evidence that gene regulation by RNA occurs at multiple levels that include assembly of transcriptional complexes and genome compartments, feedback regulation of active genes, silencing of genes, and control of protein kinases. We thus provide an RNA-centric view of transcriptional regulation that must reside alongside the more traditional DNA-protein-centric perspectives on gene regulation and genome architecture.
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Affiliation(s)
- Jonathan E Henninger
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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5
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Ranjan G, Sehgal P, Scaria V, Sivasubbu S. SCAR-6 elncRNA locus epigenetically regulates PROZ and modulates coagulation and vascular function. EMBO Rep 2024:10.1038/s44319-024-00272-w. [PMID: 39358551 DOI: 10.1038/s44319-024-00272-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 09/03/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
In this study, we characterize a novel lncRNA-producing gene locus that we name Syntenic Cardiovascular Conserved Region-Associated lncRNA-6 (scar-6) and functionally validate its role in coagulation and cardiovascular function. A 12-bp deletion of the scar-6 locus in zebrafish (scar-6gib007Δ12/Δ12) results in cranial hemorrhage and vascular permeability. Overexpression, knockdown and rescue with the scar-6 lncRNA modulates hemostasis in zebrafish. Molecular investigation reveals that the scar-6 lncRNA acts as an enhancer lncRNA (elncRNA), and controls the expression of prozb, an inhibitor of factor Xa, through an enhancer element in the scar-6 locus. The scar-6 locus suppresses loop formation between prozb and scar-6 sequences, which might be facilitated by the methylation of CpG islands via the prdm14-PRC2 complex whose binding to the locus might be stabilized by the scar-6 elncRNA transcript. Binding of prdm14 to the scar-6 locus is impaired in scar-6gib007Δ12/Δ12 zebrafish. Finally, activation of the PAR2 receptor in scar-6gib007Δ12/Δ12 zebrafish triggers NF-κB-mediated endothelial cell activation, leading to vascular dysfunction and hemorrhage. We present evidence that the scar-6 locus plays a role in regulating the expression of the coagulation cascade gene prozb and maintains vascular homeostasis.
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Affiliation(s)
- Gyan Ranjan
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Paras Sehgal
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Vinod Scaria
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Vishwanath Cancer Care Foundation, Mumbai, India.
- Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110024, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
- Vishwanath Cancer Care Foundation, Mumbai, India.
- Dr. D. Y Patil Medical College, Hospital and Research Centre, Pune, India.
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6
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Pourmehran Y, Sadri F, Hosseini SF, Mohammadi Y, Rezaei Z. Exploring the influence of non-coding RNAs on NF-κB signaling pathway regulation in ulcerative colitis. Biomed Pharmacother 2024; 179:117390. [PMID: 39243424 DOI: 10.1016/j.biopha.2024.117390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 08/20/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024] Open
Abstract
The gastrointestinal tract is chronically inflamed in ulcerative colitis (UC), which has a complicated etiology involving immunological, environmental, and genetic factors. The inflammatory response that is typical of UC is significantly regulated via the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signaling pathway. Latest research has displayed that NF-κB signaling is controlled by three main types of non-coding RNAs (ncRNAs): circular RNAs (circRNAs), long non-coding RNAs (lncRNAs), and microRNAs (miRNAs). These ncRNAs can change the expression of key genes within the NF-κB pathway by acting as molecular sponges, transcriptional regulators, and epigenetic modifiers. This review synthesizes current knowledge on the functions by which ncRNAs modulate NF-κB signaling in UC, discusses their potential as biomarkers for disease prognosis and diagnosis, and explores their therapeutic potential. Understanding the intricate interactions between ncRNAs and NF-κB signaling may provide novel insights into UC pathogenesis and targeted therapeutic strategies.
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Affiliation(s)
- Yasaman Pourmehran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Farzad Sadri
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran; Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| | - Seyede Fatemeh Hosseini
- Faculty member, Tabas School of Nursing, Birjand University of medical sciences, Birjand, Iran
| | - Yaser Mohammadi
- Department of Biochemistry, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Rezaei
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran; Department of Biology, University of Sistan and Baluchestan, ZahedanIran.
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7
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Lin Y, Zhao W, Pu R, Lv Z, Xie H, Li Y, Zhang Z. Long non‑coding RNAs as diagnostic and prognostic biomarkers for colorectal cancer (Review). Oncol Lett 2024; 28:486. [PMID: 39185489 PMCID: PMC11342420 DOI: 10.3892/ol.2024.14619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
Colorectal cancer (CRC) ranks as the 3rd most common cancer globally and is the 2nd leading cause of cancer-related death. Owing to the lack of specific early symptoms and the limitations of existing early diagnostic methods, most patients with CRC are diagnosed at advanced stages. To overcome these challenges, researchers have increasingly focused on molecular biomarkers, with particular interest in long non-coding RNAs (lncRNAs). These non-protein-coding RNAs, which exceed 200 nucleotides in length, play critical roles in the development and progression of CRC. The stability and detectability of lncRNAs in the circulatory system make them promising candidate biomarkers. The analysis of circulating lncRNAs in peripheral blood represents a potential option for minimally invasive diagnostic tests based on liquid biopsy samples. The present review aimed to evaluate the efficacy of lncRNAs with altered expression levels in peripheral blood as diagnostic markers for CRC. Additionally, the clinical significance of lncRNAs as prognostic markers for this disease were summarized.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ruonan Pu
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
| | - Ying Li
- Department of Ultrasonography, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, Fujian 361009, P.R. China
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8
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Niazi F, Parker KA, Mason SJ, Singh S, Schiemann WP, Valadkhan S. Induction of Invasive Basal Phenotype in Triple-Negative Breast Cancers by Long Noncoding RNA BORG. Cancers (Basel) 2024; 16:3241. [PMID: 39335212 PMCID: PMC11430157 DOI: 10.3390/cancers16183241] [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: 06/21/2024] [Revised: 08/30/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND/OBJECTIVES Long noncoding RNAs (lncRNAs) are known to play key roles in breast cancers; however, detailed mechanistic studies of lncRNA function have not been conducted in large cohorts of breast cancer tumors, nor has inter-donor and inter-subtype variability been taken into consideration for these analyses. Here we provide the first identification and annotation of the human BORG lncRNA gene. METHODS/RESULTS Using multiple tumor cohorts of human breast cancers, we show that while BORG expression is strongly induced in breast tumors as compared to normal breast tissues, the extent of BORG induction varies widely between breast cancer subtypes and even between different tumors within the same subtype. Elevated levels of BORG in breast tumors are associated with the acquisition of core cancer aggression pathways, including those associated with basal tumor and pluripotency phenotypes and with epithelial-mesenchymal transition (EMT) programs. While a subset of BORG-associated pathways was present in high BORG-expressing tumors across all breast cancer subtypes, many were specific to tumors categorized as triple-negative breast cancers. Finally, we show that genes induced by heterologous expression of BORG in murine models of TNBC both in vitro and in vivo strongly overlap with those associated with high BORG expression levels in human TNBC tumors. CONCLUSION Our findings implicate human BORG as a novel driver of the highly aggressive basal TNBC tumor phenotype.
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Affiliation(s)
- Farshad Niazi
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA; (F.N.); (S.J.M.)
| | - Kimberly A. Parker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Sara J. Mason
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA; (F.N.); (S.J.M.)
| | - Salendra Singh
- Center for Immunotherapy and Precision Immuno-Oncology (CITI), Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - William P. Schiemann
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
| | - Saba Valadkhan
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA; (F.N.); (S.J.M.)
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA;
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9
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Yan Z, Chu W, Sheng Y, Tang K, Wang S, Liu Y, Wong WF. Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-Terminal Coding Sequences. ACS Synth Biol 2024; 13:2960-2968. [PMID: 39229974 DOI: 10.1021/acssynbio.4c00371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology codesigned few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then performs feature extraction using attention mechanisms, before constructing a time-series network for predicting gene expression intensity, and finally a direct search algorithm identifies the optimal NCS with limited training data. We took green fluorescent protein (GFP) expressed by Bacillus subtilis as a reporting protein of NCSs, and employed the fluorescence enhancement factor as the metric of NCS optimization. Within just six iterative experiments, our model generated an NCS (MLD62) that increased average GFP expression by 5.41-fold, outperforming the state-of-the-art NCS designs. Extending our findings beyond GFP, we showed that our engineered NCS (MLD62) can effectively boost the production of N-acetylneuraminic acid by enhancing the expression of the crucial rate-limiting GNA1 gene, demonstrating its practical utility. We have open-sourced our NCS expression database and experimental procedures for public use.
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Affiliation(s)
- Zhanglu Yan
- School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Weiran Chu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Yuhua Sheng
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Kaiwen Tang
- School of Computing, National University of Singapore, Singapore 117417, Singapore
| | - Shida Wang
- Department of Mathematics, National University of Singapore, Singapore 119077, Singapore
| | - Yanfeng Liu
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Weng-Fai Wong
- School of Computing, National University of Singapore, Singapore 117417, Singapore
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Zhao X, Zhao F, Yan L, Wu J, Fang Y, Wang C, Xin Z, Yang X. Long non-coding ribonucleic acid SNHG18 induced human granulosa cell apoptosis via disruption of glycolysis in ovarian aging. J Ovarian Res 2024; 17:185. [PMID: 39272131 PMCID: PMC11395969 DOI: 10.1186/s13048-024-01510-4] [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: 03/13/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND In-depth understanding of dynamic expression profiles of human granulosa cells (GCs) during follicular development will contribute to the diagnostic and targeted interventions for female infertility. However, genome-scale analysis of long non-coding ribonucleic acid (lncRNA) in GCs across diverse developmental stages is challenging. Meanwhile, further research is needed to determine how aberrant lncRNA expression participates in ovarian diseases. METHODS Granulosa cell-related lncRNAs data spanning five follicular development stages were retrieved and filtered from the NCBI dataset (GSE107746). Stage-specific lncRNA expression patterns and mRNA-lncRNA co-expression networks were identified with bioinformatic approaches. Subsequently, the expression pattern of SNHG18 was detected in GCs during ovarian aging. And SNHG18 siRNA or overexpression plasmids were transfected to SVOG cells in examining the regulatory roles of SNHG18 in GC proliferation and apoptosis. Moreover, whether PKCɛ/SNHG18 signaling take part in GC glycolysis via ENO1 were verified in SVOG cells. RESULTS We demonstrated that GC-related lncRNAs were specifically expressed across different developmental stages, and coordinated crucial biological functions like mitotic cell cycle and metabolic processes in the folliculogenesis. Thereafter, we noticed a strong correlation of PRKCE and SNHG18 expression in our analysis. With downregulated SNHG18 of GCs identified in the context of ovarian aging, SNHG18 knockdown could further induce cell apoptosis, retard cell proliferation and exacerbate DNA damage in SVOG cell. Moreover, downregulated PKCɛ/SNHG18 pathway interrupted the SVOG cell glycolysis by lowering the ENO1 expression. CONCLUSIONS Altogether, our results revealed that folliculogenesis-related lncRNA SNHG18 participated in the pathogenesis of ovarian aging, which may provide novel biomarkers for ovarian function and new insights for the infertility treatment.
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Affiliation(s)
- Xuehan Zhao
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Feiyan Zhao
- Department of Obstetrics and Gynecology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, 100020, China
| | - Long Yan
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Jiaqi Wu
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
- Key Laboratory of Organ Regeneration and Reconstruction, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ying Fang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Cong Wang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China
| | - Zhimin Xin
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
| | - Xiaokui Yang
- Department of Human Reproductive Medicine, Beijing Obstetrics and Gynecology Hospital, Beijing Maternal and Child Health Care Hospital, Capital Medical University, Beijing, 100026, China.
