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Ballesio F, Pepe G, Ausiello G, Novelletto A, Helmer-Citterich M, Gherardini PF. Human lncRNAs harbor conserved modules embedded in different sequence contexts. Noncoding RNA Res 2024; 9:1257-1270. [PMID: 39040814 PMCID: PMC11261117 DOI: 10.1016/j.ncrna.2024.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/24/2024] Open
Abstract
We analyzed the structure of human long non-coding RNA (lncRNAs) genes to investigate whether the non-coding transcriptome is organized in modular domains, as is the case for protein-coding genes. To this aim, we compared all known human lncRNA exons and identified 340 pairs of exons with high sequence and/or secondary structure similarity but embedded in a dissimilar sequence context. We grouped these pairs in 106 clusters based on their reciprocal similarities. These shared modules are highly conserved between humans and the four great ape species, display evidence of purifying selection and likely arose as a result of recent segmental duplications. Our analysis contributes to the understanding of the mechanisms driving the evolution of the non-coding genome and suggests additional strategies towards deciphering the functional complexity of this class of molecules.
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Affiliation(s)
- Francesco Ballesio
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gerardo Pepe
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Gabriele Ausiello
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
| | - Andrea Novelletto
- Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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3
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Liu Y, Wang Y, Yu Z, Wang Z. Impacts of TP53TG1 in cancer-associated fibroblasts-derived exosomes on epithelial-mesenchymal transition capacity of colorectal carcinoma cells by targeting miR-330-3p. Heliyon 2024; 10:e30301. [PMID: 38707274 PMCID: PMC11068805 DOI: 10.1016/j.heliyon.2024.e30301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/07/2024] Open
Abstract
Objective This research aims at clarifying the action and mechanisms of action of TP53TG1 in cancer-associated fibroblasts (CAF)-derived exosomes (EXs) on colorectal carcinoma (CRC) cells. Methods CAF and CAF-EXs isolated from CRC tissues were incubated with CRC SW480 cells to determine alterations in biological behavior, epithelial-mesenchymal transition (EMT) capacity, and TP53TG1 and miR-330-3p expression. In addition, a dual luciferase reporter (DLR) assay was conducted to verify the connection between TP53TG1 and miR-330-3p, and the impacts of the two genes on CRC cells were analyzed. Results CRC-CAF-EXs extracted from CRC tissues were successfully identified and were able to promote SW480 multiplication, invasiveness, migration, and EMT ability while inhibiting apoptosis (P < 0.05). In addition, TP53TG1 increased and miR-330-3p decreased in SW480 when cultured with CRC-CAF-EXs (P < 0.05). The DLR assay identified notably reduced fluorescence activity of TP53TG1-WT after transfection with miR-330-3p-mimics (P < 0.05). Furthermore, SW480 cell multiplication, invasiveness and migration were found to be enhanced and the apoptosis decreased after up-regulating TP53TG1, while suppressing TP53TG1 and up-regulating miR-330-3p contributed to quite the opposite effect (P < 0.05). Moreover, by elevating TP53TG1 and miR-330-3p simultaneously, we found a cell activity similar to the NC group (P > 0.05). Conclusion By targeting miR-330-3p, TP53TG1 in CRC-CAF-EXs can enhance CRC cell activity and EMT capacity and inhibit apoptosis.
