1
|
Wang S, Qi X, Liu D, Xie D, Jiang B, Wang J, Wang X, Wu G. The implications for urological malignancies of non-coding RNAs in the the tumor microenvironment. Comput Struct Biotechnol J 2024; 23:491-505. [PMID: 38249783 PMCID: PMC10796827 DOI: 10.1016/j.csbj.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
Urological malignancies are a major global health issue because of their complexity and the wide range of ways they affect patients. There's a growing need for in-depth research into these cancers, especially at the molecular level. Recent studies have highlighted the importance of non-coding RNAs (ncRNAs) – these don't code for proteins but are crucial in controlling genes – and the tumor microenvironment (TME), which is no longer seen as just a background factor but as an active player in cancer progression. Understanding how ncRNAs and the TME interact is key for finding new ways to diagnose and predict outcomes in urological cancers, and for developing new treatments. This article reviews the basic features of ncRNAs and goes into detail about their various roles in the TME, focusing specifically on how different ncRNAs function and act in urological malignancies.
Collapse
Affiliation(s)
- Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaochen Qi
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Deqian Xie
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Bowen Jiang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| |
Collapse
|
2
|
Ocampo D, Damon LJ, Sanford L, Holtzen SE, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of p53 to DNA. Life Sci Alliance 2024; 7:e202402638. [PMID: 38969365 PMCID: PMC11231577 DOI: 10.26508/lsa.202402638] [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: 02/01/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 07/07/2024] Open
Abstract
Zn2+ is an essential metal required by approximately 850 human transcription factors. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Using ATAC-seq to profile regions of accessible chromatin coupled with transcription factor enrichment analysis, we examined how increases and decreases in the labile zinc pool affect chromatin accessibility and transcription factor enrichment. We found 685 transcription factor motifs were differentially enriched, corresponding to 507 unique transcription factors. The pattern of perturbation and the types of transcription factors were notably different at promoters versus intergenic regions, with zinc-finger transcription factors strongly enriched in intergenic regions in elevated Zn2+ To test whether ATAC-seq and transcription factor enrichment analysis predictions correlate with changes in transcription factor binding, we used ChIP-qPCR to profile six p53 binding sites. We found that for five of the six targets, p53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc alter chromatin accessibility and transcription factor binding to DNA.
Collapse
Affiliation(s)
- Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Leah J Damon
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Samuel E Holtzen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Mary A Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Robin D Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| |
Collapse
|
3
|
Zhang X, Yang F, Zhu T, Zhao X, Zhang J, Wen J, Zhang Y, Wang G, Ren X, Chen A, Wang X, Wang L, Lv X, Yang W, Qu C, Wang H, Ning Z, Qu L. Whole genome resequencing reveals genomic regions related to red plumage in ducks. Poult Sci 2024; 103:103694. [PMID: 38663207 PMCID: PMC11068611 DOI: 10.1016/j.psj.2024.103694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 05/07/2024] Open
Abstract
Plumage color is a characteristic trait of ducks that originates as a result of natural and artificial selection. As a conspicuous phenotypic feature, it is a breed characteristic. Previous studies have identified some genes associated with the formation of black and white plumage in ducks. However, studies on the genetic basis underlying the red plumage phenotype in ducks are limited. Here, genome-wide association analysis (GWAS) and selection signal detection (Fst, θπ ratio, and cross-population composite likelihood ratio [XP-CLR]) were conducted to identify candidate regions and genes underlying duck plumage color phenotype. Selection signal detection revealed 29 overlapping genes (including ENPP1 and ULK1) significantly associated with red plumage color in Ji'an Red ducks. ENSAPLG00000012679, ESRRG, and SPATA5 were identified as candidate genes associated with red plumage using GWAS. Selection signal detection revealed that 19 overlapping genes (including GMDS, PDIA6, and ODC1) significantly correlated with light brown plumage in Brown Tsaiya ducks. GWAS to narrow down the significant regions further revealed nine candidate genes (AKT1, ATP6V1C2, GMDS, LRP4, MAML3, PDIA6, PLD5, TMEM63B, and TSPAN8). Notably, in Brown Tsaiya ducks, GMDS, ODC1, and PDIA6 exhibit significantly differentiated allele frequencies among other feather-colored ducks, while in Ji'an Red ducks, ENSAPLG00000012679 has different allele frequency distributions compared with that in other feather-colored ducks. This study offers new insights into the variation and selection of the red plumage phenotype using GWAS and selective signals.