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11
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Díaz CR, Hernández-Huerta MT, Mayoral LPC, Villegas MEA, Zenteno E, Cruz MM, Mayoral EPC, Del Socorro Pina Canseco M, Andrade GM, Castellanos MÁ, Matías Salvador JM, Cruz Parada E, Martínez Barras A, Cruz Fernández JN, Scott-Algara D, Pérez-Campos E. Non-Coding RNAs and Innate Immune Responses in Cancer. Biomedicines 2024; 12:2072. [PMID: 39335585 PMCID: PMC11429077 DOI: 10.3390/biomedicines12092072] [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: 07/23/2024] [Revised: 08/27/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Non-coding RNAs (ncRNAs) and the innate immune system are closely related, acting as defense mechanisms and regulating gene expression and innate immunity. Both are modulators in the initiation, development and progression of cancer. We aimed to review the major types of ncRNAs, including small interfering RNAs (siRNAs), microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and long non-coding RNAs (lncRNAs), with a focus on cancer, innate immunity, and inflammation. We found that ncRNAs are closely related to innate immunity, epigenetics, chronic inflammation, and cancer and share properties such as inducibility, specificity, memory, and transfer. These similarities and interrelationships suggest that ncRNAs and modulators of trained immunity, together with the control of chronic inflammation, can be combined to develop novel therapeutic approaches for personalized cancer treatment. In conclusion, the close relationship between ncRNAs, the innate immune system, and inflammation highlights their importance in cancer pathways and their potential as targets for novel therapeutic strategies.
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Affiliation(s)
| | - María Teresa Hernández-Huerta
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCyT), Facultad de Medicina y Cirugía, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Laura Pérez-Campos Mayoral
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | | | - Edgar Zenteno
- Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Ciudad de México 04510, Mexico
| | | | - Eduardo Pérez-Campos Mayoral
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - María Del Socorro Pina Canseco
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Gabriel Mayoral Andrade
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | | | | | - Eli Cruz Parada
- Tecnológico Nacional de México/IT Oaxaca, Oaxaca 68030, Mexico
| | | | - Jaydi Nora Cruz Fernández
- Centro de Investigación, Facultad de Medicina UNAM-UABJO, Universidad Autónoma "Benito Juárez" de Oaxaca (UABJO), Oaxaca 68020, Mexico
| | - Daniel Scott-Algara
- Unité de Biologie Cellulaire des Lymphocytes and Direction of International Affairs, Institut Pasteur, 75015 Paris, France
| | - Eduardo Pérez-Campos
- Tecnológico Nacional de México/IT Oaxaca, Oaxaca 68030, Mexico
- Laboratorio de Patología Clínica "Dr. Eduardo Pérez Ortega", Oaxaca 68000, Mexico
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12
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Desideri F, Grazzi A, Lisi M, Setti A, Santini T, Colantoni A, Proietti G, Carvelli A, Tartaglia GG, Ballarino M, Bozzoni I. CyCoNP lncRNA establishes cis and trans RNA-RNA interactions to supervise neuron physiology. Nucleic Acids Res 2024; 52:9936-9952. [PMID: 38989616 PMCID: PMC11381359 DOI: 10.1093/nar/gkae590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/30/2024] [Accepted: 07/03/2024] [Indexed: 07/12/2024] Open
Abstract
The combination of morphogenetic and transcription factors together with the synergic aid of noncoding RNAs and their cognate RNA binding proteins contribute to shape motor neurons (MN) identity. Here, we extend the noncoding perspective of human MN, by detailing the molecular and biological activity of CyCoNP (as Cytoplasmic Coordinator of Neural Progenitors) a highly expressed and MN-enriched human lncRNA. Through in silico prediction, in vivo RNA purification and loss of function experiments followed by RNA-sequencing, we found that CyCoNP sustains a specific neuron differentiation program, required for the physiology of both neuroblastoma cells and hiPSC-derived MN, which mainly involves miR-4492 and NCAM1 mRNA. We propose a novel lncRNA-mediated 'dual mode' of action, in which CyCoNP acts in trans as a classical RNA sponge by sequestering miR-4492 from its pro-neuronal targets, including NCAM1 mRNA, and at the same time it plays an additional role in cis by interacting with NCAM1 mRNA and regulating the availability and localization of the miR-4492 in its proximity. These data highlight novel insights into the noncoding RNA-mediated control of human neuron physiology and point out the importance of lncRNA-mediated interactions for the spatial distribution of regulatory molecules.
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Affiliation(s)
- Fabio Desideri
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Alessandro Grazzi
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michela Lisi
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Adriano Setti
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Tiziana Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Colantoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Gabriele Proietti
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Andrea Carvelli
- Department of Neuroscience, The Scripps Research institute, La Jolla, CA 92037, USA
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genova, Italy
| | - Monica Ballarino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Irene Bozzoni
- Center for Life Nano- & Neuro-Science of Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy
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13
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Bedre R, Kavuri NR, Ramasamy M, Irigoyen S, Nelson A, Rajkumar MS, Mandadi K. Long intergenic non-coding RNAs modulate proximal protein-coding gene expression and tolerance to Candidatus Liberibacter spp. in potatoes. Commun Biol 2024; 7:1095. [PMID: 39242868 PMCID: PMC11379938 DOI: 10.1038/s42003-024-06763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 08/21/2024] [Indexed: 09/09/2024] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) are emerging as regulators of protein-coding genes (PCGs) in many plant and animal developmental processes and stress responses. In this study, we characterize the genome-wide lincRNAs in potatoes responsive to a vascular bacterial disease presumably caused by Candidatus Liberibacter solanacearum (CLso). Approximately 4397 lincRNAs were detected in healthy and infected potato plants at various stages of zebra chip (ZC) disease progression. Of them, ~65% (2844) were novel lincRNAs, and less than 1% (9) were orthologs of Arabidopsis and rice based on reciprocal BLAST analysis, suggesting species-specific expansion. Among the proximal lincRNAs within 50 kbp from a PCG, ~49% were transcribed from the same strand, while ~39% and ~15% followed convergent (head-to-head) and divergent (tail-to-tail) orientations, respectively. Approximately 30% (1308) were differentially expressed following CLso infection, with substantial changes occurring 21 days after infection (DAI). Weighted Gene Co-expression Network Analysis (WGCNA) of lincRNAs and PCGs identified 46 highly correlated lincRNA-PCG pairs exhibiting co-up or co-downregulation. Furthermore, overexpression of selected lincRNAs in transgenic potato hairy roots resulted in perturbation of neighboring PCG expression and conferred tolerance to CLso infection. Our results provide novel insights into potato lincRNAs' identity, expression dynamics, and functional relevance to CLso infection.
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Affiliation(s)
- Renesh Bedre
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Naga Rajitha Kavuri
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA
- Department of Plant Pathology and Microbiology, Texas A&M University System, College Station, TX, USA
| | - Manikandan Ramasamy
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Sonia Irigoyen
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Andrew Nelson
- Boyce Thompson Institute, Cornell University, Ithaca, NY, USA
| | - Mohan Singh Rajkumar
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Kranthi Mandadi
- Texas A&M AgriLife Research & Extension Center, Texas A&M University System, Weslaco, TX, USA.
- Department of Plant Pathology and Microbiology, Texas A&M University System, College Station, TX, USA.
- Institute for Advancing Health Through Agriculture, Texas A&M AgriLife, College Station, TX, USA.
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14
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Yoon JH, Byun HJ, Kim SY, Jung DH, Lee SK. Exosomal LINC00853 promotes progression of gastric cancer via the MAP17/PDZK1/AKT signaling pathway. Noncoding RNA Res 2024; 9:876-886. [PMID: 38586313 PMCID: PMC10997811 DOI: 10.1016/j.ncrna.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024] Open
Abstract
Although rare, there is ongoing research into biomarkers that predict the onset and recurrence of gastric cancer, particularly focusing on substances found in exosomes. Long non-coding RNAs (lncRNAs) have garnered attention for their potential in diagnosing gastric cancer. This study investigates the role of lncRNAs in gastric cancer, focusing on their presence in exosomes as potential biomarkers for the disease's onset and recurrence. We utilized the ArrayStar Human LncRNA array 2.0 to analyze lncRNA expression in tissues from early-stage gastric cancer patients. Our analysis highlighted LINC00853, which was significantly upregulated in cancer tissues and implicated in promoting epithelial-mesenchymal transition via the MAP17/PDZK1/AKT pathway. Functional studies on AGS and MKN74 gastric cancer cell lines demonstrated that LINC00853 facilitates cell proliferation, invasion, and migration. Additionally, RNA immunoprecipitation and electrophoretic mobility shift assays confirmed LINC00853 interaction with MAP17. Importantly, LINC00853 was also detected in exosomes from both patient samples and cell lines, and its downregulation led to decreased tumorigenicity in AGS cells. These findings suggest that both cellular and exosomal LINC00853 contribute to gastric cancer pathogenesis and may serve as valuable biomarkers for the disease.
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Affiliation(s)
| | | | - Seo Yeon Kim
- Department of Internal Medicine, Yonsei Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
| | - Da Hyun Jung
- Department of Internal Medicine, Yonsei Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
| | - Sang Kil Lee
- Department of Internal Medicine, Yonsei Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, South Korea
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15
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Camilleri-Robles C, Amador R, Tiebe M, Teleman A, Serras F, Guigó R, Corominas M. Long non-coding RNAs involved in Drosophila development and regeneration. NAR Genom Bioinform 2024; 6:lqae091. [PMID: 39157585 PMCID: PMC11327875 DOI: 10.1093/nargab/lqae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/12/2024] [Accepted: 07/19/2024] [Indexed: 08/20/2024] Open
Abstract
The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, gene expression, splicing, mRNA degradation, and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon cell death induction. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.
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Affiliation(s)
- Carlos Camilleri-Robles
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Raziel Amador
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marcel Tiebe
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ) Heidelberg, Division B140, 69120 Heidelberg, Germany
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
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16
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Wu Z, Zou J, Xie H, Wang J, Huang Y, Liu F, Xing C. LncRNA ALMS1-IT1 modulates ferroptosis and immune evasion in colorectal cancer through activating STAT3. J Cell Mol Med 2024; 28:e70103. [PMID: 39334527 PMCID: PMC11436373 DOI: 10.1111/jcmm.70103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 08/31/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Colorectal cancer (CRC) represents a significant malignancy within the digestive system, characterized by high incidence and mortality rates. In recent years, molecular targeted therapy has been introduced as a supplementary strategy in CRC management, complementing traditional modalities such as surgery, radiation and chemotherapy. The identification of novel therapeutic targets for CRC remains critically important. Ferroptosis, a unique form of programmed cell death distinct from apoptosis and necrosis, is characterized by cellular damage resulting from iron-induced lipid peroxidation, leading to cell death. This study utilizes a combination of bioinformatics analysis and clinical specimen validation to demonstrate that the long non-coding RNA (lncRNA) ALMS1-IT1 is significantly upregulated in CRC tissues and strongly associated with ferroptosis. Through a series of experimental investigations, we have determined that ALMS1-IT1 negatively regulates ferroptosis in CRC cells, thereby promoting cancer growth and metastasis, acting as an oncogenic factor. Furthermore, we explored the molecular interactions of ALMS1-IT1, revealing its role in activating STAT3 protein phosphorylation. This activation enhances the immune evasion capabilities of CRC cells. Rescue experiments indicated that STAT3 activation is essential for ALMS1-IT1's suppression of ferroptosis, immune evasion and oncogenic behaviour in CRC. Our findings underscore the critical biological role of ALMS1-IT1 in the progression of CRC and suggest its potential as a target for drug development.
