Biochimica et Biophysica Acta-Gene Regulatory Mechanisms最新文献

{"title":"Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis","authors":"Ezaz Ahmad ,&nbsp;Anirban Mitra ,&nbsp;Wareed Ahmed ,&nbsp;Varsha Mahapatra ,&nbsp;Shubhada R. Hegde ,&nbsp;Claudia Sala ,&nbsp;Stewart T. Cole ,&nbsp;Valakunja Nagaraja","doi":"10.1016/j.bbagrm.2023.194923","DOIUrl":"10.1016/j.bbagrm.2023.194923","url":null,"abstract":"<div><p><span><span>Intrinsic and Rho-dependent transcription termination mechanisms regulate gene expression and recycle </span>RNA polymerase in bacteria. Both the modes are well studied in </span><em>Escherichia coli</em><span>, and a few other organisms. The understanding of Rho function is limited in most other bacteria including mycobacteria. Here, we highlight the dominance of Rho-dependent termination in mycobacteria and validate Rho as a key regulatory factor. The lower abundance of intrinsic terminators, high cellular levels of Rho, and its genome-wide association with a majority of transcriptionally active genes indicate the pronounced role of Rho-mediated termination in </span><span><em>Mycobacterium tuberculosis</em></span> (<em>Mtb</em><span>). Rho modulates the termination of RNA synthesis<span> for both protein-coding and stable RNA genes in </span></span><em>Mtb</em><span><span>. Concordantly, the depletion of Rho in mycobacteria impact its growth and enhances the transcription read-through at 3′ ends of the transcription units. We demonstrate that MtbRho is catalytically active in the presence of RNA with varied secondary structures. These properties suggest an evolutionary adaptation of Rho as the efficient and preponderant mode </span>of transcription termination in mycobacteria.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194923"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9897408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"“MiR-7 controls cholesterol biosynthesis through posttranscriptional regulation of DHCR24 expression”","authors":"Mario Fernández-de Frutos ,&nbsp;Virginia Pardo-Marqués ,&nbsp;Marta Torrecilla-Parra ,&nbsp;Patricia Rada ,&nbsp;Ana Pérez-García ,&nbsp;Yolanda Martín-Martín ,&nbsp;Gema de la Peña ,&nbsp;Ana Gómez ,&nbsp;Ana Toledano-Zaragoza ,&nbsp;Diego Gómez-Coronado ,&nbsp;María José Casarejos ,&nbsp;José M. Solís ,&nbsp;Noemí Rotllan ,&nbsp;Óscar Pastor ,&nbsp;María Dolores Ledesma ,&nbsp;Ángela M. Valverde ,&nbsp;Rebeca Busto ,&nbsp;Cristina M. Ramírez","doi":"10.1016/j.bbagrm.2023.194938","DOIUrl":"10.1016/j.bbagrm.2023.194938","url":null,"abstract":"<div><p><span><span><span><span>Dysregulation of cholesterol homeostasis is associated with several pathologies including cardiovascular diseases and neurological disorders such as Alzheimer's disease (AD). </span>MicroRNAs<span> (miRNAs) have emerged as key post-transcriptional regulators of cholesterol metabolism. We previously established the role of miR-7 in regulating insulin resistance and </span></span>amyloidosis, which represents a common pathological feature between type 2 diabetes and AD. We show here an additional metabolic function of miR-7 in </span>cholesterol biosynthesis<span>. We found that miR-7 blocks the last steps of the cholesterol biosynthetic pathway </span></span><em>in vitro</em> by targeting relevant genes including DHCR24 and SC5D posttranscriptionally. Intracranial infusion of miR-7 on an adeno-associated viral vector reduced the expression of DHCR24 in the brain of wild-type mice, supporting <em>in vivo</em> miR-7 targeting. We also found that cholesterol regulates endogenous levels of miR-7 <em>in vitro</em><span>, correlating with transcriptional regulation through SREBP2 binding to its promoter region. In parallel to SREBP2 inhibition, the levels of miR-7 and hnRNPK (the host gene of miR-7) were concomitantly reduced in brain in a mouse model of Niemann Pick type C1 disease and in murine fatty liver, which are both characterized by intracellular cholesterol accumulation. Taken together, the results establish a novel regulatory feedback loop by which miR-7 modulates cholesterol homeostasis at the posttranscriptional level, an effect that could be exploited for therapeutic interventions against prevalent human diseases.