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Affiliation(s)
- Yawei Liu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Medical School, Nanjing University, Nanjing, 210008, China
| | - Youwei Wang
- Bengbu Medical College, Bengbu, Anhui, 233030, China
| | - Zhijuan Yu
- Hubei University of Science and Technology, Xianning, Hubei, 437000, China
| | - Ziheng Wang
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Taipa, Macao SAR, China
- Suzhou Industrial Park Monash Research Institute of Science and Technology, Suzhou, Jiangsu, 215000, China
- The School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
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4
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Fenton CG, Ray MK, Paulssen RH. Challenges in Defining a Reference Set of Differentially Expressed lncRNAs in Ulcerative Colitis by Meta-Analysis. Curr Issues Mol Biol 2024; 46:3164-3174. [PMID: 38666928 PMCID: PMC11049510 DOI: 10.3390/cimb46040198] [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: 03/05/2024] [Revised: 03/27/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
The study aimed to identify common differentially expressed lncRNAs from manually curated ulcerative colitis (UC) gene expression omnibus (GEO) datasets. Nine UC transcriptomic datasets of clearly annotated human colonic biopsies were included in the study. The datasets were manually curated to select active UC samples and controls. R packages geneknitR, gprofiler, clusterProfiler were used for gene symbol annotation. The R EdgeR package was used to analyze differential expression. This resulted in a total of nineteen lncRNAs that were differentially expressed in at least three datasets of the nine GEO datasets. Several of the differentially expressed lncRNAs found in UC were associated with promoting colorectal cancer (CRC) through regulating gene expression, epithelial to mesenchymal transition (EMT), cell cycle progression, and by promoting tumor proliferation, invasion, and migration. The expression of several lncRNAs varied between disease states and tissue locations within the same disease state. The identified differentially expressed lncRNAs may function as general markers for active UC independent of biopsy location, age, gender, or treatment, thereby representing a comparative resource for future comparisons using available GEO UC datasets.
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Affiliation(s)
- Christopher G. Fenton
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Mithlesh Kumar Ray
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
| | - Ruth H. Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway; (C.G.F.); (M.K.R.)
- Genomic Support Centre Tromsø (GSCT), Department of Clinical Medicine, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
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5
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Alemi F, Poornajaf Y, Hosseini F, Vahedian V, Gharekhani M, Shoorei H, Taheri M. Interaction between lncRNAs and RNA-binding proteins (RBPs) influences DNA damage response in cancer chemoresistance. Mol Biol Rep 2024; 51:308. [PMID: 38366290 DOI: 10.1007/s11033-024-09288-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024]
Abstract
The DNA damage response (DDR) is a crucial cellular signaling pathway activated in response to DNA damage, including damage caused by chemotherapy. Chemoresistance, which refers to the resistance of cancer cells to the effects of chemotherapy, poses a significant challenge in cancer treatment. Understanding the relationship between DDR and chemoresistance is vital for devising strategies to overcome this resistance and improve treatment outcomes. Long non-coding RNAs (lncRNAs) are a class of RNA molecules that do not code for proteins but play important roles in various biological processes, including cancer development and chemoresistance. RNA-binding proteins (RBPs) are a group of proteins that bind to RNA molecules and regulate their functions. The interaction between lncRNAs and RBPs has been found to regulate gene expression at the post-transcriptional level, thereby influencing various cellular processes, including DDR signaling pathways. Multiple studies have demonstrated that lncRNAs can interact with RBPs to modulate the expression of genes involved in cancer chemoresistance by impacting DDR signaling pathways. Conversely, RBPs can regulate the expression and function of lncRNAs involved in DDR. Exploring these interactions can provide valuable insights for the development of innovative therapeutic approaches to overcome chemoresistance in cancer patients. This review article aims to summarize recent research on the interaction between lncRNAs and RBPs during cancer chemotherapy, with a specific focus on DDR pathways.
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Affiliation(s)
- Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Poornajaf
- Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Foroogh Hosseini
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - Vahid Vahedian
- Department of Medical Clinic, Division of Hematology/Oncology and Cellular Therapy, Faculty of Medicine, University of Sao Paulo (FMUSP), Sao Paulo, Brazil
| | - Mahdi Gharekhani
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hamed Shoorei
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.
- Rooyesh Infertility Center, Birjand University of Medical Sciences, Birjand, Iran.
- Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany.