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Affiliation(s)
- Zhaoying Wu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Junwei Zou
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Hao Xie
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Jie Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Yong Huang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Fei Liu
- Department of Gastroenterology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chungen Xing
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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17
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Stasevich EM, Simonova AV, Bogomolova EA, Murashko MM, Uvarova AN, Zheremyan EA, Korneev KV, Schwartz AM, Kuprash DV, Demin DE. Cut from the same cloth: RNAs transcribed from regulatory elements. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195049. [PMID: 38964653 DOI: 10.1016/j.bbagrm.2024.195049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/25/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
A certain degree of chromatin openness is necessary for the activity of transcription-regulating regions within the genome, facilitating accessibility to RNA polymerases and subsequent synthesis of regulatory element RNAs (regRNAs) from these regions. The rapidly increasing number of studies underscores the significance of regRNAs across diverse cellular processes and diseases, challenging the paradigm that these transcripts are non-functional transcriptional noise. This review explores the multifaceted roles of regRNAs in human cells, encompassing rather well-studied entities such as promoter RNAs and enhancer RNAs (eRNAs), while also providing insights into overshadowed silencer RNAs and insulator RNAs. Furthermore, we assess notable examples of shorter regRNAs, like miRNAs, snRNAs, and snoRNAs, playing important roles. Expanding our discourse, we deliberate on the potential usage of regRNAs as biomarkers and novel targets for cancer and other human diseases.
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Affiliation(s)
- E M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A V Simonova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Bogomolova
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - M M Murashko
- Laboratory of Intracellular Signaling in Health and Disease, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Moscow Center for Advanced Studies, Moscow, Russia
| | - A N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - E A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - K V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - A M Schwartz
- Department of Human Biology, University of Haifa, Haifa, Israel
| | - D V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - D E Demin
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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18
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Wen Y, Lei W, Zhang J, Liu Q, Li Z. Advances in understanding the role of lncRNA in ferroptosis. PeerJ 2024; 12:e17933. [PMID: 39210921 PMCID: PMC11361268 DOI: 10.7717/peerj.17933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
LncRNA is a type of transcript with a length exceeding 200 nucleotides, which was once considered junk transcript with no biological function during the transcription process. In recent years, lncRNA has been shown to act as an important regulatory factor at multiple levels of gene expression, affecting various programmed cell death modes including ferroptosis. Ferroptosis, as a new form of programmed cell death, is characterized by a deficiency of cysteine or inactivation of glutathione peroxidase, leading to depletion of glutathione, aggregation of iron ions, and lipid peroxidation. These processes are influenced by many physiological processes, such as the Nrf2 pathway, autophagy, p53 pathway and so on. An increasing number of studies have shown that lncRNA can block the expression of specific molecules through decoy effect, guide specific proteins to function, or promote interactions between molecules as scaffolds. These modes of action regulate the expression of key factors in iron metabolism, lipid metabolism, and antioxidant metabolism through epigenetic or genetic regulation, thereby regulating the process of ferroptosis. In this review, we snapshotted the regulatory mechanism of ferroptosis as an example, emphasizing the regulation of lncRNA on these pathways, thereby helping to fully understand the evolution of ferroptosis in cell fate.
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Affiliation(s)
- Yating Wen
- Pathogenic Biology Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Wenbo Lei
- Pathogenic Biology Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jie Zhang
- Pathogenic Biology Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Qiong Liu
- Pathogenic Biology Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Zhongyu Li
- Pathogenic Biology Institute, Hengyang Medical College, University of South China, Hengyang, Hunan, China
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19
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Refael T, Sudman M, Golan G, Pnueli L, Naik S, Preger-Ben Noon E, Henn A, Kaplan A, Melamed P. An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context. Cell Mol Life Sci 2024; 81:361. [PMID: 39158745 PMCID: PMC11335282 DOI: 10.1007/s00018-024-05398-7] [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: 05/23/2024] [Revised: 07/21/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Genome-wide studies have demonstrated regulatory roles for diverse non-coding elements, but their precise and interrelated functions have often remained enigmatic. Addressing the need for mechanistic insight, we studied their roles in expression of Lhb which encodes the pituitary gonadotropic hormone that controls reproduction. We identified a bi-directional enhancer in gonadotrope-specific open chromatin, whose functional eRNA (eRNA2) supports permissive chromatin at the Lhb locus. The central untranscribed region of the enhancer contains an iMotif (iM), and is bound by Hmgb2 which stabilizes the iM and directs transcription specifically towards the functional eRNA2. A distinct downstream lncRNA, associated with an inducible G-quadruplex (G4) and iM, also facilitates Lhb expression, following its splicing in situ. GnRH activates Lhb transcription and increased levels of all three RNAs, eRNA2 showing the highest response, while estradiol, which inhibits Lhb, repressed levels of eRNA2 and the lncRNA. The levels of these regulatory RNAs and Lhb mRNA correlate highly in female mice, though strikingly not in males, suggesting a female-specific function. Our findings, which shed new light on the workings of non-coding elements and non-canonical DNA structures, reveal novel mechanisms regulating transcription which have implications not only in the central control of reproduction but also for other inducible genes.
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Affiliation(s)
- Tal Refael
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Sudman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gil Golan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sujay Naik
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Ella Preger-Ben Noon
- Department of Genetics and Developmental Biology, The Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Arnon Henn
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Ariel Kaplan
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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20
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Maqbool M, Hussain MS, Shaikh NK, Sultana A, Bisht AS, Agrawal M. Noncoding RNAs in the COVID-19 Saga: An Untold Story. Viral Immunol 2024; 37:269-286. [PMID: 38968365 DOI: 10.1089/vim.2024.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024] Open
Affiliation(s)
- Mudasir Maqbool
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, India
| | - Md Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Nusrat K Shaikh
- Department of Quality Assurance, Smt. N. M. Padalia Pharmacy College, Ahmedabad, India
| | - Ayesha Sultana
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya University, Mangalore, India
| | - Ajay Singh Bisht
- Shri Guru Ram Rai University School of Pharmaceutical Sciences, Dehradun, India
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K. R. Mangalam University, Gurugram, India
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21
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Ma X, Mei S, Wuyun Q, Zhou L, Cai Z, Ding H, Yan J. Super-enhancer-driven LncRNA PPARα-seRNA exacerbates glucolipid metabolism and diabetic cardiomyopathy via recruiting KDM4B. Mol Metab 2024; 86:101978. [PMID: 38950776 PMCID: PMC11277359 DOI: 10.1016/j.molmet.2024.101978] [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: 04/07/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/03/2024] Open
Abstract
OBJECTIVE Aberrant glucolipid metabolism in the heart is a characteristic factor in diabetic cardiomyopathy (DbCM). Super-enhancers-driven noncoding RNAs (seRNAs) are emerging as powerful regulators in the progression of cardiac diseases. However, the functions of seRNAs in DbCM have not been fully elucidated. METHODS Super enhancers and their associated seRNAs were screened and identified by H3K27ac ChIP-seq data in the Encyclopedia of DNA Elements (ENCODE) dataset. A dual-luciferase reporter assay was performed to analyze the function of super-enhancers on the transcription of peroxisome proliferator-activated receptor α-related seRNA (PPARα-seRNA). A DbCM mouse model was established using db/db leptin receptor-deficient mice. Adeno-associated virus serotype 9-seRNA (AAV9-seRNA) was injected via the tail vein to evaluate the role of seRNA in DbCM. The underlying mechanism was explored through RNA pull-down, RNA and chromatin immunoprecipitation, and chromatin isolation by RNA purification. RESULTS PPARα-seRNA was regulated by super-enhancers and its levels were increased in response to high glucose and palmitic acid stimulation in cardiomyocytes. Functionally, PPARα-seRNA overexpression aggravated lipid deposition, reduced glucose uptake, and repressed energy production. In contrast, PPARα-seRNA knockdown ameliorated metabolic disorder in vitro. In vivo, overexpression of PPARα-seRNA exacerbated cardiac metabolic disorder and deteriorated cardiac dysfunction, myocardial fibrosis, and hypertrophy in DbCM. Mechanistically, PPARα-seRNA bound to the histone demethylase KDM4B (Lysine-specific demethylase 4B) and decreased H3K9me3 levels in the promoter region of PPARα, ultimately enhancing its transcription. CONCLUSIONS Our study revealed the pivotal function of a super-enhancer-driven long noncoding RNA (lncRNA), PPARα-seRNA, in the deterioration of cardiac function and the exacerbation of metabolic abnormalities in diabetic cardiomyopathy, which recruited KDM4B to the promoter region of PPARα and repression of its transcription. This suggests a promising therapeutic strategy for the treatment of DbCM.
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Affiliation(s)
- Xiaozhu Ma
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Shuai Mei
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Qidamugai Wuyun
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Li Zhou
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Ziyang Cai
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, China.
| | - Jiangtao Yan
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, China.
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22
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Rajabi D, Khanmohammadi S, Rezaei N. The role of long noncoding RNAs in amyotrophic lateral sclerosis. Rev Neurosci 2024; 35:533-547. [PMID: 38452377 DOI: 10.1515/revneuro-2023-0155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/18/2024] [Indexed: 03/09/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease with a poor prognosis leading to death. The diagnosis and treatment of ALS are inherently challenging due to its complex pathomechanism. Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides involved in different cellular processes, incisively gene expression. In recent years, more studies have been conducted on lncRNA classes and interference in different disease pathologies, showing their promising contribution to diagnosing and treating neurodegenerative diseases. In this review, we discussed the role of lncRNAs like NEAT1 and C9orf72-as in ALS pathogenesis mechanisms caused by mutations in different genes, including TAR DNA-binding protein-43 (TDP-43), fused in sarcoma (FUS), superoxide dismutase type 1 (SOD1). NEAT1 is a well-established lncRNA in ALS pathogenesis; hence, we elaborate on its involvement in forming paraspeckles, stress response, inflammatory response, and apoptosis. Furthermore, antisense lncRNAs (as-lncRNAs), a key group of transcripts from the opposite strand of genes, including ZEB1-AS1 and ATXN2-AS, are discussed as newly identified components in the pathology of ALS. Ultimately, we review the current standing of using lncRNAs as biomarkers and therapeutic agents and the future vision of further studies on lncRNA applications.
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Affiliation(s)
- Darya Rajabi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
| | - Shaghayegh Khanmohammadi
- School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children's Medical Center, No 63, Gharib Ave, Keshavarz Blv, Tehran, 1419733151, Iran
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Felestin St., Keshavarz Blvd., Tehran, 1416634793, Iran
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23
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Petroulia S, Hockemeyer K, Tiwari S, Berico P, Shamloo S, Banijamali SE, Vega-Saenz de Miera E, Gong Y, Thandapani P, Wang E, Schulz M, Tsirigos A, Osman I, Aifantis I, Imig J. CRISPR-inhibition screen for lncRNAs linked to melanoma growth and metastasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604899. [PMID: 39211068 PMCID: PMC11361079 DOI: 10.1101/2024.07.24.604899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Melanoma being one of the most common and deadliest skin cancers, has been rising since the past decade. Patients at advanced stages of the disease have very poor prognoses, as opposed to at the earlier stages. Nowadays the standard-of-care of advanced melanoma is resection followed by immune checkpoint inhibition based immunotherapy. However, a substantial proportion of patients either do not respond or develop resistances. This underscores a need for novel approaches and therapeutic targets as well as a better understanding of the mechanisms of melanoma pathogenesis. Long non-coding RNAs (lncRNAs) comprise a poorly characterized class of functional players and promising targets in promoting malignancy. Certain lncRNAs have been identified to play integral roles in melanoma progression and drug resistances, however systematic screens to uncover novel functional lncRNAs are scarce. Here, we profile differentially expressed lncRNAs in patient derived short-term metastatic cultures and BRAF-MEK-inhibition resistant cells. We conduct a focused growth-related CRISPR-inhibition screen of overexpressed lncRNAs, validate and functionally characterize lncRNA hits with respect to cellular growth, invasive capacities and apoptosis in vitro as well as the transcriptomic impact of our lead candidate the novel lncRNA XLOC_030781. In sum, we extend the current knowledge of ncRNAs and their potential relevance on melanoma. Significance Previously considered as transcriptional noise, lncRNAs have emerged as novel players in regulating many cellular aspects in health and disease including melanoma. However, the number and as well as the extent of functional significance of most lncRNAs remains elusive. We provide a comprehensive strategy to identify functionally relevant lncRNAs in melanoma by combining expression profiling with CRISPR-inhibition growths screens lowering the experimental effort. We also provide a larger resource of differentially expressed lncRNAs with potential implications in melanoma growth and invasion. Our results broaden the characterized of lncRNAs as potential targets for future therapeutic applications.