Collapse
Affiliation(s)
- Xinye Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Fangxi Yang
- Beijing Nankou Duck Breeding Technology Co., Ltd., Beijing, China
| | - Tao Zhu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiurong Zhao
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinxin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Junhui Wen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xufang Ren
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Anqi Chen
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Daxing District, Beijing, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, China
| | - Huie Wang
- College of Animal Science, Tarim University, Xinjiang, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
4
|
Armstrong L, Willoughby CE, McKenna DJ. The Suppression of the Epithelial to Mesenchymal Transition in Prostate Cancer through the Targeting of MYO6 Using MiR-145-5p. Int J Mol Sci 2024; 25:4301. [PMID: 38673886 PMCID: PMC11050364 DOI: 10.3390/ijms25084301] [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: 03/19/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Aberrant expression of miR-145-5p has been observed in prostate cancer where is has been suggested to play a tumor suppressor role. In other cancers, miR-145-5p acts as an inhibitor of epithelial-to-mesenchymal transition (EMT), a key molecular process for tumor progression. However, the interaction between miR-145-5p and EMT remains to be elucidated in prostate cancer. In this paper the link between miR-145-5p and EMT in prostate cancer was investigated using a combination of in silico and in vitro analyses. miR-145-5p expression was significantly lower in prostate cancer cell lines compared to normal prostate cells. Bioinformatic analysis of The Cancer Genome Atlas prostate adenocarcinoma (TCGA PRAD) data showed significant downregulation of miR-145-5p in prostate cancer, correlating with disease progression. Functional enrichment analysis significantly associated miR-145-5p and its target genes with EMT. MYO6, an EMT-associated gene, was identified and validated as a novel target of miR-145-5p in prostate cancer cells. In vitro manipulation of miR-145-5p levels significantly altered cell proliferation, clonogenicity, migration and expression of EMT-associated markers. Additional TCGA PRAD analysis suggested miR-145-5p tumor expression may be useful predictor of disease recurrence. In summary, this is the first study to report that miR-145-5p may inhibit EMT by targeting MYO6 in prostate cancer cells. The findings suggest miR-145-5p could be a useful diagnostic and prognostic biomarker for prostate cancer.
Collapse
Affiliation(s)
| | | | - Declan J. McKenna
- Genomic Medicine Research Group, Ulster University, Cromore Road, Coleraine BT52 1SA, UK; (L.A.); (C.E.W.)
| |
Collapse
|
5
|
Zhang W, Zhu F, Zhu J, Liu K. Phospholipase D, a Novel Therapeutic Target Contributes to the Pathogenesis of Neurodegenerative and Neuroimmune Diseases. Anal Cell Pathol (Amst) 2024; 2024:6681911. [PMID: 38487684 PMCID: PMC10940030 DOI: 10.1155/2024/6681911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 01/10/2024] [Accepted: 02/14/2024] [Indexed: 03/17/2024] Open
Abstract
Phospholipase D (PLD) is an enzyme that consists of six isoforms (PLD1-PLD6) and has been discovered in different organisms including bacteria, viruses, plants, and mammals. PLD is involved in regulating a wide range of nerve cells' physiological processes, such as cytoskeleton modulation, proliferation/growth, vesicle trafficking, morphogenesis, and development. Simultaneously, PLD, which also plays an essential role in the pathogenesis of neurodegenerative and neuroimmune diseases. In this review, family members, characterizations, structure, functions and related signaling pathways, and therapeutic values of PLD was summarized, then five representative diseases including Alzheimer disease (AD), Parkinson's disease (PD), etc. were selected as examples to tell the involvement of PLD in these neurological diseases. Notably, recent advances in the development of tools for studying PLD therapy envisaged novel therapeutic interventions. Furthermore, the limitations of PLD based therapy were also analyzed and discussed. The content of this review provided a thorough and reasonable basis for further studies to exploit the potential of PLD in the treatment of neurodegenerative and neuroimmune diseases.