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Burdennyy AM, Filippova EA, Lukina SS, Ivanova NA, Pronina IV, Loginov VI, Kazubskaya TP, Kushlinskii NE, Braga EA. DNA Methylation of a Group of Long Non-Coding RNA Genes at Different Stages of Ovarian Cancer Dissemination. Bull Exp Biol Med 2024; 176:495-500. [PMID: 38492100 DOI: 10.1007/s10517-024-06054-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 03/18/2024]
Abstract
There are three types of metastases in ovarian cancer: lymphogenous, hematogenous, and peritoneal. Dissemination of the tumor in the peritoneum is directly related with the development of ascites and a poor prognosis. The purpose of this study is to determine changes in the methylation level of a group of long non-coding RNA (lncRNA) genes at different stages of ovarian cancer progression. The methylation level of 7 lncRNA genes (LINC00472, LINC00886, MAFG-DT, SNHG1, SNHG6, TP53TG1, and TUG1) was studied by quantitative methyl-specific PCR in 93 samples of ovarian tumors and 75 paired samples of histologically normal tissue, as well as in 29 peritoneal macroscopic metastases. Using the nonparametric Mann-Whitney test, a significant (p<0.001) increase in the level of methylation of the LINC00886, SNHG1, SNHG6, and TUG1 genes in the tumor tissue was shown. For the LINC00472, LINC00886, and SNHG6 genes, a significant relationship was found with the clinical stage (p≤0.001), as well as with the appearance of metastases for the LINC00472 (p<0.001) and SNHG6 (p=0.005) genes. There was a significant increase in the level of methylation of MAFG-DT and TP53TG1 (p<0.001) genes, as well as a decrease in LINC00886 (p=0.003) in peritoneal metastases relative to the primary focus. Methylation of the LINC00472 and SNHG6 genes can be considered as a factor in initiating ovarian cancer metastasis, and methylation of the LINC00886, MAFG-DT, and TP53TG1 genes as a colonization factor for metastases in the peritoneum. Thus, a relationship between methylation of a group of lncRNA genes at different stages of ovarian cancer dissemination was shown, which is important for understanding the mechanisms of these processes and for developing innovative approaches to ovarian cancer therapy.
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Affiliation(s)
- A M Burdennyy
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.
| | - E A Filippova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - S S Lukina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - N A Ivanova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - I V Pronina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - T P Kazubskaya
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
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7
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Bao-Caamano A, Costa-Fraga N, Cayrefourcq L, Rodriguez-Casanova A, Muinelo-Romay L, López-López R, Alix-Panabières C, Díaz-Lagares A. Epigenomic reprogramming of therapy-resistant circulating tumor cells in colon cancer. Front Cell Dev Biol 2023; 11:1291179. [PMID: 38188020 PMCID: PMC10771310 DOI: 10.3389/fcell.2023.1291179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/28/2023] [Indexed: 01/09/2024] Open
Abstract
Therapy resistance is a major challenge in colorectal cancer management. Epigenetic changes, such as DNA methylation, in tumor cells are involved in the development of acquired resistance during treatment. Here, we characterized the DNA methylation landscape of colon circulating tumor cells (CTCs) during cancer progression and therapy resistance development. To this aim, we used nine permanent CTC lines that were derived from peripheral blood samples of a patient with metastatic colon cancer collected before treatment initiation (CTC-MCC-41) and during treatment and cancer progression (CTC-MCC-41.4 and CTC-MCC-41.5 [A-G]). We analyzed the DNA methylome of these nine CTC lines using EPIC arrays and also assessed the association between DNA methylation and gene expression profiles. We confirmed DNA methylation and gene expression results by pyrosequencing and RT-qPCR, respectively. The global DNA methylation profiles were different in the pre-treatment CTC line and in CTC lines derived during therapy resistance development. These resistant CTC lines were characterized by a more hypomethylated profile compared with the pre-treatment CTC line. Most of the observed DNA methylation differences were localized at CpG-poor regions and some in CpG islands, shore regions and promoters. We identified a distinctive DNA methylation signature that clearly differentiated the pre-treatment CTC line from the others. Of note, the genes involved in this signature were associated with cancer-relevant pathways, including PI3K/AKT, MAPK, Wnt signaling and metabolism. We identified several epigenetically deregulated genes associated with therapy resistance in CTCs, such as AP2M1. Our results bring new knowledge on the epigenomic landscape of therapy-resistant CTCs, providing novel mechanisms of resistance as well as potential biomarkers and therapeutic targets for advanced CRC management.