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24
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Kim J, Diaz LF, Miller MJ, Leadem B, Krivega I, Dean A. An enhancer RNA recruits KMT2A to regulate transcription of Myb. Cell Rep 2024; 43:114378. [PMID: 38889007 PMCID: PMC11369905 DOI: 10.1016/j.celrep.2024.114378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/20/2024] Open
Abstract
The Myb proto-oncogene encodes the transcription factor c-MYB, which is critical for hematopoiesis. Distant enhancers of Myb form a hub of interactions with the Myb promoter. We identified a long non-coding RNA (Myrlin) originating from the -81-kb murine Myb enhancer. Myrlin and Myb are coordinately regulated during erythroid differentiation. Myrlin TSS deletion using CRISPR-Cas9 reduced Myrlin and Myb expression and LDB1 complex occupancy at the Myb enhancers, compromising enhancer contacts and reducing RNA Pol II occupancy in the locus. In contrast, CRISPRi silencing of Myrlin left LDB1 and the Myb enhancer hub unperturbed, although Myrlin and Myb expressions were downregulated, decoupling transcription and chromatin looping. Myrlin interacts with the KMT2A/MLL1 complex. Myrlin CRISPRi compromised KMT2A occupancy in the Myb locus, decreasing CDK9 and RNA Pol II binding and resulting in Pol II pausing in the Myb first exon/intron. Thus, Myrlin directly participates in activating Myb transcription by recruiting KMT2A.
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Affiliation(s)
- Juhyun Kim
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Luis F Diaz
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Oregon Health and Sciences University, Portland, OR 97239, USA
| | - Matthew J Miller
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; University of Iowa Medical School, Iowa City, IA 52242, USA
| | - Benjamin Leadem
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; GeneDx, Gaithersburg, MD 20877, USA
| | - Ivan Krivega
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Sonothera, South San Francisco, CA 94080, USA
| | - Ann Dean
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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25
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Liu Y, Lv H, Liu X, Xu L, Li T, Zhou H, Zhu H, Hao C, Lin C, Zhang Y. The RP11-417E7.1/THBS2 signaling pathway promotes colorectal cancer metastasis by activating the Wnt/β-catenin pathway and facilitating exosome-mediated M2 macrophage polarization. J Exp Clin Cancer Res 2024; 43:195. [PMID: 39020380 PMCID: PMC11253389 DOI: 10.1186/s13046-024-03107-7] [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: 02/17/2024] [Accepted: 06/22/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Metastasis is the major cause of colorectal cancer (CRC) mortality. Emerging evidence suggests that long noncoding RNAs (lncRNAs) drive cancer metastasis and that their regulatory pathways could be targeted for preventing metastasis. However, the underlying mechanisms of lncRNAs in CRC metastasis remain poorly understood. METHODS Microarray analysis was used to screen for differentially expressed lncRNAs. Transwell assays, fibronectin cell adhesion assays, and mouse metastasis models were utilized to evaluate the metastatic capacities of CRC in vitro and in vivo. Chromatin isolation by RNA purification, chromatin immunoprecipitation and chromosome conformation capture were applied to investigate the underlying mechanism involved. qRT‒PCR and transmission electron microscopy were performed to confirm macrophage polarization and the presence of cancer-derived exosomes. RESULTS The lncRNA RP11-417E7.1 was screened and identified as a novel metastasis-associated lncRNA that was correlated with a poor prognosis. RP11-417E7.1 enhances the metastatic capacity of CRC cells in vivo and in vitro. Mechanistically, RP11-417E7.1 binding with High mobility group A1 (HMGA1) promotes neighboring thrombospondin 2 (THBS2) transcription via chromatin loop formation between its promoter and enhancer, which activates the Wnt/β-catenin signaling pathway and facilitates CRC metastasis. Furthermore, exosomes derived from CRC cells transport THBS2 into macrophages, thereby inducing the M2 polarization of macrophages to sustain the prometastatic microenvironment. Notably, netropsin, a DNA-binding drug, suppresses chromatin loop formation mediated by RP11-417E7.1 at the THBS2 locus and significantly inhibits CRC metastasis in vitro and in vivo. CONCLUSIONS This study revealed the novel prometastatic function and mechanism of the lncRNA RP11-417E7.1, which provides a potential prognostic indicator and therapeutic target in CRC.
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Affiliation(s)
- Yunze Liu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, 221000, China
| | - Heng Lv
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Xin Liu
- Department of Endocrinology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
- Department of Biology and Biochemistry, Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX, 77204, USA
| | - Lei Xu
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Tiankang Li
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Hui Zhou
- Department of Gastrointestinal Surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan, 410013, China
| | - Hongmei Zhu
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Chuanchuan Hao
- Department of Traditional Chinese Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Changwei Lin
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
- Department of Gastrointestinal Surgery, The Third XiangYa Hospital of Central South University, Changsha, Hunan, 410013, China.
| | - Yi Zhang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China.
- Institute of Digestive Diseases, Xuzhou Medical University, Xuzhou, 221000, China.
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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26
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Fahad M, Tariq L, Muhammad S, Wu L. Underground communication: Long non-coding RNA signaling in the plant rhizosphere. PLANT COMMUNICATIONS 2024; 5:100927. [PMID: 38679911 PMCID: PMC11287177 DOI: 10.1016/j.xplc.2024.100927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as integral gene-expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota, as well as nutrient acquisition and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface. A comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. Looking ahead, we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.
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Affiliation(s)
- Muhammad Fahad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Leeza Tariq
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sajid Muhammad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liang Wu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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27
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Peng Y, Zhu M, Gong Y, Wang C. Identification and functional prediction of lncRNAs associated with intramuscular lipid deposition in Guangling donkeys. Front Vet Sci 2024; 11:1410109. [PMID: 39036793 PMCID: PMC11258529 DOI: 10.3389/fvets.2024.1410109] [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: 03/31/2024] [Accepted: 05/30/2024] [Indexed: 07/23/2024] Open
Abstract
Many studies have shown that long non-coding RNAs (lncRNAs) play key regulatory roles in various biological processes. However, the importance and molecular regulatory mechanisms of lncRNAs in donkey intramuscular fat deposition remain to be further investigated. In this study, we used published transcriptomic data from the longissimus dorsi muscle of Guangling donkeys to identify lncRNAs and obtained 196 novel lncRNAs. Compared with the coding genes, the novel lncRNAs and the known lncRNAs exhibited some typical features, such as shorter transcript length and smaller exons. A total of 272 coding genes and 52 lncRNAs were differentially expressed between the longissimus dorsi muscles of the low-fat and high-fat groups. The differentially expressed genes were found to be involved in various biological processes related to lipid metabolism. The potential target genes of differentially expressed lncRNAs were predicted by cis and trans. Functional analysis of lncRNA targets showed that some lncRNAs may act on potential target genes involved in lipid metabolism processes and regulate lipid deposition in the longissimus dorsi muscle. This study provides valuable information for further investigation of the molecular mechanisms of lipid deposition traits in donkeys, which may improve meat traits and facilitate the selection process of donkeys in future breeding.
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Affiliation(s)
- Yongdong Peng
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
| | | | | | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Agricultural Science and Engineering School, Liaocheng University, Liaocheng, China
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28
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Lin Y, Zhao W, Lv Z, Xie H, Li Y, Zhang Z. The functions and mechanisms of long non-coding RNA in colorectal cancer. Front Oncol 2024; 14:1419972. [PMID: 39026978 PMCID: PMC11254705 DOI: 10.3389/fonc.2024.1419972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
CRC poses a significant challenge in the global health domain, with a high number of deaths attributed to this disease annually. If CRC is detected only in its advanced stages, the difficulty of treatment increases significantly. Therefore, biomarkers for the early detection of CRC play a crucial role in improving patient outcomes and increasing survival rates. The development of a reliable biomarker for early detection of CRC is particularly important for timely diagnosis and treatment. However, current methods for CRC detection, such as endoscopic examination, blood, and stool tests, have certain limitations and often only detect cases in the late stages. To overcome these constraints, researchers have turned their attention to molecular biomarkers, which are considered a promising approach to improving CRC detection. Non-invasive methods using biomarkers such as mRNA, circulating cell-free DNA, microRNA, LncRNA, and proteins can provide more reliable diagnostic information. These biomarkers can be found in blood, tissue, stool, and volatile organic compounds. Identifying molecular biomarkers with high sensitivity and specificity for the early and safe, economic, and easily measurable detection of CRC remains a significant challenge for researchers.
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Affiliation(s)
- Yuning Lin
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Wenzhen Zhao
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Zhenyi Lv
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Hongyan Xie
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
| | - Ying Li
- Ultrasonography Department, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, China
| | - Zhongying Zhang
- Medical Laboratory, Xiamen Humanity Hospital, Fujian Medical University, Xiamen, China
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29
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Andersen RE, Alkuraya IF, Ajeesh A, Sakamoto T, Mena EL, Amr SS, Romi H, Kenna MA, Robson CD, Wilch ES, Nalbandian K, Piña-Aguilar R, Walsh CA, Morton CC. Chromosomal structural rearrangements implicate long non-coding RNAs in rare germline disorders. Hum Genet 2024; 143:921-938. [PMID: 39060644 PMCID: PMC11294402 DOI: 10.1007/s00439-024-02693-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024]
Abstract
In recent years, there has been increased focus on exploring the role the non-protein-coding genome plays in Mendelian disorders. One class of particular interest is long non-coding RNAs (lncRNAs), which has recently been implicated in the regulation of diverse molecular processes. However, because lncRNAs do not encode protein, there is uncertainty regarding what constitutes a pathogenic lncRNA variant, and thus annotating such elements is challenging. The Developmental Genome Anatomy Project (DGAP) and similar projects recruit individuals with apparently balanced chromosomal abnormalities (BCAs) that disrupt or dysregulate genes in order to annotate the human genome. We hypothesized that rearrangements disrupting lncRNAs could be the underlying genetic etiology for the phenotypes of a subset of these individuals. Thus, we assessed 279 cases with BCAs and selected 191 cases with simple BCAs (breakpoints at only two genomic locations) for further analysis of lncRNA disruptions. From these, we identified 66 cases in which the chromosomal rearrangements directly disrupt lncRNAs. In 30 cases, no genes of any other class aside from lncRNAs are directly disrupted, consistent with the hypothesis that lncRNA disruptions could underly the phenotypes of these individuals. Strikingly, the lncRNAs MEF2C-AS1 and ENSG00000257522 are each disrupted in two unrelated cases. Furthermore, we experimentally tested the lncRNAs TBX2-AS1 and MEF2C-AS1 and found that knockdown of these lncRNAs resulted in decreased expression of the neighboring transcription factors TBX2 and MEF2C, respectively. To showcase the power of this genomic approach for annotating lncRNAs, here we focus on clinical reports and genetic analysis of seven individuals with likely developmental etiologies due to lncRNA disruptions.