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194938"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9898423","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RelB represses miR-193a-5p expression to promote the phenotypic transformation of vascular smooth muscle cells in aortic aneurysm","authors":"Yisi Liu ,&nbsp;Xiaoxiang Tian ,&nbsp;Dan Liu ,&nbsp;Xiaolin Zhang ,&nbsp;Chenghui Yan ,&nbsp;Yaling Han","doi":"10.1016/j.bbagrm.2023.194926","DOIUrl":"10.1016/j.bbagrm.2023.194926","url":null,"abstract":"<div><p>Aortic aneurysm (AA) is a potentially fatal disease with the possibility of rupture, causing high mortality rates with no effective drugs for the treatment of AA. The mechanism of AA, as well as its therapeutic potential to inhibit aneurysm expansion, has been minimally explored. Small non-coding RNA (miRNAs and miRs) is emerging as a new fundamental regulator of gene expression. This study aimed to explore the role and mechanism of miR-193a-5p in abdominal aortic aneurysms (AAA). In AAA vascular tissue and Angiotensin II (Ang II)-treated vascular smooth muscle cells (VSMCs), the expression of miR-193a-5 was determined using real-time quantitative PCR (RT-qPCR). Western blotting was used to detect the effects of miR-193a-5p on PCNA, CCND1, CCNE1, and CXCR4. To detect the effect of miR-193a-5p on the proliferation and migration of VSMCs, CCK-8, and EdU immunostaining, flow cytometry, wound healing, and Transwell Chamber analysis were performed. In vitro results suggest that overexpression of miR-193a-5p inhibited the proliferation and migration of VSMCs, and its inhibition aggravated their proliferation and migration. In VSMCs, miR-193a-5p mediated proliferation by regulating CCNE1 and CCND1 genes and migration by regulating CXCR4. Further, in the Ang II-induced abdominal aorta of mice, the expression of miR-193a-5p was reduced and significantly downregulated in the serum of patients with aortic aneurysm (AA). In vitro studies confirmed that Ang II-induced downregulation of miR-193a-5p in VSMCs by upregulation of the expression of the transcriptional repressor RelB in the promoter region. This study may provide new intervention targets for the prevention and treatment of AA.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194926"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9913915","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"PKI: A bioinformatics method of quantifying the importance of nodes in gene regulatory network via a pseudo knockout index","authors":"Yijuan Wang ,&nbsp;Chao Liu ,&nbsp;Xu Qiao ,&nbsp;Xianhua Han ,&nbsp;Zhi-Ping Liu","doi":"10.1016/j.bbagrm.2023.194911","DOIUrl":"10.1016/j.bbagrm.2023.194911","url":null,"abstract":"<div><h3>Background</h3><p>Gene regulatory network<span> (GRN) is a model that characterizes the complex relationships between genes and thereby provides an informatics environment to measure the importance of nodes. The evaluation of important nodes in a GRN can effectively refer to their functional implications severing as key players in particular biological processes<span>, such as master regulator and driver gene. Currently, it is mainly based on network topological parameters and focuses only on evaluating a single node individually. However, genes and products play their functions by interacting with each other. It is worth noting that the effects of gene combinations in GRN are not simply additive. Key combinations discovery is of significance in revealing gene sets with important functions. Recently, with the development of single-cell RNA-sequencing (scRNA-seq) technology, we can quantify gene expression profiles of individual cells that provide the potential to identify crucial nodes in gene regulations regarding specific condition, e.g., stem cell differentiation.</span></span></p></div><div><h3>Results</h3><p><span>In this paper, we propose a bioinformatics method, called Pseudo Knockout Importance (PKI), to quantify the importance of node and node sets in a specific GRN structure using time-course scRNA-seq data. First, we construct ordinary differential equations to approach the gene regulations during cell differentiation. Then we design gene pseudo knockout experiments and define PKI score evaluation criteria based on the coefficient of determination. The importance of nodes can be described as the influence on the ODE system of removing variables. For key gene combinations, PKI is derived as a combinatorial optimization problem of quantifying the </span><em>in silico</em><span> gene knockout effects.