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Affiliation(s)
- Aida Bao-Caamano
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Laure Cayrefourcq
- Laboratory of Rare Human Circulating Cells–The Liquid Biopsy Lab, University Medical Center of Montpellier, Montpellier, France
- Centre for Ecological and Evolutionary Cancer Research, Maladies infectieuses et vecteurs: génétique, èvolution et contrôle, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Aitor Rodriguez-Casanova
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells–The Liquid Biopsy Lab, University Medical Center of Montpellier, Montpellier, France
- Centre for Ecological and Evolutionary Cancer Research, Maladies infectieuses et vecteurs: génétique, èvolution et contrôle, University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
| | - Angel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, Madrid, Spain
- Department of Clinical Analysis, University Hospital Complex of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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8
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Ying Z, Wenjing S, Jing B, Songbin F, Kexian D. Advances in long non-coding RNA regulating drug resistance of cancer. Gene 2023; 887:147726. [PMID: 37625566 DOI: 10.1016/j.gene.2023.147726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/19/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
Drug resistance is one of the main challenges in cancer treatment. Long non coding RNAs (lncRNAs) play a complex and precise regulatory role in regulating drug resistance of cancer. The common ways of lncRNA regulating drug resistance of cancer involve ATP binding transporter overexpression, abnormal DNA damage response, tumor cell apoptosis, accumulation of epithelial mesenchymal transformation and cancer stem cell formation. Moreover, studies on exosomal lncRNAs regulating cancer drug resistance are developed in recent years. Further study on the role and mechanism of lncRNAs drug resistance in cancer will help clinical cancer treatment program and explore new treatment methods. This paper reviews recent advances in lncRNAs regulating drug resistance of cancer, especially the role of exosomal lncRNAs.
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Affiliation(s)
- Zhang Ying
- Key laboratory of preservation of human genetic resources and disease control in China, Harbin Medical University, Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Sun Wenjing
- Key laboratory of preservation of human genetic resources and disease control in China, Harbin Medical University, Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Bai Jing
- Key laboratory of preservation of human genetic resources and disease control in China, Harbin Medical University, Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Fu Songbin
- Key laboratory of preservation of human genetic resources and disease control in China, Harbin Medical University, Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China
| | - Dong Kexian
- Key laboratory of preservation of human genetic resources and disease control in China, Harbin Medical University, Ministry of Education, Harbin 150081, China; Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.
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9
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Bao-Caamano A, Costa-Fraga N, Cayrefourcq L, Jácome MA, Rodriguez-Casanova A, Muinelo-Romay L, López-López R, Alix-Panabières C, Díaz-Lagares A. Epigenomic analysis reveals a unique DNA methylation program of metastasis-competent circulating tumor cells in colorectal cancer. Sci Rep 2023; 13:15401. [PMID: 37717096 PMCID: PMC10505142 DOI: 10.1038/s41598-023-42037-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/04/2023] [Indexed: 09/18/2023] Open
Abstract
Circulating tumor cells (CTCs) and epigenetic alterations are involved in the development of metastasis from solid tumors, such as colorectal cancer (CRC). The aim of this study was to characterize the DNA methylation profile of metastasis-competent CTCs in CRC. The DNA methylome of the human CRC-derived cell line CTC-MCC-41 was analyzed and compared with primary (HT29, Caco2, HCT116, RKO) and metastatic (SW620 and COLO205) CRC cells. The association between methylation and the transcriptional profile of CTC-MCC-41 was also evaluated. Differentially methylated CpGs were validated with pyrosequencing and qMSP. Compared to primary and metastatic CRC cells, the methylation profile of CTC-MCC-41 was globally different and characterized by a slight predominance of hypomethylated CpGs mainly distributed in CpG-poor regions. Promoter CpG islands and shore regions of CTC-MCC-41 displayed a unique methylation profile that was associated with the transcriptional program and relevant cancer pathways, mainly Wnt signaling. The epigenetic regulation of relevant genes in CTC-MCC-41 was validated. This study provides new insights into the epigenomic landscape of metastasis-competent CTCs, revealing biological information for metastasis development, as well as new potential biomarkers and therapeutic targets for CRC patients.
