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Shah JA, Miao Y, Chu J, Chen W, Zhao Q, Cai C, Khattak S, Wang F, Jin J. Feedback Modulation between Human INO80 Chromatin Remodeling Complex and miR-372 in HCT116 Cells. Int J Mol Sci 2023; 24:10685. [PMID: 37445863 DOI: 10.3390/ijms241310685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/15/2023] Open
Abstract
Human INO80 chromatin remodeling complex (INO80 complex) as a transcription cofactor is widely involved in gene transcription regulation and is frequently highly expressed in tumor cells. However, few reports exist on the mutual regulatory mechanism between INO80 complex and non-coding microRNAs. Herein, we showed evidence that the INO80 complex transcriptionally controls microRNA-372 (miR-372) expression through RNA-Seq analysis and a series of biological experiments. Knocking down multiple subunits in the INO80 complex, including the INO80 catalytic subunit, YY1, Ies2, and Arp8, can significantly increase the expression level of miR-372. Interestingly, mimicking miR-372 expression in HCT116 cells, in turn, post-transcriptionally suppressed INO80 and Arp8 expression at both mRNA and protein levels, indicating the existence of a mutual regulatory mechanism between the INO80 complex and miR-372. The target relationship between miR-372 and INO80 complex was verified using luciferase assays in HCT116 colon cancer cells. As expected, miR-372 mimics significantly suppressed the luciferase activity of pMIR-luc/INO80 and pMIR-luc/Arp8 3'-UTR in cells. In contrast, the miR-372 target sites in the 3'-UTRs linked to the luciferase reporter were mutagenized, and both mutant sites lost their response to miR-372. Furthermore, the mutual modulation between the INO80 complex and miR-372 was involved in cell proliferation and the p53/p21 signaling pathway, suggesting the synergistic anti-tumor role of the INO80 complex and miR372. Our results will provide a solid theoretical basis for exploring miR-372 as a biological marker of tumorigenesis.
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Affiliation(s)
- Junaid Ali Shah
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yujuan Miao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jinmeng Chu
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Wenqi Chen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Qingzhi Zhao
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Chengyu Cai
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Saadullah Khattak
- Henan International Joint Laboratory for Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Fei Wang
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun 130012, China
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2
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Boyero L, Noguera-Uclés JF, Castillo-Peña A, Salinas A, Sánchez-Gastaldo A, Alonso M, Benedetti JC, Bernabé-Caro R, Paz-Ares L, Molina-Pinelo S. Aberrant Methylation of the Imprinted C19MC and MIR371-3 Clusters in Patients with Non-Small Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15051466. [PMID: 36900258 PMCID: PMC10000578 DOI: 10.3390/cancers15051466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/02/2023] Open
Abstract
Epigenetic mechanisms have emerged as an important contributor to tumor development through the modulation of gene expression. Our objective was to identify the methylation profile of the imprinted C19MC and MIR371-3 clusters in patients with non-small cell lung cancer (NSCLC) and to find their potential target genes, as well as to study their prognostic role. DNA methylation status was analyzed in a NSCLC patient cohort (n = 47) and compared with a control cohort including COPD patients and non-COPD subjects (n = 23) using the Illumina Infinium Human Methylation 450 BeadChip. Hypomethylation of miRNAs located on chromosome 19q13.42 was found to be specific for tumor tissue. We then identified the target mRNA-miRNA regulatory network for the components of the C19MC and MIR371-3 clusters using the miRTargetLink 2.0 Human tool. The correlations of miRNA-target mRNA expression from primary lung tumors were analyzed using the CancerMIRNome tool. From those negative correlations identified, we found that a lower expression of 5 of the target genes (FOXF2, KLF13, MICA, TCEAL1 and TGFBR2) was significantly associated with poor overall survival. Taken together, this study demonstrates that the imprinted C19MC and MIR371-3 miRNA clusters undergo polycistronic epigenetic regulation leading to deregulation of important and common target genes with potential prognostic value in lung cancer.