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Affiliation(s)
- Rebecca E Andersen
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ibrahim F Alkuraya
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Abna Ajeesh
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tyler Sakamoto
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard College, Cambridge, MA, USA
| | - Elijah L Mena
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Sami S Amr
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hila Romi
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margaret A Kenna
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
| | - Caroline D Robson
- Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology, Boston Children's Hospital, Boston, MA, USA
- Department of Radiology, Boston Children's Hospital, Boston, MA, USA
| | - Ellen S Wilch
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Katarena Nalbandian
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Raul Piña-Aguilar
- Harvard Medical School, Boston, MA, USA
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Cynthia C Morton
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- University of Manchester, Manchester Center for Audiology and Deafness, Manchester, UK.
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30
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Das S, Zea Rojas MP, Tran EJ. Novel insights on the positive correlation between sense and antisense pairs on gene expression. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1864. [PMID: 39087253 DOI: 10.1002/wrna.1864] [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: 11/30/2023] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 08/02/2024]
Abstract
A considerable proportion of the eukaryotic genome undergoes transcription, leading to the generation of noncoding RNA molecules that lack protein-coding information and are not subjected to translation. These noncoding RNAs (ncRNAs) are well recognized to have essential roles in several biological processes. Long noncoding RNAs (lncRNAs) represent the most extensive category of ncRNAs found in the human genome. Much research has focused on investigating the roles of cis-acting lncRNAs in the regulation of specific target gene expression. In the majority of instances, the regulation of sense gene expression by its corresponding antisense pair occurs in a negative (discordant) manner, resulting in the suppression of the target genes. The notion that a negative correlation exists between sense and antisense pairings is, however, not universally valid. In fact, several recent studies have reported a positive relationship between corresponding cis antisense pairs within plants, budding yeast, and mammalian cancer cells. The positive (concordant) correlation between anti-sense and sense transcripts leads to an increase in the level of the sense transcript within the same genomic loci. In addition, mechanisms such as altering chromatin structure, the formation of R loops, and the recruitment of transcription factors can either enhance transcription or stabilize sense transcripts through their antisense pairs. The primary objective of this work is to provide a comprehensive understanding of both aspects of antisense regulation, specifically focusing on the positive correlation between sense and antisense transcripts in the context of eukaryotic gene expression, including its implications towards cancer progression. This article is categorized under: RNA Processing > 3' End Processing Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.
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Affiliation(s)
- Subhadeep Das
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | | | - Elizabeth J Tran
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
- Purdue University Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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Bohrer C, Varon E, Peretz E, Reinitz G, Kinor N, Halle D, Nissan A, Shav-Tal Y. CCAT1 lncRNA is chromatin-retained and post-transcriptionally spliced. Histochem Cell Biol 2024; 162:91-107. [PMID: 38763947 PMCID: PMC11227459 DOI: 10.1007/s00418-024-02294-w] [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] [Accepted: 04/22/2024] [Indexed: 05/21/2024]
Abstract
Super-enhancers are unique gene expression regulators widely involved in cancer development. Spread over large DNA segments, they tend to be found next to oncogenes. The super-enhancer c-MYC locus forms long-range chromatin looping with nearby genes, which brings the enhancer and the genes into proximity, to promote gene activation. The colon cancer-associated transcript 1 (CCAT1) gene, which is part of the MYC locus, transcribes a lncRNA that is overexpressed in colon cancer cells through activation by MYC. Comparing different types of cancer cell lines using RNA fluorescence in situ hybridization (RNA FISH), we detected very prominent CCAT1 expression in HeLa cells, observed as several large CCAT1 nuclear foci. We found that dozens of CCAT1 transcripts accumulate on the gene locus, in addition to active transcription occurring from the gene. The accumulating transcripts are released from the chromatin during cell division. Examination of CCAT1 lncRNA expression patterns on the single-RNA level showed that unspliced CCAT1 transcripts are released from the gene into the nucleoplasm. Most of these unspliced transcripts were observed in proximity to the active gene but were not associated with nuclear speckles in which unspliced RNAs usually accumulate. At larger distances from the gene, the CCAT1 transcripts appeared spliced, implying that most CCAT1 transcripts undergo post-transcriptional splicing in the zone of the active gene. Finally, we show that unspliced CCAT1 transcripts can be detected in the cytoplasm during splicing inhibition, which suggests that there are several CCAT1 variants, spliced and unspliced, that the cell can recognize as suitable for export.
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Affiliation(s)
- Chaya Bohrer
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eli Varon
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Eldar Peretz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Gita Reinitz
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Kinor
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - David Halle
- Biochemistry Laboratory, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Aviram Nissan
- Ziv Medical Center, Safed, Israel
- Surgical Innovation Laboratory, The Chaim Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina and Everard Goodman Faculty of Life Sciences and Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel.
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Weiss M, Hettrich S, Hofmann T, Hachim S, Günther S, Braun T, Boettger T. Mitolnc controls cardiac BCAA metabolism and heart hypertrophy by allosteric activation of BCKDH. Nucleic Acids Res 2024; 52:6629-6646. [PMID: 38567728 PMCID: PMC11194096 DOI: 10.1093/nar/gkae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/12/2024] [Accepted: 03/19/2024] [Indexed: 06/25/2024] Open
Abstract
Enzyme activity is determined by various different mechanisms, including posttranslational modifications and allosteric regulation. Allosteric activators are often metabolites but other molecules serve similar functions. So far, examples of long non-coding RNAs (lncRNAs) acting as allosteric activators of enzyme activity are missing. Here, we describe the function of mitolnc in cardiomyocytes, a nuclear encoded long non-coding RNA, located in mitochondria and directly interacting with the branched-chain ketoacid dehydrogenase (BCKDH) complex to increase its activity. The BCKDH complex is critical for branched-chain amino acid catabolism (BCAAs). Inactivation of mitolnc in mice reduces BCKDH complex activity, resulting in accumulation of BCAAs in the heart and cardiac hypertrophy via enhanced mTOR signaling. We found that mitolnc allosterically activates the BCKDH complex, independent of phosphorylation. Mitolnc-mediated regulation of the BCKDH complex constitutes an important additional layer to regulate the BCKDH complex in a tissue-specific manner, evading direct coupling of BCAA metabolism to ACLY-dependent lipogenesis.
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Affiliation(s)
- Maria Weiss
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Sara Hettrich
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Theresa Hofmann
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Salma Hachim
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Stefan Günther
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Thomas Braun
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
| | - Thomas Boettger
- Max Planck Institute for Heart- and Lung Research, Department of Cardiac Development and Remodelling, Ludwigstr. 43, D-61231 Bad Nauheim, Germany
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Xie B, Wu Y, Wang S, Ruan L, Liu X. Expression profile of long noncoding RNAs and comprehensive analysis of lncRNA-cisTF-DGE regulation in condyloma acuminatum. BMC Med Genomics 2024; 17:167. [PMID: 38902760 PMCID: PMC11188504 DOI: 10.1186/s12920-024-01938-z] [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: 11/16/2023] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
OBJECTIVE To identify differentially expressed long noncoding RNAs (lncRNAs) in condyloma acuminatum (CA) and to explore their probable regulatory mechanisms by establishing coexpression networks. METHODS High-throughput RNA sequencing was performed to assess genome-wide lncRNA expression in CA and paired adjacent mucosal tissue. The expression of candidate lncRNAs and their target genes in larger CA specimens was validated using real-time quantitative reverse transcriptase polymerase chain reaction (RT‒qPCR). Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used for the functional enrichment analysis of these candidate lncRNAs and differential mRNAs. The coexpressed mRNAs of the candidate lncRNAs, calculated by Pearson's correlation coefficient, were also analysed using GO and KEGG analysis. In addition, the interactions among differentially expressed lncRNAs (DElncRNAs)-cis-regulatory transcription factors (cisTFs)-differentially expressed genes (DEGs) were analysed and their network was constructed. RESULTS A total of 546 lncRNAs and 2553 mRNAs were found to be differentially expressed in CA compared to the paired control. Functional enrichment analysis revealed that the DEGs coexpressed with DElncRNAs were enriched in the terms of cell adhesion and keratinocyte differentiation, and the pathways of ECM-receptor interaction, local adhesion, PI3K/AKT and TGF-ß signaling. We further constructed the network among DElncRNAs-cisTFs-DEGs and found that these 95 DEGs were mainly enriched in GO terms of epithelial development, regulation of transcription or gene expression. Furthermore, the expression of 3 pairs of DElncRNAs and cisTFs, EVX1-AS and HOXA13, HOXA11-AS and EVX1, and DLX6-AS and DLX5, was validated with a larger number of specimens using RT‒qPCR. CONCLUSION CA has a specific lncRNA profile, and the differentially expressed lncRNAs play regulatory roles in mRNA expression through cis-acting TFs, which provides insight into their regulatory networks. It will be useful to understand the pathogenesis of CA to provide new directions for the prevention, clinical treatment and efficacy evaluation of CA.
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Affiliation(s)
- Bo Xie
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, Zhejiang Province, 310003, China
| | - Yinhua Wu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, Zhejiang Province, 310003, China
| | - Su Wang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, Zhejiang Province, 310003, China
| | - Liming Ruan
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, Zhejiang Province, 310003, China.
- Department of Dermatology, Beilun People's Hospital of Ningbo City, 1288# Lushan East Road, Ningbo, Zhejiang Province, 310058, China.
| | - Xiaoyan Liu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, 79# Qingchun Road, Hangzhou, Zhejiang Province, 310003, China.
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Hong S, Zhang Y, Wang D, Wang H, Zhang H, Jiang J, Chen L. Disulfidptosis-related lncRNAs signature predicting prognosis and immunotherapy effect in lung adenocarcinoma. Aging (Albany NY) 2024; 16:9972-9989. [PMID: 38862217 PMCID: PMC11210254 DOI: 10.18632/aging.205911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/22/2024] [Indexed: 06/13/2024]
Abstract
PURPOSE Lung adenocarcinoma (LUAD) is a prevalent malignant tumor worldwide, with high incidence and mortality rates. However, there is still a lack of specific and sensitive biomarkers for its early diagnosis and targeted treatment. Disulfidptosis is a newly identified mode of cell death that is characteristic of disulfide stress. Therefore, exploring the correlation between disulfidptosis-related long non-coding RNAs (DRGs-lncRNAs) and patient prognosis can provide new molecular targets for LUAD patients. METHODS The study analysed the transcriptome data and clinical data of LUAD patients in The Cancer Genome Atlas (TCGA) database, gene co-expression, and univariate Cox regression methods were used to screen for DRGs-lncRNAs related to prognosis. The risk score model of lncRNA was established by univariate and multivariate Cox regression models. TIMER, CIBERSORT, CIBERSORT-ABS, and other methods were used to analyze immune infiltration and further evaluate immune function analysis, immune checkpoints, and drug sensitivity. Real-time polymerase chain reaction (RT-PCR) was performed to detect the expression of DRGs-lncRNAs in LUAD cell lines. RESULTS A total of 108 lncRNAs significantly associated with disulfidptosis were identified. A prognostic model was constructed by screening 10 lncRNAs with independent prognostic significance through single-factor Cox regression analysis, LASSO regression analysis, and multiple-factor Cox regression analysis. Survival analysis of patients through the prognostic model showed that there were obvious survival differences between the high- and low-risk groups. The risk score of the prognostic model can be used as an independent prognostic factor independent of other clinical traits, and the risk score increases with stage. Further analysis showed that the prognostic model was also different from tumor immune cell infiltration, immune function, and immune checkpoint genes in the high- and low-risk groups. Chemotherapy drug susceptibility analysis showed that high-risk patients were more sensitive to Paclitaxel, 5-Fluorouracil, Gefitinib, Docetaxel, Cytarabine, and Cisplatin. Additionally, RT-PCR analysis demonstrated differential expression of DRGs-lncRNAs between LUAD cell lines and the human bronchial epithelial cell line. CONCLUSIONS The prognostic model of DRGs-lncRNAs constructed in this study has certain accuracy and reliability in predicting the survival prognosis of LUAD patients, and provides clues for the interaction between disulfidptosis and LUAD immunotherapy.