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Grants
- ISCIII and the European Regional Development Fund (FEDER), reference number PI18/00307. Juan Rodés, Instituto de Salud Carlos III (ISCIII) and Servizo Galego de Saúde (SERGAS), reference number JR17/00016
- PFIS, Instituto de Salud Carlos III (ISCIII) and Fondo Social Europeo, reference number FI19/00240
- Xunta de Galicia, reference number IN606A-2020/004
- Axencia Galega de Innovación (GAIN), Vicepresidencia Segunda e Consellería de Economía, Empresa e Innovación. Reference number IN853B 2018/03
- ISCIII and the European Regional Development Fund (FEDER), reference number PI18/00307. Instituto de Salud Carlos III (ISCII), reference number CP20/00129
- European Union Horizon 2020 Research and Innovation program under the Marie Skłodowska-Curie grant agreement No. 765492, The National Institute of Cancer (INCa, http://www.e-cancer.fr), SIRIC Montpellier Cancer Grant INCa_Inserm_DGOS_12553, and the ERA-NET TRANSCAN 2 JTC 2016 PROLIPSY, la Fondation ARC pour la Recherche sur le cancer and les Fonds de dotation AFER pour la recherche médicale
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Affiliation(s)
- Aida Bao-Caamano
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Laure Cayrefourcq
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, IURC, 641, Avenue du Doyen Gaston Giraud, 34093, Montpellier Cedex 5, France
- CREEC, MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
| | - María Amalia Jácome
- Department of Mathematics, MODES Group, CITIC, Faculty of Science, Universidade da Coruña, A Coruña, Spain
| | - Aitor Rodriguez-Casanova
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Laura Muinelo-Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Rafael López-López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain.
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706, Santiago de Compostela, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain.
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain.
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, IURC, 641, Avenue du Doyen Gaston Giraud, 34093, Montpellier Cedex 5, France.
- CREEC, MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France.
- European Liquid Biopsy Society (ELBS), Hamburg, Germany.
| | - Angel Díaz-Lagares
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain.
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain.
- Department of Clinical Analysis, University Hospital Complex of Santiago de Compostela (CHUS), 15706 Santiago de Compostela, Spain.
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10
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Chu F, Wu P, Mu M, Hu S, Niu C. MGCG regulates glioblastoma tumorigenicity via hnRNPK/ATG2A and promotes autophagy. Cell Death Dis 2023; 14:443. [PMID: 37460467 DOI: 10.1038/s41419-023-05959-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 06/12/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023]
Abstract
Glioblastoma (GBM) is the most common malignant primary brain cancer in adults and has constantly been a focus of research. Long noncoding RNAs (lncRNAs) play important roles in the development of cancers. To illustrate the role of lncRNAs in the development of glioblastoma, high-throughput RNA sequencing was performed to obtain the transcripts using three freshly isolated tumor tissue samples from GBM patients and three normal brain tissue samples from the traumatic brain of patients. Then, a lncRNA, MGCG (MGC70870 is expressed at a high level in glioblastoma), which has not been reported previously in GBM, was found to be associated with the prognosis of patients. The results of bioinformatic analysis showed that MGCG was correlated with autophagy and positively correlated with the expression of the autophagy-related gene ATG2A. The data of mass spectrometry demonstrated that the hnRNPK protein was a direct target interacting with MGCG, and MGCG/hnRNPK promoted the development of GBM by enhancing the translation of ATG2A and autophagy. In conclusion, the present study showed that MGCG has the potential to promote the development of GBM and may become a candidate for molecular diagnostics and treatment of tumors.