Collapse
Affiliation(s)
- Weiwei Zhang
- Neuroscience Center, Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Feiqi Zhu
- Cognitive Impairment Ward of Neurology Department, The Third Affiliated Hospital of Shenzhen University Medical College, Shenzhen, China
| | - Jie Zhu
- Neuroscience Center, Department of Neurology, The First Hospital of Jilin University, Changchun, China
- Department of Neurobiology, Care Sciences and Society, Karolinska Institute, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Kangding Liu
- Neuroscience Center, Department of Neurology, The First Hospital of Jilin University, Changchun, China
| |
Collapse
|
6
|
Damon LJ, Ocampo D, Sanford L, Jones T, Allen MA, Dowell RD, Palmer AE. Cellular zinc status alters chromatin accessibility and binding of transcription factor p53 to genomic sites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.20.567954. [PMID: 38045276 PMCID: PMC10690171 DOI: 10.1101/2023.11.20.567954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Zinc (Zn2+) is an essential metal required by approximately 2500 proteins. Nearly half of these proteins act on DNA, including > 850 human transcription factors, polymerases, DNA damage response factors, and proteins involved in chromatin architecture. How these proteins acquire their essential Zn2+ cofactor and whether they are sensitive to changes in the labile Zn2+ pool in cells remain open questions. Here, we examine how changes in the labile Zn2+ pool affect chromatin accessibility and transcription factor binding to DNA. We observed both increases and decreases in accessibility in different chromatin regions via ATAC-seq upon treating MCF10A cells with elevated Zn2+ or the Zn2+-specific chelator tris(2-pyridylmethyl)amine (TPA). Transcription factor enrichment analysis was used to correlate changes in chromatin accessibility with transcription factor motifs, revealing 477 transcription factor motifs that were differentially enriched upon Zn2+ perturbation. 186 of these transcription factor motifs were enriched in Zn2+ and depleted in TPA, and the majority correspond to Zn2+ finger transcription factors. We selected TP53 as a candidate to examine how changes in motif enrichment correlate with changes in transcription factor occupancy by ChIP-qPCR. Using publicly available ChIP-seq and nascent transcription datasets, we narrowed the 50,000+ ATAC-seq peaks to 2164 TP53 targets and subsequently selected 6 high-probability TP53 binding sites for testing. ChIP-qPCR revealed that for 5 of the 6 targets, TP53 binding correlates with the local accessibility determined by ATAC-seq. These results demonstrate that changes in labile zinc directly alter chromatin accessibility and transcription factor binding to DNA.
Collapse
Affiliation(s)
- Leah J. Damon
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Daniel Ocampo
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
| | - Lynn Sanford
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Taylor Jones
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
| | - Mary A. Allen
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Robin D. Dowell
- Department of Molecular, Cellular, Developmental Biology, University of Colorado, Boulder, 80309
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| | - Amy E. Palmer
- Department of Biochemistry, University of Colorado, Boulder, CO 80303
- BioFrontiers Institute, University of Colorado, Boulder, CO 80303
| |
Collapse
|
7
|
Wolf A, Tanguy E, Wang Q, Gasman S, Vitale N. Phospholipase D and cancer metastasis: A focus on exosomes. Adv Biol Regul 2023; 87:100924. [PMID: 36272918 DOI: 10.1016/j.jbior.2022.100924] [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: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/10/2022] [Indexed: 03/01/2023]
Abstract
In mammals, phospholipase D (PLD) enzymes involve 6 isoforms, of which only three have established lipase activity to produce the signaling lipid phosphatidic acid (PA). This phospholipase activity has been postulated to contribute to cancer progression for over three decades now, but the exact mechanisms involved have yet to be uncovered. Indeed, using various models, an altered PLD activity has been proposed altogether to increase cell survival rate, promote angiogenesis, boost rapamycin resistance, and favor metastasis. Although for some part, the molecular pathways by which this increase in PA is pro-oncogenic are partially known, the pleiotropic functions of PA make it quite difficult to distinguish which among these simple signaling pathways is responsible for each of these PLD facets. In this review, we will describe an additional potential contribution of PA generated by PLD1 and PLD2 in the biogenesis, secretion, and uptake of exosomes. Those extracellular vesicles are now viewed as membrane vehicles that carry informative molecules able to modify the fate of receiving cells at distance from the original tumor to favor homing of metastasis. The perspectives for a better understanding of these complex role of PLDs will be discussed.
Collapse
Affiliation(s)
- Alexander Wolf
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Emeline Tanguy
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Qili Wang
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Stéphane Gasman
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France
| | - Nicolas Vitale
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, Strasbourg, France.
| |
Collapse
|
8
|
Matulić M, Gršković P, Petrović A, Begić V, Harabajsa S, Korać P. miRNA in Molecular Diagnostics. Bioengineering (Basel) 2022; 9:bioengineering9090459. [PMID: 36135005 PMCID: PMC9495386 DOI: 10.3390/bioengineering9090459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/05/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized.