</span></p></div><div><h3>Conclusions</h3><p><span>Here, we focus our analyses on the specific GRN of embryonic stem cells with time series gene expression profile. To verify the effectiveness and advantage of PKI method, we compare its node importance rankings with other twelve kinds of centrality-based methods, such as degree and Latora closeness. For key node combinations, we compare the results with the method based on minimum dominant set. Moreover, the famous combinations of transcription factors in </span>induced pluripotent stem cell are also employed to verify the vital gene combinations identified by PKI. These results demonstrate the reliability and superiority of the proposed method.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194911"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9541644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alzheimer's disease-associated mutant ubiquitin (UBB+1) is secreted through an autophagosome-like vesicle-mediated unconventional pathway","authors":"Ajay R. Wagh,&nbsp;Prasad Sulakshane,&nbsp;Michael H. Glickman","doi":"10.1016/j.bbagrm.2023.194936","DOIUrl":"https://doi.org/10.1016/j.bbagrm.2023.194936","url":null,"abstract":"<div><p><span>Misfolded protein aggregation at both intracellular and extracellular milieus is thought to be the major etiology of Alzheimer's disease (AD). UBB</span>⁺¹, a frameshift variant of the ubiquitin B gene (UBB) results in a folded ubiquitin domain fused to a flexible unstructured extension. Accumulation of UBB⁺¹ in extracellular plaques in the brains of AD patients undoubtedly suggests a role of the ubiquitin-proteasome system in AD. However, the exact mechanism of extracellular secretion of UBB⁺¹ remains unknown.</p><p>In an attempt to understand the molecular mechanism of UBB⁺¹<span> secretion, we performed a survey of secretory pathways and identified the involvement of unconventional autophagosome-mediated UBB</span>⁺¹ secretion. Expression of UBB⁺¹<span><span> was sufficient to stimulate LC3B/Atg8 conversion from LC3B-I to LC3B-II, which indicates initiation of the autophagy pathway. Furthermore, deficiency of ATG5 - a key player in </span>autophagosome formation - inhibited UBB</span>⁺¹ secretion. Based on immunofluorescence 3D structured illumination (SIM) microscopy and co-immunoprecipitation, we provide evidence that UBB⁺¹<span> is associated with the secretory autophagosome marker, SEC22B, while HSP90 possibly acts as a carrier. Using LC-MS/MS and mutagenesis we found that in cells, UBB</span>⁺¹<span><span><span> is ubiquitinated on lysine 11, 29, and 48, however, this ubiquitination does not contribute to its secretion. By contrast, </span>proteasome or </span>lysosome inhibition slightly enhanced secretion. Taken together, this study suggests that by ridding cells of UBB</span>⁺¹, secretory autophagosomes may alleviate the cellular stress associated with UBB⁺¹, yet simultaneously mediate the spreading of a mutant specie with disordered characteristics to the extracellular milieu.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194936"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49865123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sirtuin4 impacts mitochondrial homeostasis in pancreatic cancer cells by reducing the stability of AlkB homolog 1 via deacetylation of the HRD1-SEL1L complex","authors":"Dongnan Ping ,&nbsp;Xiaofan Pu ,&nbsp;Guoping Ding ,&nbsp;Chaolei Zhang ,&nbsp;Junbin Jin ,&nbsp;Chengjie Xu ,&nbsp;Jiazheng Liu ,&nbsp;Shengnan Jia ,&nbsp;Liping Cao","doi":"10.1016/j.bbagrm.2023.194941","DOIUrl":"10.1016/j.bbagrm.2023.194941","url":null,"abstract":"<div><p><span><span><span>Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant tumor with a poor prognosis. As a tumor inhibitor, the specific tumor suppressor mechanism of Sirtuin4(SIRT4) in PDAC remains elusive. In this study, SIRT4 was found to inhibit PDAC by impacting mitochondrial </span>homeostasis. SIRT4 deacetylated lysine 547 of SEL1L and increased the protein level of an E3 </span>ubiquitin ligase<span> HRD1. As a central member of ER-associated protein degradation (ERAD), HRD1-SEL1L complex is recently reported to regulate the mitochondria, though the mechanism is not fully delineated. Here, we found the increase in SEL1L-HRD1 complex decreased the stability of a mitochondrial protein, ALKBH1. Downregulation of ALKBH1 subsequently blocked the transcription of mitochondrial DNA-coded genes, and resulted in mitochondrial damage. Lastly, a putative SIRT4 stimulator, Entinostat, was identified, which upregulated the expression of SIRT4 and effectively inhibited pancreatic cancer </span></span><em>in vivo</em> and <em>in vitro</em>.