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Affiliation(s)
- Fang Chu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China
- Anhui Key Laboratory of Brain Function and Diseases, Hefei, Anhui, 230001, P.R. China
| | - Pengfei Wu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China
- Anhui Key Laboratory of Brain Function and Diseases, Hefei, Anhui, 230001, P.R. China
| | - Maolin Mu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China
- Anhui Key Laboratory of Brain Function and Diseases, Hefei, Anhui, 230001, P.R. China
| | - Shanshan Hu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China.
- Anhui Key Laboratory of Brain Function and Diseases, Hefei, Anhui, 230001, P.R. China.
- Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, Anhui, 230001, P.R. China.
- Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, Anhui, 230001, P.R. China.
| | - Chaoshi Niu
- Department of Neurosurgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, P.R. China.
- Anhui Key Laboratory of Brain Function and Diseases, Hefei, Anhui, 230001, P.R. China.
- Anhui Provincial Stereotactic Neurosurgical Institute, Hefei, Anhui, 230001, P.R. China.
- Anhui Provincial Clinical Research Center for Neurosurgical Disease, Hefei, Anhui, 230001, P.R. China.
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11
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Yang Z, Cai Y, Mao S, Wu Q, Zhu M, Cao X, Wei B, Tian JM, Bao X, Ye X, Chen J, Wang S, Yu Y, Zhang H, Sun X, Cui ZN, Li YS, Wang H. Discovery of 2,5-disubstituted furan derivatives featuring a benzamide motif for overcoming P-glycoprotein mediated multidrug resistance in MCF-7/ADR cell. Eur J Med Chem 2023; 257:115462. [PMID: 37229830 DOI: 10.1016/j.ejmech.2023.115462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/05/2023] [Accepted: 05/05/2023] [Indexed: 05/27/2023]
Abstract
P-glycoprotein (P-gp) is one of the drug efflux transporters that triggers multidrug resistance (MDR) in cells. Herein, by utilizing the strategies of active skeleton splicing and structural optimization on the lead compound 5 m, a total of 50 novel 2,5-disubstituted furan derivatives were designed, synthesized, and screened for P-gp inhibitory activity. The structure-activity relationship analysis enabled the identification of an important pharmacophore N-phenylbenzamide, which resulted in the discovery of a promising drug lead compound Ⅲ-8. Ⅲ-8 possesses broad-spectrum reversal activity and low toxicity in MCF-7/ADR cells. Western blot and Rh123 accumulation assay demonstrated that Ⅲ-8 displayed the reversal activity by inhibiting P-gp efflux. Molecular docking analysis indicated a potent affinity of Ⅲ-8 to P-gp by forming H-bond interactions with residues Asn 721 and Met 986. Ⅲ-8 was determined to be a highly effective and safe P-gp inhibitor in an MCF-7/ADR xenograft mouse model.
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Affiliation(s)
- Zhikun Yang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yue Cai
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Shen Mao
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Qihao Wu
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA; Institute of Biomolecular Design &Discovery, Yale University, West Haven, CT, 06516, USA
| | - Mengdi Zhu
- Research Center of Analysis and Measurement, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoji Cao
- Research Center of Analysis and Measurement, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jin-Miao Tian
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoze Bao
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xinyi Ye
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jianwei Chen
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Sijia Wang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yanlei Yu
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Huawei Zhang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xuanrong Sun
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zi-Ning Cui
- National Key Laboratory of Green Pesticide, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China.
| | - Ya-Sheng Li
- Department of Infectious Diseases & Anhui Center for Surveillance of Bacterial Resistance, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
| | - Hong Wang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology, Hangzhou, 310014, China.