Collapse
Affiliation(s)
- Maja Matulić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Paula Gršković
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Andreja Petrović
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Institute of Clinical Pathology and Cytology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Valerija Begić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Primary School “Sesvetski Kraljevec”, 10361 Sesvetski Kraljevec, Croatia
| | - Suzana Harabajsa
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Department of Pathology and Cytology, Division of Pulmonary Cytology Jordanovac, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4606-278
| |
Collapse
|
9
|
Ding R, Hong W, Huang L, Shao J, Yu W, Xu X. Examination of the effects of microRNA-145-5p and phosphoserine aminotransferase 1 in colon cancer. Bioengineered 2022; 13:12794-12806. [PMID: 35615948 PMCID: PMC9275947 DOI: 10.1080/21655979.2022.2071010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Previous studies manifested that microRNA-145-5p is pivotal in the development of various cancers. Nevertheless, the potential function of microRNA-145-5p in colorectal cancer remains unclear. This study attempted to investigate the potential role and possible mechanism of microRNA-145-5p in colon cancer. MicroRNA-145-5p and phosphoserine aminotransferase 1 (PSAT1) levels in colon cancer cells were assayed via quantitative reverse transcription polymerase chain reaction (qRT-PCR). Cell proliferation and cell cycle status were assessed using Cell Counting Kit-8, colony formation, and flow cytometry. The target binding relationship of microRNA-145-5p and PSAT1 was identified using bioinformatics analysis and dual-luciferase reporter gene assay. The result of qRT-PCR disclosed that microRNA-145-5p was markedly down-regulated and PSAT1 level was up-regulated in colon cancer cell lines. Besides, enforced microRNA-145-5p level repressed proliferation of colon cancer cells, and cells were arrested in G0-G1 phase. Bioinformatics analysis and dual-luciferase reporter genes confirmed that PSAT1 was a downstream target of microRNA-145-5p. Enforced PSAT1 level remarkably modulated cell cycle and fostered cell proliferation. Furthermore, rescue experiments displayed that microRNA-145-5p restrained cell cycle progression and cell proliferation and forced PSAT1 level could partially reverse this process. Taken together, our findings demonstrated that microRNA-145-5p repressed colon cancer cell cycle progression and cell proliferation via targeting PSAT1. Our findings identified microRNA-145-5p as an essential tumor repressor gene in colon cancer and may provide a novel biomarker for colon cancer.
Collapse
Affiliation(s)
- Ruliang Ding
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| | - Weiwen Hong
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| | - Liang Huang
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| | - Jinfan Shao
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| | - Wenfeng Yu
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| | - Xijuan Xu
- Department of Anorectal Surgery, Taizhou First People's Hospital, Taizhou, Zhejiang Province, China
| |
Collapse
|
10
|
Zhou Y, Cai W, Lu H. Overexpression of microRNA-145 enhanced docetaxel sensitivity in breast cancer cells via inactivation of protein kinase B gamma-mediated phosphoinositide 3-kinase -protein kinase B pathway. Bioengineered 2022; 13:11310-11320. [PMID: 35499128 PMCID: PMC9278436 DOI: 10.1080/21655979.2022.2068756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Chemoresistance is a major challenge for the treatment of breast cancer (BC). Previous studies showed that miR-145 level decreases in chemoresistant BC tissues. Nevertheless, the biological function of miR-145 on docetaxel resistance of BC cells remains unclear, which is what our research attempted to clarify. RT-qPCR analyzed miR-145 level, and cell viability and colony formation assays assessed the impact of miR-145 on docetaxel resistance. Molecular mechanisms of miR-145-mediated docetaxel sensitivity were examined by Luciferase reporter assay and Western Blot assessed the function of AKT3 and PI3K/AKT signaling. Our research found that miR-145 expression presented significant downregulation in docetaxel-resistant BC cells. Meanwhile, miR-145 overexpression facilitated the docetaxel sensitivity of BC cells in vivo and in vitro, while the miR-145 inhibitor decreased the sensitivity of BC cells to docetaxel. We also observed that miR-145 inhibited docetaxel resistance mainly via downregulation of the AKT3 expression and further inhibited PI3K/AKT pathway. To conclude, this research provides a novel strategy for improving chemosensitivity through the newly identified miR-145-AKT3/PI3K-AKT signaling pathway in BC.