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Affiliation(s)
- Suifeng Hong
- Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315400, China
| | - Yu Zhang
- Department of Oncology Radiation, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200433, China
| | - Dongfeng Wang
- Dongying People’s Hospital (Dongying Hospital of Shandong Provincial Hospital Group), Dongying, Shandong 257091, China
| | - Huaying Wang
- Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315400, China
| | - Huihui Zhang
- Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315400, China
| | - Jing Jiang
- Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315400, China
| | - Liping Chen
- Department of Respiratory and Critical Care Medicine, The Affiliated People’s Hospital of Ningbo University, Ningbo 315400, China
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Lee U, Mozeika SM, Zhao L. A Synergistic, Cultivator Model of De Novo Gene Origination. Genome Biol Evol 2024; 16:evae103. [PMID: 38748819 PMCID: PMC11152449 DOI: 10.1093/gbe/evae103] [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] [Accepted: 05/12/2024] [Indexed: 06/07/2024] Open
Abstract
The origin and fixation of evolutionarily young genes is a fundamental question in evolutionary biology. However, understanding the origins of newly evolved genes arising de novo from noncoding genomic sequences is challenging. This is partly due to the low likelihood that several neutral or nearly neutral mutations fix prior to the appearance of an important novel molecular function. This issue is particularly exacerbated in large effective population sizes where the effect of drift is small. To address this problem, we propose a regulation-focused, cultivator model for de novo gene evolution. This cultivator-focused model posits that each step in a novel variant's evolutionary trajectory is driven by well-defined, selectively advantageous functions for the cultivator genes, rather than solely by the de novo genes, emphasizing the critical role of genome organization in the evolution of new genes.
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Affiliation(s)
- UnJin Lee
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Shawn M Mozeika
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
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Zang H, Guo S, Dong S, Song Y, Li K, Fan X, Qiu J, Zheng Y, Jiang H, Wu Y, Lü Y, Chen D, Guo R. Construction of a Full-Length Transcriptome of Western Honeybee Midgut Tissue and Improved Genome Annotation. Genes (Basel) 2024; 15:728. [PMID: 38927663 PMCID: PMC11202838 DOI: 10.3390/genes15060728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/22/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Honeybees are an indispensable pollinator in nature with pivotal ecological, economic, and scientific value. However, a full-length transcriptome for Apis mellifera, assembled with the advanced third-generation nanopore sequencing technology, has yet to be reported. Here, nanopore sequencing of the midgut tissues of uninoculated and Nosema ceranae-inoculated A. mellifera workers was conducted, and the full-length transcriptome was then constructed and annotated based on high-quality long reads. Next followed improvement of sequences and annotations of the current reference genome of A. mellifera. A total of 5,942,745 and 6,664,923 raw reads were produced from midguts of workers at 7 days post-inoculation (dpi) with N. ceranae and 10 dpi, while 7,100,161 and 6,506,665 raw reads were generated from the midguts of corresponding uninoculated workers. After strict quality control, 6,928,170, 6,353,066, 5,745,048, and 6,416,987 clean reads were obtained, with a length distribution ranging from 1 kb to 10 kb. Additionally, 16,824, 17,708, 15,744, and 18,246 full-length transcripts were respectively detected, including 28,019 nonredundant ones. Among these, 43,666, 30,945, 41,771, 26,442, and 24,532 full-length transcripts could be annotated to the Nr, KOG, eggNOG, GO, and KEGG databases, respectively. Additionally, 501 novel genes (20,326 novel transcripts) were identified for the first time, among which 401 (20,255), 193 (13,365), 414 (19,186), 228 (12,093), and 202 (11,703) were respectively annotated to each of the aforementioned five databases. The expression and sequences of three randomly selected novel transcripts were confirmed by RT-PCR and Sanger sequencing. The 5' UTR of 2082 genes, the 3' UTR of 2029 genes, and both the 5' and 3' UTRs of 730 genes were extended. Moreover, 17,345 SSRs, 14,789 complete ORFs, 1224 long non-coding RNAs (lncRNAs), and 650 transcription factors (TFs) from 37 families were detected. Findings from this work not only refine the annotation of the A. mellifera reference genome, but also provide a valuable resource and basis for relevant molecular and -omics studies.
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Affiliation(s)
- He Zang
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Sijia Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Shunan Dong
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Yuxuan Song
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Kunze Li
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Xiaoxue Fan
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Jianfeng Qiu
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Yidi Zheng
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (H.J.); (Y.W.)
| | - Ying Wu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China; (H.J.); (Y.W.)
| | - Yang Lü
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157000, China;
| | - Dafu Chen
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Bee Science and Biomedicine, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.Z.); (S.G.); (S.D.); (Y.S.); (K.L.); (X.F.); (J.Q.); (Y.Z.); (D.C.)
- National & Local United Engineering Laboratory of Natural Biotoxin, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Song XW, He WX, Su T, Li CJ, Jiang LL, Huang SQ, Li SH, Guo ZF, Zhang BL. Abnormal expression of PRKAG2-AS1 in endothelial cells induced inflammation and apoptosis by reducing PRKAG2 expression. Noncoding RNA Res 2024; 9:536-546. [PMID: 38511052 PMCID: PMC10950609 DOI: 10.1016/j.ncrna.2024.02.012] [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: 10/18/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
PRKAG2 is required for the maintenance of cellular energy balance. PRKAG2-AS1, a long non-coding RNA (lncRNA), was found within the promoter region of PRKAG2. Despite the extensive expression of PRKAG2-AS1 in endothelial cells, the precise function and mechanism of this gene in endothelial cells have yet to be elucidated. The localization of PRKAG2-AS1 was predominantly observed in the nucleus, as revealed using nuclear and cytoplasmic fractionation and fluorescence in situ hybridization. The manipulation of PRKAG2-AS1 by knockdown and overexpression within the nucleus significantly altered PRKAG2 expression in a cis-regulatory manner. The expression of PRKAG2-AS1 and its target genes, PRKAG2b and PRKAG2d, was down-regulated in endothelial cells subjected to oxLDL and Hcy-induced injury. This finding suggests that PRKAG2-AS1 may be involved in the mechanism behind endothelial injury. The suppression of PRKAG2-AS1 specifically in the nucleus led to an upregulation of inflammatory molecules such as cytokines, adhesion molecules, and chemokines in endothelial cells. Additionally, this nuclear suppression of PRKAG2-AS1 facilitated the adherence of THP1 cells to endothelial cells. We confirmed the role of nuclear knockdown PRKAG2-AS1 in the induction of apoptosis and inhibition of cell proliferation, migration, and lumen formation through flow cytometry, TUNEL test, CCK8 assay, and cell scratching. Finally, it was determined that PRKAG2-AS1 exerts direct control over the transcription of PRKAG2 by its binding to their promoters. In conclusion, downregulation of PRKAG2-AS1 suppressed the proliferation and migration, promoted inflammation and apoptosis of endothelial cells, and thus contributed to the development of atherosclerosis resulting from endothelial cell injury.
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Affiliation(s)
- Xiao-Wei Song
- Department of Anesthesiology, Shidong Hospital of Shanghai, University of Shanghai for Science and Technology, Shanghai, China
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wen-Xia He
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Ting Su
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chang-Jin Li
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Li-Li Jiang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Song-Qun Huang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Song-Hua Li
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-Fu Guo
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Bi-Li Zhang
- Department of Cardiology, Changhai Hospital, Second Military Medical University, Shanghai, China
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38
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Mylarshchikov D, Nikolskaya A, Bogomaz O, Zharikova A, Mironov A. BaRDIC: robust peak calling for RNA-DNA interaction data. NAR Genom Bioinform 2024; 6:lqae054. [PMID: 38774512 PMCID: PMC11106031 DOI: 10.1093/nargab/lqae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 04/29/2024] [Accepted: 05/09/2024] [Indexed: 05/24/2024] Open
Abstract
Chromatin-associated non-coding RNAs play important roles in various cellular processes by targeting genomic loci. Two types of genome-wide NGS experiments exist to detect such targets: 'one-to-al', which focuses on targets of a single RNA, and 'all-to-al', which captures targets of all RNAs in a sample. As with many NGS experiments, they are prone to biases and noise, so it becomes essential to detect 'peaks'-specific interactions of an RNA with genomic targets. Here, we present BaRDIC-Binomial RNA-DNA Interaction Caller-a tailored method to detect peaks in both types of RNA-DNA interaction data. BaRDIC is the first tool to simultaneously take into account the two most prominent biases in the data: chromatin heterogeneity and distance-dependent decay of interaction frequency. Since RNAs differ in their interaction preferences, BaRDIC adapts peak sizes according to the abundances and contact patterns of individual RNAs. These features enable BaRDIC to make more robust predictions than currently applied peak-calling algorithms and better handle the characteristic sparsity of all-to-all data. The BaRDIC package is freely available at https://github.com/dmitrymyl/BaRDIC.
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Affiliation(s)
- Dmitry E Mylarshchikov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Arina I Nikolskaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Olesja D Bogomaz
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
| | - Anastasia A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskiye Gory, Moscow 119234, Russia
- Kharkevich Institute for Information Transmission Problems RAS, Bolshoy Karetny per., Moscow 127051, Russia
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He J, Kang L. Regulation of insect behavior by non-coding RNAs. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1106-1118. [PMID: 38443665 DOI: 10.1007/s11427-023-2482-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 03/07/2024]
Abstract
The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes. Over the past several decades, accumulating studies have unveiled the roles of non-coding RNAs (ncRNAs) in regulating insect behaviors. ncRNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli. ncRNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes. However, a comprehensive review of ncRNAs' roles in regulating insect behaviors has yet to be conducted. Here, we present the recent progress in our understanding of how ncRNAs regulate various insect behaviors, including flight and movement, social behavior, reproduction, learning and memory, and feeding. We refine the intricate mechanisms by which ncRNAs modulate the function of neural, motor, reproductive, and other physiological systems, as well as gene expression in insects like fruit flies, social insects, locusts, and mosquitos. Furthermore, we discuss potential avenues for future studies in ncRNA-mediated insect behaviors.
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Affiliation(s)
- Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, 071002, China.