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12
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Mitra R, Adams CM, Eischen CM. Decoding the lncRNAome Across Diverse Cellular Stresses Reveals Core p53-effector Pan-cancer Suppressive lncRNAs. CANCER RESEARCH COMMUNICATIONS 2023; 3:842-859. [PMID: 37377895 PMCID: PMC10173889 DOI: 10.1158/2767-9764.crc-22-0473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/17/2023] [Accepted: 04/26/2023] [Indexed: 06/29/2023]
Abstract
Despite long non-coding RNAs (lncRNAs) emerging as key contributors to malignancies, their transcriptional regulation, tissue-type expression under different conditions, and functions remain largely unknown. Developing a combined computational and experimental framework, which integrates pan-cancer RNAi/CRISPR screens, and genomic, epigenetic, and expression profiles (including single-cell RNA sequencing), we report across multiple cancers, core p53-transcriptionally regulated lncRNAs, which were thought to be primarily cell/tissue-specific. These lncRNAs were consistently directly transactivated by p53 with different cellular stresses in multiple cell types and associated with pan-cancer cell survival/growth suppression and patient survival. Our prediction results were verified through independent validation datasets, our own patient cohort, and cancer cell experiments. Moreover, a top predicted p53-effector tumor-suppressive lncRNA (we termed PTSL) inhibited cell proliferation and colony formation by modulating the G2 regulatory network, causing G2 cell-cycle arrest. Therefore, our results elucidated previously unreported, high-confidence core p53-targeted lncRNAs that suppress tumorigenesis across cell types and stresses. Significance Identification of pan-cancer suppressive lncRNAs transcriptionally regulated by p53 across different cellular stresses by integrating multilayered high-throughput molecular profiles. This study provides critical new insights into the p53 tumor suppressor by revealing the lncRNAs in the p53 cell-cycle regulatory network and their impact on cancer cell growth and patient survival.
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Affiliation(s)
- Ramkrishna Mitra
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Clare M. Adams
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christine M. Eischen
- Department of Pharmacology, Physiology, and Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
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13
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Samec M, Mazurakova A, Lucansky V, Koklesova L, Pecova R, Pec M, Golubnitschaja O, Al-Ishaq RK, Caprnda M, Gaspar L, Prosecky R, Gazdikova K, Adamek M, Büsselberg D, Kruzliak P, Kubatka P. Flavonoids attenuate cancer metabolism by modulating Lipid metabolism, amino acids, ketone bodies and redox state mediated by Nrf2. Eur J Pharmacol 2023; 949:175655. [PMID: 36921709 DOI: 10.1016/j.ejphar.2023.175655] [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: 01/03/2023] [Revised: 02/20/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023]
Abstract
Metabolic reprogramming of cancer cells is a common hallmark of malignant transformation. The preference for aerobic glycolysis over oxidative phosphorylation in tumors is a well-studied phenomenon known as the Warburg effect. Importantly, metabolic transformation of cancer cells also involves alterations in signaling cascades contributing to lipid metabolism, amino acid flux and synthesis, and utilization of ketone bodies. Also, redox regulation interacts with metabolic reprogramming during malignant transformation. Flavonoids, widely distributed phytochemicals in plants, exert various beneficial effects on human health through modulating molecular cascades altered in the pathological cancer phenotype. Recent evidence has identified numerous flavonoids as modulators of critical components of cancer metabolism and associated pathways interacting with metabolic cascades such as redox balance. Flavonoids affect lipid metabolism by regulating fatty acid synthase, redox balance by modulating nuclear factor-erythroid factor 2-related factor 2 (Nrf2) activity, or amino acid flux and synthesis by phosphoglycerate mutase 1. Here, we discuss recent preclinical evidence evaluating the impact of flavonoids on cancer metabolism, focusing on lipid and amino acid metabolic cascades, redox balance, and ketone bodies.