Collapse
Affiliation(s)
- Ying Zhou
- Department of Oncology, Suzhou Ninth People’s Hospital, Suzhou, Jiangsu, China
| | - Wei Cai
- Department of Oncology, Suzhou Ninth People’s Hospital, Suzhou, Jiangsu, China
| | - Hailin Lu
- Department of Oncology, Suzhou Ninth People’s Hospital, Suzhou, Jiangsu, China
| |
Collapse
|
11
|
Hsieh YH, Yu FJ, Nassef Y, Liu CJ, Chen YS, Lin CY, Feng JL, Wu MH. Targeting of Mcl-1 Expression by MiRNA-3614-5p Promotes Cell Apoptosis of Human Prostate Cancer Cells. Int J Mol Sci 2022; 23:ijms23084194. [PMID: 35457012 PMCID: PMC9029607 DOI: 10.3390/ijms23084194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/03/2022] [Accepted: 04/08/2022] [Indexed: 02/01/2023] Open
Abstract
MicroRNA (miRNA) acts as a critical regulator of growth in various human malignancies. However, the role of miRNA-3614 in the progression of human prostate cancer remains unknown. In this study, our results demonstrated that miRNA-3614-5p exerts a significant inhibitory effect on cell viability and colony formation and induces sub-G1 cell cycle arrest and apoptosis in human prostate cancer cells. Myeloid cell leukemia-1 (Mcl-1) acts as a master regulator of cell survival. Using the miRNA databases, miRNA-3614-5p was found to regulate Mcl-1 expression by targeting positions of the Mcl-1-3′ UTR. The reduction of Mcl-1 expression by miRNA-3614-5p was further confirmed using an immunoblotting assay. Pro-apoptotic caspase-3 and poly (ADP-ribose) polymerase (PARP) were significantly activated by miRNA-3614-5p to generate cleaved caspase-3 (active caspase-3) and cleaved PARP (active PARP), accompanied by the inhibited Mcl-1 expression. These findings were the first to demonstrate the anti-growth effects of miRNA-3614-5p through downregulating Mcl-1 expression in human prostate cancer cells.
Collapse
Affiliation(s)
- Yi-Hsien Hsieh
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-H.H.); (Y.N.); (Y.-S.C.)
- Department of Medical Research, Chung Shan Medical University Hospital, Taichung 40201, Taiwan
| | - Fang-Jung Yu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (F.-J.Y.); (C.-J.L.)
- Department of Medicine, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yasser Nassef
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-H.H.); (Y.N.); (Y.-S.C.)
| | - Chung-Jung Liu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan; (F.-J.Y.); (C.-J.L.)
- Regenetative Medicine and Cell Therapy Research Center, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yong-Syuan Chen
- Institute of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan; (Y.-H.H.); (Y.N.); (Y.-S.C.)
| | - Ching-Yi Lin
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan;
| | - Jia-Liang Feng
- Laboratory Department, Chung-Kang Branch, Cheng-Ching General Hospital, Taichung 40764, Taiwan
- Department of Medicinal Botanicals and Health Applications, Da-Yeh University, Chunghua 515006, Taiwan
- Correspondence: (J.-L.F.); (M.-H.W.)
| | - Min-Hua Wu
- Laboratory Department, Chung-Kang Branch, Cheng-Ching General Hospital, Taichung 40764, Taiwan
- Department of Medicinal Botanicals and Health Applications, Da-Yeh University, Chunghua 515006, Taiwan
- Correspondence: (J.-L.F.); (M.-H.W.)