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194941"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9596953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced gene regulation by cooperation between mRNA decay and gene transcription","authors":"José García-Martínez ,&nbsp;Abhyudai Singh ,&nbsp;Daniel Medina ,&nbsp;Sebastián Chávez ,&nbsp;José E. Pérez-Ortín","doi":"10.1016/j.bbagrm.2023.194910","DOIUrl":"10.1016/j.bbagrm.2023.194910","url":null,"abstract":"<div><p>It has become increasingly clear in the last few years that gene expression in eukaryotes is not a linear process from mRNA synthesis in the nucleus to translation and degradation in the cytoplasm, but works as a circular one where the mRNA level is controlled by crosstalk between nuclear transcription and cytoplasmic decay pathways. One of the consequences of this crosstalk is the approximately constant level of mRNA. This is called mRNA buffering and happens when transcription and mRNA degradation act at compensatory rates. However, if transcription and mRNA degradation act additively, enhanced gene expression regulation occurs. In this work, we analyzed new and previously published genomic datasets obtained for several yeast mutants related to either transcription or mRNA decay that are not known to play any role in the other process. We show that some, which were presumed only transcription factors (Sfp1) or only decay factors (Puf3, Upf2/3), may represent examples of RNA-binding proteins (RBPs) that make specific crosstalk to enhance the control of the mRNA levels of their target genes by combining additive effects on transcription and mRNA stability. These results were mathematically modeled to see the effects of RBPs when they have positive or negative effects on mRNA synthesis and decay rates. We found that RBPs can be an efficient way to buffer or enhance gene expression responses depending on their respective effects on transcription and mRNA stability.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194910"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9897396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Histone H4K20 monomethylation enables recombinant nucleosome methylation by PRMT1 in vitro","authors":"Alice Shi Ming Li ,&nbsp;Charles Homsi ,&nbsp;Eric Bonneil ,&nbsp;Pierre Thibault ,&nbsp;Alain Verreault ,&nbsp;Masoud Vedadi","doi":"10.1016/j.bbagrm.2023.194922","DOIUrl":"10.1016/j.bbagrm.2023.194922","url":null,"abstract":"<div><p><span><span>Protein arginine methyltransferases<span> (PRMTs) catalyze the transfer of methyl groups to specific arginine residues of histones and nonhistone proteins. There are nine members in the PRMT family (PRMT1 to PRMT9), and </span></span>PRMT1<span> is a dominant member catalyzing majority of arginine methylation in the cell. However, none of the PRMTs is active with recombinant nucleosome as substrate </span></span><em>in vitro</em><span>. Here, we report the discovery of the first in class novel crosstalk between histone H4 lysine 20 (H4K20) monomethylation on nucleosome by SETD8 and histone H4 arginine 3 (H4R3) methylation by PRMT1 </span><em>in vitro</em>. Full kinetic characterization and mass spectrometry analysis indicated that PRMT1 is only active with recombinant nucleosomes monomethylated at H4K20 by SETD8. These data suggests that the level of activity of PRMT1 could potentially be regulated selectively by SETD8 in various pathways, providing a new approach for discovery of selective regulators of PRMT1 activity.