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40
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Luo H, Jing H, Chen W. An extensive overview of the role of lncRNAs generated from immune cells in the etiology of cancer. Int Immunopharmacol 2024; 133:112063. [PMID: 38677091 DOI: 10.1016/j.intimp.2024.112063] [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: 02/03/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024]
Abstract
Long non-coding RNAs (lncRNAs) are involved in the control of critical tumor-suppressor and oncogenic pathways in cancer. These types of non-coding RNAs could affect both immune and cancer cells. The thorough analysis of lncRNAs derived from immune cells and the incorporation of new findings significantly advance our understanding of the complex role of lncRNAs in the context of cancer. This work highlights the promise of lncRNAs for translational therapeutic approaches while also establishing a solid foundation for comprehending the complex link between lncRNAs and cancer through a coherent narrative. The main findings of this article are that types of lncRNAs derived from immune cells, such as MM2P and MALAT1, can affect the behaviors of cancer cells, like invasion, angiogenesis, and proliferation. As research in this area grows, the therapeutic potential of targeting these lncRNAs offers promising opportunities for expanding our understanding of cancer biology and developing cutting-edge, precision-based therapies for cancer therapy.
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Affiliation(s)
- Hong Luo
- Department of Oncology, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, Jiangsu Province, China.
| | - Hailiang Jing
- Department of Integrative Medicine, Yancheng Branch of Nanjing Drum Tower Hospital, Yancheng, Jiangsu Province, China
| | - Wei Chen
- Department of Oncology, Tumor Hospital Affiliated to Nantong University, Nantong, Jiangsu Province, China
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41
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Li X, Hou Z, Meng S, Jia Q, Xing S, Wang Z, Chen M, Xu H, Li M, Cai H. LncRNA BlncAD1 Modulates Bovine Adipogenesis by Binding to MYH10, PI3K/Akt Signaling Pathway, and miR-27a-5p/CDK6 Axis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:11094-11110. [PMID: 38661523 DOI: 10.1021/acs.jafc.4c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Research on adipogenesis will help to improve the meat quality of livestock. Long noncoding RNAs (lncRNAs) are involved in mammalian adipogenesis as epigenetic modulators. In this study, we analyzed lncRNA expression during bovine adipogenesis and detected 195 differentially expressed lncRNAs, including lncRNA BlncAD1, which was significantly upregulated in mature bovine adipocytes. Gain- and loss-of-function experiments confirmed that BlncAD1 promoted the proliferation, apoptosis, and differentiation of bovine preadipocytes. RNA pull-down revealed that the nonmuscle myosin 10 (MYH10) is a potential binding protein of BlncAD1. Then, we elucidated that loss of BlncAD1 caused increased ubiquitination of MYH10, which confirmed that BlncAD1 regulates adipogenesis by enhancing the stability of the MYH10 protein. Western blotting was used to demonstrate that BlncAD1 activated the PI3K/Akt signaling pathway. Bioinformatic analysis and dual-luciferase reporter assays indicated that BlncAD1 competitively absorbed miR-27a-5p. The overexpression and interference of miR-27a-5p in bovine preadipocytes displayed that miR-27a-5p inhibited proliferation, apoptosis, and differentiation. Further results suggested that miR-27a-5p targeted the CDK6 gene and that BlncAD1 controlled the proliferation of bovine preadipocytes by modulating the miR-27a-5p/CDK6 axis. This study revealed the complex mechanisms of BlncAD1 underlying bovine adipogenesis for the first time, which would provide useful information for genetics and breeding improvement of Chinese beef cattle.
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Affiliation(s)
- Xin Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhongyi Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shengbo Meng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shanshan Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhitong Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Mengjuan Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Ming Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hanfang Cai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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42
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Agrawal S, Buyan A, Severin J, Koido M, Alam T, Abugessaisa I, Chang HY, Dostie J, Itoh M, Kere J, Kondo N, Li Y, Makeev VJ, Mendez M, Okazaki Y, Ramilowski JA, Sigorskikh AI, Strug LJ, Yagi K, Yasuzawa K, Yip CW, Hon CC, Hoffman MM, Terao C, Kulakovskiy IV, Kasukawa T, Shin JW, Carninci P, de Hoon MJL. Annotation of nuclear lncRNAs based on chromatin interactions. PLoS One 2024; 19:e0295971. [PMID: 38709794 PMCID: PMC11073715 DOI: 10.1371/journal.pone.0295971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/02/2023] [Indexed: 05/08/2024] Open
Abstract
The human genome is pervasively transcribed and produces a wide variety of long non-coding RNAs (lncRNAs), constituting the majority of transcripts across human cell types. Some specific nuclear lncRNAs have been shown to be important regulatory components acting locally. As RNA-chromatin interaction and Hi-C chromatin conformation data showed that chromatin interactions of nuclear lncRNAs are determined by the local chromatin 3D conformation, we used Hi-C data to identify potential target genes of lncRNAs. RNA-protein interaction data suggested that nuclear lncRNAs act as scaffolds to recruit regulatory proteins to target promoters and enhancers. Nuclear lncRNAs may therefore play a role in directing regulatory factors to locations spatially close to the lncRNA gene. We provide the analysis results through an interactive visualization web portal at https://fantom.gsc.riken.jp/zenbu/reports/#F6_3D_lncRNA.
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Affiliation(s)
- Saumya Agrawal
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Andrey Buyan
- Autosome.org, Russia
- FANTOM Consortium, Dolgoprudny, Russia
| | - Jessica Severin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaru Koido
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Howard Y. Chang
- Center for Personal Dynamic Regulome, Stanford University, Stanford, California, United States of America
| | - Josée Dostie
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Center, McGill University, Montréal, Québec, Canada
| | - Masayoshi Itoh
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Japan
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Stem Cells and Metabolism Research Program, University of Helsinki and Folkhälsan Research Center, Helsinki, Finland
| | - Naoto Kondo
- RIKEN Center for Life Science Technologies, Yokohama, Japan
| | - Yunjing Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | | | - Mickaël Mendez
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Yasushi Okazaki
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jordan A. Ramilowski
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | | | - Lisa J. Strug
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Department of Statistical Sciences, University of Toronto, Ontario, Canada
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ken Yagi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kayoko Yasuzawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chi Wai Yip
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chung Chau Hon
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michael M. Hoffman
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Takeya Kasukawa
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Jay W. Shin
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
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43
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Cao L, Wang X, Li X, Ma L, Li Y. Identification of Co-diagnostic Genes for Heart Failure and Hepatocellular Carcinoma Through WGCNA and Machine Learning Algorithms. Mol Biotechnol 2024; 66:1229-1245. [PMID: 38236461 DOI: 10.1007/s12033-023-01025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/06/2023] [Indexed: 01/19/2024]
Abstract
This research delves into the intricate relationship between hepatocellular carcinoma (HCC) and heart failure (HF) by exploring shared genetic characteristics and molecular processes. Employing advanced methodologies such as differential analysis, weighted correlation network analysis (WGCNA), and algorithms like Random Forest (RF), Least Absolute Shrinkage Selection (LASSO), and XGBoost, we meticulously identified modular differential genes (DEGs) associated with both HF and HCC. Gene Set Variation Analysis (GSVA) and single sample gene set enrichment analysis (ssGSEA) were employed to unveil underlying biological mechanisms. The study revealed 88 core genes shared between HF and HCC, indicating a common mechanism. Enrichment analysis emphasized the roles of immune responses and inflammation in both diseases. Leveraging XGBoost, we crafted a robust multigene diagnostic model (including FCN3, MAP2K1, AP3M2, CDH19) with an area under the curve (AUC) > 0.9, showcasing exceptional predictive accuracy. GSVA and ssGSEA analyses unveiled the involvement of immune cells and metabolic pathways in the pathogenesis of HF and HCC. This research uncovers a pivotal interplay between HF and HCC, highlighting shared pathways and key genes, offering promising insights for future clinical treatments and experimental research endeavors.
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Affiliation(s)
- Lizhi Cao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
- University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xiaoying Wang
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China
| | - Xin Li
- Physical Examination Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
| | - Linlin Ma
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China.
- University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Yanfei Li
- Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai, 201318, China.
- University of Shanghai for Science and Technology, Shanghai, 200093, China.
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44
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Mably JD, Wang DZ. Long non-coding RNAs in cardiac hypertrophy and heart failure: functions, mechanisms and clinical prospects. Nat Rev Cardiol 2024; 21:326-345. [PMID: 37985696 PMCID: PMC11031336 DOI: 10.1038/s41569-023-00952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/16/2023] [Indexed: 11/22/2023]
Abstract
The surge in reports describing non-coding RNAs (ncRNAs) has focused attention on their possible biological roles and effects on development and disease. ncRNAs have been touted as previously uncharacterized regulators of gene expression and cellular processes, possibly working to fine-tune these functions. The sheer number of ncRNAs identified has outpaced the capacity to characterize each molecule thoroughly and to reliably establish its clinical relevance; it has, nonetheless, created excitement about their potential as molecular targets for novel therapeutic approaches to treat human disease. In this Review, we focus on one category of ncRNAs - long non-coding RNAs - and their expression, functions and molecular mechanisms in cardiac hypertrophy and heart failure. We further discuss the prospects for this specific class of ncRNAs as novel targets for the diagnosis and treatment of these conditions.
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Affiliation(s)
- John D Mably
- Center for Regenerative Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Da-Zhi Wang
- Center for Regenerative Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- USF Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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45
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Kumar V, Sabaté-Cadenas X, Soni I, Stern E, Vias C, Ginsberg D, Romá-Mateo C, Pulido R, Dodel M, Mardakheh FK, Shkumatava A, Shaulian E. The lincRNA JUNI regulates the stress-dependent induction of c-Jun, cellular migration and survival through the modulation of the DUSP14-JNK axis. Oncogene 2024; 43:1608-1619. [PMID: 38565943 PMCID: PMC11108773 DOI: 10.1038/s41388-024-03021-4] [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: 01/22/2024] [Revised: 03/17/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Cancer cells employ adaptive mechanisms to survive various stressors, including genotoxic drugs. Understanding the factors promoting survival is crucial for developing effective treatments. In this study, we unveil a previously unexplored long non-coding RNA, JUNI (JUN-DT, LINC01135), which is upregulated by genotoxic drugs through the activation of stress-activated MAPKs, JNK, and p38 and consequently exerts positive control over the expression of its adjacent gene product c-Jun, a well-known oncoprotein, which transduces signals to multiple transcriptional outputs. JUNI regulates cellular migration and has a crucial role in conferring cellular resistance to chemotherapeutic drugs or UV radiation. Depletion of JUNI markedly increases the sensitivity of cultured cells and spheroids to chemotherapeutic agents. We identified 57 proteins interacting with JUNI. The activity of one of them the MAPK phosphatase and inhibitor, DUSP14, is counteracted by JUNI, thereby, facilitating efficient JNK phosphorylation and c-Jun induction when cells are exposed to UV radiation. The antagonistic interplay with DUSP14 contributes not only to c-Jun induction but also augments the survival of UV-exposed cells. In summary, we introduce JUNI as a novel stress-inducible regulator of c-Jun, positioning it as a potential target for enhancing the sensitivity of cancer cells to chemotherapy.
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Affiliation(s)
- Vikash Kumar
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Xavier Sabaté-Cadenas
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Isha Soni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
| | - Esther Stern
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel
- Gene Therapy Institute, Hadassah Hebrew University Medical Center and Faculty of Medicine, Hebrew University, Jerusalem, 9112102, Israel
| | - Carine Vias
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
| | - Doron Ginsberg
- The Mina and Everard Goodman, Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel
| | - Carlos Romá-Mateo
- Department of Physiology, Facultat de Medicina i Odontologia, Universitat de València & Fundación Instituto de Investigación Sanitaria INCLIVA, 46010, Valencia, Spain
| | - Rafael Pulido
- Biobizkaia Health Research Institute, Barakaldo, 48903 Spain; & Ikerbasque, The Basque Foundation for Science, 48009, Bilbao, Spain
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London, EC1M 6BQ, UK
| | - Alena Shkumatava
- Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, 75005, France
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Eitan Shaulian
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, 9112102, Jerusalem, Israel.