| |
Collapse
|
12
|
Wang H, Lian X, Gao W, Gu J, Shi H, Ma Y, Li Y, Fan Y, Wang Q, Wang L. Long noncoding RNA H19 suppresses cardiac hypertrophy through the MicroRNA-145-3p/SMAD4 axis. Bioengineered 2022; 13:3826-3839. [PMID: 35139769 PMCID: PMC8973863 DOI: 10.1080/21655979.2021.2017564] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 02/08/2023] Open
Abstract
Sustained cardiac hypertrophy (CH) contributes to many heart diseases. Long noncoding RNAs (lncRNAs) collectively play critical roles in cardiovascular diseases (CVDs). However, the roles of lncRNA H19 in CH are still unclear. A CH model was constructed utilizing isoproterenol (ISO). We demonstrated H19 could participate in regulating ISO-induced CH development both in vivo and in vitro. The online databases DIANA and TargetScan were used to predict the targets of H19 and MicroRNA-145-3p (miR-145-3p), respectively. Luciferase reporter assay was used to verify the downstream targets. The results showed that H19 was decreased under ISO stimulation. The H19 overexpression resulted in significant decrease in mouse heart size and weight, left ventricular systolic dysfunction, left ventricular posterior wall thickness and cardiac hypertrophic growth, while promoted the increase of left ventricular ejection fraction and left ventricle fraction shortening. H19 also inhibited protein expression levels of CH markers, such as atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and MYH7. Luciferase assays results showed that miR-145-3p was a target of H19 and SMAD4 was a target of miR-145-3p. We found that H19 regulated SMAD4 by sponging miR-145-3p. Knockout of miR-145-3p or overexpression of SMAD4 facilitated H19-induced decreases in ANP, BNP, and MYH7. Collectively, our findings have indicated that the H19/miR-145-3p/SMAD4 axis should be a negative regulator involved in CH progression.
Collapse
Affiliation(s)
- Hao Wang
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqing Lian
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Gao
- Department of Geriatrics, Sir Run Run Hospital of Nanjing Medical University, Nanjing, China
| | - Jie Gu
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haojie Shi
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yao Ma
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yafei Li
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Fan
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiming Wang
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liansheng Wang
- Department of Cardiology, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| |
Collapse
|
13
|
Role of miRNA-145, 148, and 185 and Stem Cells in Prostate Cancer. Int J Mol Sci 2022; 23:ijms23031626. [PMID: 35163550 PMCID: PMC8835890 DOI: 10.3390/ijms23031626] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/11/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that play a role in cancer linked to the regulation of important cellular processes and pathways involving tumorigenesis, cell proliferation, differentiation, and apoptosis. A lot of human miRNA sequences have been identified which are linked to cancer pathogenesis. MicroRNAs, in prostate cancer (PC), play a relevant role as biomarkers, show a specific profile, and have been used as therapeutic targets. Prostate cancer (PC) is the most frequently diagnosed cancer in men. Clinical diagnoses among the gold standards for PC diagnosis and monitoring are prostate-specific antigen (PSA) testing, digital rectal examination, and prostate needle biopsies. PSA screening still has a large grey area of patients, which leads to overdiagnosis. Therefore, new biomarkers are needed to improve existing diagnostic tools. The miRNA expression profiles from tumour versus normal tissues are helpful and exhibit significant differences not only between cancerous and non-cancerous tissues, but also between different cancer types and subtypes. In this review, we focus on the role of miRNAs-145, 148, and 185 and their correlation with stem cells in prostate cancer pathogenesis. MiR-145, by modulating multiple oncogenes, regulates different cellular processes in PC, which are involved in the transition from localised to metastatic disease. MiR-148 is downregulated in high-grade tumours, suggesting that the miR-148-3 family might act as tumour suppressors in PC as a potential biomarker for detecting this disease. MiR-185 regulation is still unclear in being able to regulate tumour processes in PC. Nevertheless, other authors confirm the role of this miRNA as a tumour suppressor, suggesting its potential use as a suitable biomarker in disease prognosis. These three miRNAs are all involved in the regulation of prostate cancer stem cell behaviour (PCSCs). Within this contest, PCSCs are often involved in the onset of chemo-resistance in PC, therefore strategies for targeting this subset of cells are strongly required to control the disease. Hence, the relationship between these two players is interesting and important in prostate cancer pathogenesis and in PCSC stemness regulation, in the attempt to pave the way for novel therapeutic targets in prostate cancer.