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Affiliation(s)
- Laura Boyero
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
| | | | - Alejandro Castillo-Peña
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
| | - Ana Salinas
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
| | - Amparo Sánchez-Gastaldo
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Miriam Alonso
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Johana Cristina Benedetti
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Reyes Bernabé-Caro
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
- Medical Oncology Department, Hospital Universitario Virgen del Rocío, 41013 Seville, Spain
| | - Luis Paz-Ares
- H12O Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre (imas12), 28029 Madrid, Spain
- Spanish Center for Biomedical Research Network in Oncology (CIBERONC), 28029 Madrid, Spain
- Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
- MD Anderson, 28033 Madrid, Spain
| | - Sonia Molina-Pinelo
- Institute of Biomedicine of Seville (IBiS), HUVR, CSIC, Universidad de Sevilla, 41013 Seville, Spain
- Spanish Center for Biomedical Research Network in Oncology (CIBERONC), 28029 Madrid, Spain
- Correspondence:
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3
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Žarković M, Hufsky F, Markert UR, Marz M. The Role of Non-Coding RNAs in the Human Placenta. Cells 2022; 11:1588. [PMID: 35563893 PMCID: PMC9104507 DOI: 10.3390/cells11091588] [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: 03/08/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
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Affiliation(s)
- Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Franziska Hufsky
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
- Aging Research Center (ARC), 07745 Jena, Germany
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Li Y, Li F, Feng C, Wu T, Chen Y, Shah JA, Wang F, Cai Y, Wang J, Jin J. MiR-372-3p Functions as a Tumor Suppressor in Colon Cancer by Targeting MAP3K2. Front Genet 2022; 13:836256. [PMID: 35432472 PMCID: PMC9006175 DOI: 10.3389/fgene.2022.836256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) as small non-coding RNA transcripts bind their complementary sequences in the 3′-untranslated region (3′-UTR) of target messenger RNAs (mRNAs) to regulate their expression. It is known that miR-372 belongs to the miR-371–373 gene cluster and has been found to be abnormally expressed in a variety of cancers, but its precise mechanism in cancer remains to be discovered. In this study, miR-372-3p expression was assessed in 153 frozen tissue samples, including primary diagnosed colon cancer and matched normal and adjacent tissues, using real time quantitative polymerase chain reaction (qPCR). An analysis of qPCR data revealed a significant reduction in miR-372-3p expression (by >2-fold) in colon cancer tissues in 51.5% (34/66) of patients. Consistent with this, mimicking the increased miR-372-3p levels in SW480 colon cancer cells significantly suppressed cell growth and proliferation. Although no direct correlation was found between the low level of miR-372-3p and certain tumor-related factors, such as p53, HRE-2, PMS2, MLH1, MSH2, MSH6, HDAC4, p21, and Wee1, in colon cancer tissues, an inverse relationship between miR-372-3p and Ki67 (a marker of proliferation) or miR-372-3p and MAP3K2(MEKK2), which plays a critical role in the MAPK signaling pathways, was confirmed using tissue samples. The target relationship between miR-372-3p and MAP3K2 was verified using luciferase assays in SW480 colon cancer cells. As expected, miR-372-3p mimics significantly suppressed the luciferase activity of pMIR-luc/MAP3K2 3′-UTR in cells, suggesting that miR-372-3p modulates the expression of MAP3K2 by directly targeting its 3′-UTR. Overall, the results obtained herein suggest that miR-372-3p may function as a tumor-suppressor miRNA in colon cancer by targeting MAP3K2.
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Affiliation(s)
- Yana Li
- School of Life Sciences, Jilin University, Changchun, China
- Department of Ophthalmology and Otorhinolaryngology, Changchun Children’s Hospital, Changchun, China
| | - Fuqiang Li
- School of Life Sciences, Jilin University, Changchun, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Chang Feng
- School of Life Sciences, Jilin University, Changchun, China
| | - Tingting Wu
- School of Life Sciences, Jilin University, Changchun, China
| | - Yuyang Chen
- School of Life Sciences, Jilin University, Changchun, China
| | | | - Fei Wang
- School of Life Sciences, Jilin University, Changchun, China
| | - Yong Cai
- School of Life Sciences, Jilin University, Changchun, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Jianfeng Wang
- Department of Radiotherapy, China-Japan Union Hospital, Jilin University, Changchun, China
- *Correspondence: Jianfeng Wang, ; Jingji Jin,
| | - Jingji Jin
- School of Life Sciences, Jilin University, Changchun, China
- School of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
- *Correspondence: Jianfeng Wang, ; Jingji Jin,
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Lobo J, van Zogchel LMJ, Nuru MG, Gillis AJM, van der Schoot CE, Tytgat GAM, Looijenga LHJ. Combining Hypermethylated RASSF1A Detection Using ddPCR with miR-371a-3p Testing: An Improved Panel of Liquid Biopsy Biomarkers for Testicular Germ Cell Tumor Patients. Cancers (Basel) 2021; 13:5228. [PMID: 34680375 PMCID: PMC8534014 DOI: 10.3390/cancers13205228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/13/2021] [Indexed: 12/22/2022] Open
Abstract
The classical serum tumor markers used routinely in the management of testicular germ cell tumor (TGCT) patients-alpha fetoprotein (AFP) and human chorionic gonadotropin (HCG)-show important limitations. miR-371a-3p is the most recent promising biomarker for TGCTs, but it is not sufficiently informative for detection of teratoma, which is therapeutically relevant. We aimed to test the feasibility of hypermethylated RASSF1A (RASSF1AM) detected in circulating cell-free DNA as a non-invasive diagnostic marker of testicular germ cell tumors, combined with miR-371a-3p. A total of 109 serum samples of patients and 29 sera of healthy young adult males were included, along with representative cell lines and tumor tissue samples. We describe a novel droplet digital polymerase chain reaction (ddPCR) method for quantitatively assessing RASSF1AM in liquid biopsies. Both miR-371a-3p (sensitivity = 85.7%) and RASSF1AM (sensitivity = 86.7%) outperformed the combination of AFP and HCG (sensitivity = 65.5%) for TGCT diagnosis. RASSF1AM detected 88% of teratomas. In this representative cohort, 14 cases were negative for miR-371a-3p, all of which were detected by RASSF1AM, resulting in a combined sensitivity of 100%. We have described a highly sensitive and specific panel of biomarkers for TGCT patients, to be validated in the context of patient follow-up and detection of minimal residual disease.
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Affiliation(s)
- João Lobo
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS—School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Lieke M. J. van Zogchel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Mohammed G. Nuru
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Ad J. M. Gillis
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
| | - C. Ellen van der Schoot
- Department of Experimental Immunohematology, Sanquin Research Amsterdam, Plesmanlaan 125, 1066 CX Amsterdam, The Netherlands; (M.G.N.); (C.E.v.d.S.)
| | - Godelieve A. M. Tytgat
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
| | - Leendert H. J. Looijenga
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, The Netherlands; (J.L.); (L.M.J.v.Z.); (A.J.M.G.)
- Lab. for Exp. Patho-Oncology (LEPO), Department of Pathology, Erasmus MC-University Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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