</p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194922"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9897407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"GLI1, a novel target of the ER stress regulator p97/VCP, promotes ATF6f-mediated activation of XBP1","authors":"Luciana L. Almada ,&nbsp;Kim Barroso ,&nbsp;Sandhya Sen ,&nbsp;Murat Toruner ,&nbsp;Ashley N. Sigafoos ,&nbsp;Glancis L. Raja Arul ,&nbsp;David R. Pease ,&nbsp;Renzo E. Vera ,&nbsp;Rachel L.O. Olson ,&nbsp;Holger W. Auner ,&nbsp;Rémy Pedeux ,&nbsp;Juan L. Iovanna ,&nbsp;Eric Chevet ,&nbsp;Martin E. Fernandez-Zapico","doi":"10.1016/j.bbagrm.2023.194924","DOIUrl":"10.1016/j.bbagrm.2023.194924","url":null,"abstract":"<div><p><span><span><span>Upon accumulation of improperly folded proteins in the Endoplasmic Reticulum (ER), the Unfolded Protein Response<span> (UPR) is triggered to restore ER homeostasis<span>. The induction of stress genes is a sine qua non condition for effective adaptive UPR. Although this requirement has been extensively described, the mechanisms underlying this process remain in part uncharacterized. Here, we show that p97/VCP, an AAA+ ATPase known to contribute to ER stress-induced gene expression, regulates the transcription factor </span></span></span>GLI1, a primary effector of Hedgehog (Hh) signaling. Under basal (non-ER stress) conditions, GLI1 is repressed by a p97/VCP-HDAC1 complex while upon </span>ER stress<span> GLI1 is induced through a mechanism requiring both USF2 binding and increase </span></span>histone acetylation<span><span> at its promoter. Interestingly, the induction of GLI1 was independent of ligand-regulated Hh signaling. Further analysis showed that GLI1 cooperates with ATF6f to induce promoter activity and expression of XBP1, a key transcription factor driving UPR. Overall, our work demonstrates a novel role for GLI1 in the regulation of ER stress gene expression and defines the interplay between p97/VCP, </span>HDAC1 and USF2 as essential players in this process.</span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194924"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9543929","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Novel splice variants of LINC00963 suppress colorectal cancer cell proliferation via miR-10a/miR-143/miR-217/miR-512-mediated regulation of PI3K/AKT and Wnt/β-catenin signaling pathways","authors":"Zahra Ghaemi,&nbsp;Seyed Javad Mowla,&nbsp;Bahram Mohammad Soltani","doi":"10.1016/j.bbagrm.2023.194921","DOIUrl":"10.1016/j.bbagrm.2023.194921","url":null,"abstract":"<div><p><span><span><span><span>Emerging evidence has shown lncRNAs play important roles in </span>signaling pathways involved in colorectal cancer (CRC) carcinogenesis. However, only a few functional lncRNAs have been extensively researched, especially in CRC-related signaling pathways. Looking for novel candidate regulators of CRC incidence and progression, using available RNA-seq and microarray datasets, LINC00963 was introduced as a bona fide oncogenic-lncRNA. Consistently, RT-qPCR results showed that LINC00963 was up-regulated in CRC tissues. However, our attempt to amplify the full-length lncRNA from cDNA resulted in the discovery of two novel variants (LINC00963-v2 &amp; LINC00963-v3) that surprisingly, were downregulated in CRC tissues, detected by RT-qPCR. Overexpression of LINC00963-v2/-v3 in HCT116 and SW480 cells resulted in downregulation of the major </span>oncogenes and upregulation of the main </span>tumor suppressor genes<span> involved in PI3K and Wnt signaling<span>, verified through RT-qPCR, western blotting, and TOPFlash assays. Mechanistic studies revealed that LINC00963-v2/-v3 exert their effect on PI3K and Wnt signaling through sponging miR-10a-5p, miR-143-3p, miR-217, and miR-512-3p, which in turn these miRNAs are fine-regulators of </span></span></span><em>PTEN</em>, <em>APC1</em>, and <em>Axin1</em><span> tumor suppressor<span><span> genes verified by dual-luciferase assay and RT-qPCR. At cellular levels, LINC00963-v2/-v3 overexpression suppressed cell proliferation, viability, and migration while increasing the apoptosis of CRC cell lines, detected by </span>PI flow cytometry, colony formation, MTT, RT-qPCR, wound-healing, Transwell, AnnexinV-PE/7AAD, caspase3/7 activity assays, and Hoechst/PI-AO/EB staining. Overall, our results indicate that LINC00963-v2 &amp; -v3 are novel tumor suppressor ceRNAs that attenuate the PI3K and Wnt pathways during CRC incidence and these lncRNAs may serve as potential targets for CRC therapy.</span></span></p></div>","PeriodicalId":55382,"journal":{"name":"Biochimica et Biophysica Acta-Gene Regulatory Mechanisms","volume":"1866 2","pages":"Article 194921"},"PeriodicalIF":4.7,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9541645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}