Collapse
|
14
|
Kattan RE, Han H, Seo G, Yang B, Lin Y, Dotson M, Pham S, Menely Y, Wang W. Interactome analysis of human phospholipase D and phosphatidic acid-associated protein network. Mol Cell Proteomics 2022; 21:100195. [PMID: 35007762 PMCID: PMC8864472 DOI: 10.1016/j.mcpro.2022.100195] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/22/2021] [Accepted: 01/06/2022] [Indexed: 01/01/2023] Open
Abstract
Mammalian phospholipase D (PLD) enzyme family consists of six members. Among them, PLD1/2/6 catalyzes phosphatidic acid (PA) production, while PLD3/4/5 has no catalytic activities. Deregulation of the PLD-PA lipid signaling has been associated with various human diseases including cancer. However, a comprehensive analysis of the regulators and effectors for this crucial lipid metabolic pathway has not been fully achieved. Using a proteomic approach, we defined the protein interaction network for the human PLD family of enzymes and PA and revealed diverse cellular signaling events involving them. Through it, we identified PJA2 as a novel E3 ubiquitin ligase for PLD1 involved in control of the PLD1-mediated mammalian target of rapamycin signaling. Additionally, we showed that PA interacted with and positively regulated sphingosine kinase 1. Taken together, our study not only generates a rich interactome resource for further characterizing the human PLD-PA lipid signaling but also connects this important metabolic pathway with numerous biological processes. Defining the interactome of human phospholipase D enzymes and phosphatidic acid. PJA2 functions as an E3 ubiquitin ligase of phospholipase D1. Phosphatidic acid interacts with and positively regulates sphingosine kinase 1.
Collapse
Affiliation(s)
- Rebecca Elizabeth Kattan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Han Han
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Gayoung Seo
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Bing Yang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Yongqi Lin
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Max Dotson
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Stephanie Pham
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Yahya Menely
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Wenqi Wang
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
| |
Collapse
|
15
|
Hong X, Mao L, Xu L, Hu Q, Jia R. Prostate-specific membrane antigen modulates the progression of prostate cancer by regulating the synthesis of arginine and proline and the expression of androgen receptors and Fos proto-oncogenes. Bioengineered 2022; 13:995-1012. [PMID: 34974814 PMCID: PMC8805960 DOI: 10.1080/21655979.2021.2016086] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The expression of prostate-specific membrane antigen (PSMA) is strikingly upregulated during oncogenesis and prostate cancer (PCa) progression, but the functions of this antigen in PCa remain unclear. Here, we constructed PSMA-knockdown LNCaP and 22rv1 cell lines and performed metabonomic and transcriptomic analyses to determine the effects of PSMA on PCa metabolism and transcription. The metabolism of arginine and proline was detected using specific kits. The mRNA and protein expression levels of the identified differentially expressed genes were quantified by RT-qPCR and Western blotting. The proliferation of each cell line was evaluated through CCK-8, EdU and colony formation assays. The migration and invasion abilities of each cell line were detected using wound healing and transwell assays, respectively. PSMA knockdown led to metabolic disorder and abnormal transcription in PCa and resulted in inhibition of the proliferation and metastasis of PCa cells in vitro and in vivo. The depletion of PSMA also promoted the biosynthesis of arginine and proline, inhibited the expression of AR and PSA, and induced the expression of c-Fos and FosB. PSMA plays an important role in the metabolism, proliferation and metastasis of human PCa and may be a promising therapeutic target.
Collapse
Affiliation(s)
- Xi Hong
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Liang Mao
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Qiang Hu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| |
Collapse
|
16
|
Li C, Zhang D, Tian S. Clinical significance of microRNA-1180-3p for colorectal cancer and effect of its alteration on cell function. Bioengineered 2021; 12:10491-10500. [PMID: 34723759 PMCID: PMC8810127 DOI: 10.1080/21655979.2021.1997694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
An early diagnosis and effective prognostic factors would greatly reduce the mortality rate of colorectal cancer (CRC). This research is intended to complete the evaluation of the prognostic value and potential role of miR-1180-3p in CRC. The miR-1180-3p levels were reduced in CRC patients’ tissues, blood, and human CRC cell lines. The ability of miR-1180-3p was explored in discrimination of CRC patients and healths and the value in overall survival estimate. The effect of miR-1180-3p dysregulation on the CRC cellular function was investigated. miR-1180-3p is downregulated in CRC tissues, blood and cells than normal ones. This lower expression was correlated with vascular invasion, lymph node metastasis, and TNM stage. With the use of ROC curve, miR-1180-3p showed discriminating ability in CRC patients and healthy subjects. With the result of Kaplan–Meier analysis and multi-multivariate Cox analysis, miR-1180-3p was an independent predictor for CRC patients’ overall survival. Utilizing CCK-8, Transwell and matrigel assays, overexpression of miR-1180-3p reduced cancer cell proliferation and mobility, but induced apoptosis, by targeting COL12A1. miR-1180-3p might function as a suppressor in CRC progression and allowed the discovery of a new biomarker for diagnosis, prognosis and therapy target for CRC.