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Cui P, Zhang Y, Wang C, Xiao B, Wang Q, Zhang L, Li H, Wu C, Tian W. Crucial role of lncRNA NONHSAG037054.2 and GABPA, and their related functional networks, in ankylosing spondylitis. Exp Ther Med 2024; 27:237. [PMID: 38628657 PMCID: PMC11019654 DOI: 10.3892/etm.2024.12525] [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: 09/09/2023] [Accepted: 02/09/2024] [Indexed: 04/19/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been previously researched in ankylosing spondylitis (AS). Nevertheless, there are few studies of lncRNAs and mRNAs associated with the pathogenesis of AS. Differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) between AS and normal samples were assessed using the R limma package. DOSE packages and 'clusterProfiler' were exploited for gene enrichment analysis. The functional association of proteins and protein interactions was assessed using the STRING database. To investigate the important genes and subnetworks in the protein-protein interaction network, the MCODE plug-in in the Cytoscape software was utilized. The gene mRNA was examined via reverse transcription-quantitative PCR. In total, 152 DEmRNAs and 204 DElncRNAs were observed between normal and AS samples. A total of 68 candidate genes related to DElncRNA were identified. These candidate genes were enriched in 30 cellular component terms, 22 molecular functions, 83 biological processes, 9 Kyoto Encyclopedia of Genes and Genomes, and 36 disease ontology pathways. NONHSAG037054.2 was the most related lncRNA to genes, and GABPA was the most connected gene to lncRNA in AS. The NCBI/GenBank accession number of the lncRNA NONHSAG037054.2 was not found because it is not included in NCBI. The information of lncRNA NONHSAG037054.2 can be found at the website (http://www.noncode.org/show_gene.php?id=NONHSAG037054 and https://www.genecards.org/cgi-bin/carddisp.pl?gene=ACAP2-IT1). In total, 13 microRNAs (miRNAs) and 46 miRNAs associated with NONHSAG037054.2 and GABPA, respectively, were found. A total of 173 RNA-binding protein genes were associated with both NONHSAG037054.2 and GABPA. In addition, GABPA was downregulated in AS samples, suggesting it may have diagnostic value in AS. In conclusion, NONHSAG037054.2 and GABPA are associated with AS. GABPA was downregulated in AS, and it could serve as a novel diagnostic factor for AS.
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Affiliation(s)
- Penglei Cui
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Yanzhuo Zhang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Chao Wang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Bin Xiao
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Qianqian Wang
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Liang Zhang
- Department of Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Hongchao Li
- Department of Rheumatology and Immunology, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Chengai Wu
- Department of Molecular Orthopaedics, Beijing Research Institute of Traumatology and Orthopaedics, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
| | - Wei Tian
- Department of Spine Surgery, Beijing Jishuitan Hospital, Capital Medical University, Beijing 100035, P.R. China
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47
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Ferrer J, Dimitrova N. Transcription regulation by long non-coding RNAs: mechanisms and disease relevance. Nat Rev Mol Cell Biol 2024; 25:396-415. [PMID: 38242953 PMCID: PMC11045326 DOI: 10.1038/s41580-023-00694-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/21/2024]
Abstract
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the control of gene transcription. Some of the best characterized lncRNAs have essential transcription cis-regulatory functions that cannot be easily accomplished by DNA-interacting transcription factors, such as XIST, which controls X-chromosome inactivation, or imprinted lncRNAs that direct allele-specific repression. A growing number of lncRNA transcription units, including CHASERR, PVT1 and HASTER (also known as HNF1A-AS1) act as transcription-stabilizing elements that fine-tune the activity of dosage-sensitive genes that encode transcription factors. Genetic experiments have shown that defects in such transcription stabilizers often cause severe phenotypes. Other lncRNAs, such as lincRNA-p21 (also known as Trp53cor1) and Maenli (Gm29348) contribute to local activation of gene transcription, whereas distinct lncRNAs influence gene transcription in trans. We discuss findings of lncRNAs that elicit a function through either activation of their transcription, transcript elongation and processing or the lncRNA molecule itself. We also discuss emerging evidence of lncRNA involvement in human diseases, and their potential as therapeutic targets.
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Affiliation(s)
- Jorge Ferrer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid, Spain.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
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48
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Zhang X, Li Z, Nie H, Huang Y, Du J, Xi Y, Guo C, Mu M, Li X, Zheng X, Xu Q, Huang D, Tu L, Cheng L. The IGF2BP2-lncRNA TRPC7-AS1 axis promotes hepatocellular carcinoma cell proliferation and invasion. Cell Signal 2024; 117:111078. [PMID: 38320625 DOI: 10.1016/j.cellsig.2024.111078] [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: 10/21/2023] [Revised: 01/16/2024] [Accepted: 02/01/2024] [Indexed: 02/08/2024]
Abstract
Hepatocellular carcinoma(HCC) is one of the most common tumors in the world. Human insulin-like growth factor 2(IGF2) mRNA binding protein 2(IGF2BP2) plays an important role in the progression of hepatocellular carcinoma. Additionally, long non-coding RNA(lncRNA) has been confirmed as a key regulator of hepatocellular carcinoma occurrence. However, the function of TRPC7-AS1 has not been verified in hepatocellular carcinoma. The research results revealed that high IGF2BP2 expression was associated with a decreased survival rate in patients with hepatocellular carcinoma. Furthermore, IGF2BP2 knockdown inhibited and IGF2BP2 overexpression promoted the cell proliferation and invasion of hepatocellular carcinoma cells. The research illuminated that IGF2BP2 regulated the expression of TRPC7-AS1, and a correlation was observed between IGF2BP2 and TRPC7-AS1 expression. TRPC7-AS1 silencing repressed and its overexpression promoted the progression of hepatocellular carcinoma. After silencing or overexpressing TRPC7-AS1, the expression of the high-mobility group AT-hook 2 (HMGA2) gene decreased or increased, respectively. IGF2BP2 enhanced the expression of TRPC7-AS1 and thus affected the expression of HMGA2, thereby promoting hepatocellular carcinoma progression.
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Affiliation(s)
- Xu Zhang
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Zilin Li
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Huizong Nie
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yue Huang
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jingyang Du
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yiling Xi
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chaoqin Guo
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Mingshan Mu
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xiangyu Li
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Xiaoliang Zheng
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China; Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, 182 Tianmushan Road, Xihu District, Hangzhou City, Zhejiang Province, China; Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, China
| | - Qiuran Xu
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, China.
| | - Dongsheng Huang
- School of Basic Medicine and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Linglan Tu
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China; Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, China.
| | - Liyan Cheng
- School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, Zhejiang, China; Zhejiang Provincial Laboratory of Experimental Animal's & Nonclinical Laboratory Studies, Hangzhou Medical College, 182 Tianmushan Road, Xihu District, Hangzhou City, Zhejiang Province, China; Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, China.
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49
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Dikmen F, Dabak T, Özgişi BD, Özenirler Ç, Kuralay SC, Çay SB, Çınar YU, Obut O, Balcı MA, Akbaba P, Aksel EG, Zararsız G, Solares E, Eldem V. Transcriptome-wide analysis uncovers regulatory elements of the antennal transcriptome repertoire of bumblebee at different life stages. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38676460 DOI: 10.1111/imb.12914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024]
Abstract
Bumblebees are crucial pollinators, providing essential ecosystem services and global food production. The success of pollination services relies on the interaction between sensory organs and the environment. The antenna functions as a versatile multi-sensory organ, pivotal in mediating chemosensory/olfactory information, and governs adaptive responses to environmental changes. Despite an increasing number of RNA-sequencing studies on insect antenna, comprehensive antennal transcriptome studies at the different life stages were not elucidated systematically. Here, we quantified the expression profile and dynamics of coding/microRNA genes of larval head and antennal tissues from early- and late-stage pupa to the adult of Bombus terrestris as suitable model organism among pollinators. We further performed Pearson correlation analyses on the gene expression profiles of the antennal transcriptome from larval head tissue to adult stages, exploring both positive and negative expression trends. The positively correlated coding genes were primarily enriched in sensory perception of chemical stimuli, ion transport, transmembrane transport processes and olfactory receptor activity. Negatively correlated genes were mainly enriched in organic substance biosynthesis and regulatory mechanisms underlying larval body patterning and the formation of juvenile antennal structures. As post-transcriptional regulators, miR-1000-5p, miR-13b-3p, miR-263-5p and miR-252-5p showed positive correlations, whereas miR-315-5p, miR-92b-3p, miR-137-3p, miR-11-3p and miR-10-3p exhibited negative correlations in antennal tissue. Notably, based on the inverse expression relationship, positively and negatively correlated microRNA (miRNA)-mRNA target pairs revealed that differentially expressed miRNAs predictively targeted genes involved in antennal development, shaping antennal structures and regulating antenna-specific functions. Our data serve as a foundation for understanding stage-specific antennal transcriptomes and large-scale comparative analysis of transcriptomes in different insects.
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Affiliation(s)
- Fatih Dikmen
- Department of Biology, Istanbul University, İstanbul, Turkey
| | - Tunç Dabak
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, USA
| | | | | | | | | | | | - Onur Obut
- Department of Biology, Istanbul University, İstanbul, Turkey
| | | | - Pınar Akbaba
- Department of Biology, Istanbul University, İstanbul, Turkey
| | - Esma Gamze Aksel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Edwin Solares
- Computer Science & Engineering Department, University of California, San Diego, California, USA
| | - Vahap Eldem
- Department of Biology, Istanbul University, İstanbul, Turkey
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50
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Lee YJ, Kim WR, Park EG, Lee DH, Kim JM, Shin HJ, Jeong HS, Roh HY, Kim HS. Exploring the Key Signaling Pathways and ncRNAs in Colorectal Cancer. Int J Mol Sci 2024; 25:4548. [PMID: 38674135 PMCID: PMC11050203 DOI: 10.3390/ijms25084548] [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: 03/29/2024] [Revised: 04/19/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer to be diagnosed, and it has a substantial mortality rate. Despite numerous studies being conducted on CRC, it remains a significant health concern. The disease-free survival rates notably decrease as CRC progresses, emphasizing the urgency for effective diagnostic and therapeutic approaches. CRC development is caused by environmental factors, which mostly lead to the disruption of signaling pathways. Among these pathways, the Wingless/Integrated (Wnt) signaling pathway, Phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) signaling pathway, Mitogen-Activated Protein Kinase (MAPK) signaling pathway, Transforming Growth Factor-β (TGF-β) signaling pathway, and p53 signaling pathway are considered to be important. These signaling pathways are also regulated by non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). They have emerged as crucial regulators of gene expression in CRC by changing their expression levels. The altered expression patterns of these ncRNAs have been implicated in CRC progression and development, suggesting their potential as diagnostic and therapeutic targets. This review provides an overview of the five key signaling pathways and regulation of ncRNAs involved in CRC pathogenesis that are studied to identify promising avenues for diagnosis and treatment strategies.
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Affiliation(s)
- Yun Ju Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Woo Ryung Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Eun Gyung Park
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Du Hyeong Lee
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Jung-min Kim
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hae Jin Shin
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyeon-su Jeong
- Department of Integrated Biological Sciences, Pusan National University, Busan 46241, Republic of Korea; (Y.J.L.); (W.R.K.); (E.G.P.); (D.H.L.); (J.-m.K.); (H.J.S.); (H.-s.J.)
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
| | - Hyun-Young Roh
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
| | - Heui-Soo Kim
- Institute of Systems Biology, Pusan National University, Busan 46241, Republic of Korea;
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 46241, Republic of Korea
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