Collapse
Affiliation(s)
- Chunlei Li
- Department of Gastroenterology, Jiaozhou Central Hospital of Qingdao, Shandong, 266300, China
| | - Dewei Zhang
- Department of 3rd General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110032, China
| | - Shoujin Tian
- Department of General Gastroenterology, Zhucheng People's Hospital, Shandong, 262200, China
| |
Collapse
|
17
|
Chu Q, Gu X, Zheng Q, Guo Z, Shan D, Wang J, Zhu H. Long noncoding RNA SNHG4: a novel target in human diseases. Cancer Cell Int 2021; 21:583. [PMID: 34717631 PMCID: PMC8557547 DOI: 10.1186/s12935-021-02292-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022] Open
Abstract
Recently, long noncoding RNAs (lncRNAs) have attracted great attention from researchers. LncRNAs are non-protein-coding RNAs of more than 200 nucleotides in length. Multiple studies have been published on the relationship between lncRNA expression and the progression of human diseases. LncRNA small nucleolar RNA host gene 4 (SNHG4), a member of the lncRNA SNHG family, is abnormally expressed in a variety of human diseases, including gastric cancer, renal cell carcinoma, glioblastoma, neuroblastoma, prostate cancer, colorectal cancer, osteosarcoma, cervical cancer, liver cancer, lung cancer, non-small-cell lung cancer, neonatal pneumonia, diabetic retinopathy, neuropathic pain, acute cerebral infarction, acute myeloid leukaemia, and endometriosis. In this paper, the structure of SNHG4 is first introduced, and then studies in humans, animal models and cells are summarized to highlight the expression and function of SNHG4 in the above diseases. In addition, the specific mechanism of SNHG4 as a competing endogenous RNA (ceRNA) is discussed. The findings indicate that SNHG4 can be used as a biomarker for disease prognosis evaluation and as a potential target for disease diagnosis and treatment.
Collapse
Affiliation(s)
- Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Qiuxian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Zixuan Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Dandan Shan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
| |
Collapse
|
18
|
Chen X, Chen Z, Wu H, Liu X, Nie F, Wang Z, Sun M. Comprehensive Genomic Characterization Analysis Identifies an Oncogenic Pseudogene RP11-3543B.1 in Human Gastric Cancer. Front Cell Dev Biol 2021; 9:743652. [PMID: 34660601 PMCID: PMC8511815 DOI: 10.3389/fcell.2021.743652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/06/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Gastrointestinal Cancer (GICs) is the most common group of malignancies, and many of its types are the leading causes of cancer related death worldwide. Pseudogenes have been revealed to have critical regulatory roles in human cancers. The objective of this study is to comprehensive characterize the pseudogenes expression profiling and identify key pseudogenes in the development of gastric cancer (GC). Methods: The pseudogenes expression profiling was analyzed in six types of GICs cancer from The Cancer Genome Atlas RNA-seq data to identify GICs cancer related pseudogenes. Meanwhile, the genomic characterization including somatic alterations of pseudogenes was analyzed. Then, CCK8 and colony formation assays were performed to evaluate the biological function of RP11-3543B.1 and miR-145 in gastric cancer cells. The mechanisms of pseudogene RP11-3543B.1 in GC cells were explored via using bioinformatics analysis, next generation sequencing and lucifarese reporter assay. Results: We identified a great number of pseudogenes with significantly altered expression in GICs, and some of these pseudogenes expressed differently among the six cancer types. The amplification or deletion in the pseudogenes-containing loci involved in the alterations of pseudogenes expression in GICs. Among these altered pseudogenes, RP11-3543B.1 is significantly upregulated in gastric cancer. Down-regulation of RP11-3543B.1 expression impaired GC cells proliferation both in vitro and in vivo. RP11-3543B.1 exerts oncogene function via targeting miR-145-5p to regulate MAPK4 expression in gastric cancer cells. Conclusion: Our study reveals the potential of pseudogenes expression as a new paradigm for investigating GI cancer tumorigenesis and discovering prognostic biomarkers for patients.
Collapse
Affiliation(s)
- Xin Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenyao Chen
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hao Wu
- Department of Oncology, First Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Xianghua Liu
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China
| | - Fengqi Nie
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Zhaoxia Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, China
| | - Ming Sun
- Suzhou Cancer Center Core Laboratory, Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| |
Collapse
|