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Affiliation(s)
- Marek Samec
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Comenius University in Bratislava, Martin, Slovakia
| | - Vincent Lucansky
- Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Lenka Koklesova
- Clinic of Obstetrics and Gynecology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01, Martin, Slovakia
| | - Renata Pecova
- Department of Pathophysiology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Martin Pec
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia
| | - Olga Golubnitschaja
- Predictive, Preventive, Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | | | - Martin Caprnda
- 1(st) Department of Internal Medicine, Faculty of Medicine, Comenius University and University Hospital, Bratislava, Slovakia
| | - Ludovit Gaspar
- Faculty of Health Sciences, University of Ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Robert Prosecky
- 2(nd) Department of Internal Medicine, Faculty of Medicine, Masaryk University and St. Anne´s University Hospital, Brno, Czech Republic; International Clinical Research Centre, St. Anne's University Hospital and Masaryk University, Brno, Czech Republic
| | - Katarina Gazdikova
- Department of Nutrition, Faculty of Nursing and Professional Health Studies, Slovak Medical University, Bratislava, Slovakia; Department of General Medicine, Faculty of Medicine, Slovak Medical University, Bratislava, Slovakia.
| | - Mariusz Adamek
- Department of Thoracic Surgery, Medical University of Silesia, Katowice, Poland
| | | | - Peter Kruzliak
- 2(nd) Department of Surgery, Faculty of Medicine, Masaryk University and St. Anne´s University Hospital, Brno, Czech Republic.
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovakia.
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14
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Fischer M, Riege K, Hoffmann S. The landscape of human p53-regulated long non-coding RNAs reveals critical host gene co-regulation. Mol Oncol 2023. [PMID: 36852646 DOI: 10.1002/1878-0261.13405] [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: 11/23/2022] [Revised: 01/20/2023] [Accepted: 02/27/2023] [Indexed: 03/01/2023] Open
Abstract
The role of long non-coding RNAs (lncRNAs) in p53-mediated tumor suppression has become increasingly appreciated in the past decade. Thus, the identification of p53-regulated lncRNAs can be a promising starting point to select and prioritize lncRNAs for functional analyses. By integrating transcriptome and transcription factor-binding data, we identified 379 lncRNAs that are recurrently differentially regulated by p53. Dissecting the mechanisms by which p53 regulates many of them, we identified sets of lncRNAs regulated either directly by p53 or indirectly through the p53-RFX7 and p53-p21-DREAM/RB:E2F pathways. Importantly, we identified multiple p53-responsive lncRNAs that are co-regulated with their protein-coding host genes, revealing an important mechanism by which p53 may regulate lncRNAs. Further analysis of transcriptome data and clinical data from cancer patients showed that recurrently p53-regulated lncRNAs are associated with patient survival. Together, the integrative analysis of the landscape of p53-regulated lncRNAs provides a powerful resource facilitating the identification of lncRNA function and displays the mechanisms of p53-dependent regulation that could be exploited for developing anticancer approaches.
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Affiliation(s)
- Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Konstantin Riege
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Steve Hoffmann
- Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
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15
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Long non-coding RNAs involved in retinoblastoma. J Cancer Res Clin Oncol 2023; 149:401-421. [PMID: 36305946 DOI: 10.1007/s00432-022-04398-z] [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: 09/12/2022] [Accepted: 10/05/2022] [Indexed: 02/03/2023]
Abstract
INTRODUCTION Retinoblastoma (RB) is the most common childhood tumor that can occur in the retina and develop in a sporadic or heritable form. Although various traditional treatment options have been used for patients with RB, identifying novel strategies for childhood cancers is necessary. MATERIAL AND METHODS Recently, molecular-based targeted therapies have opened a greater therapeutic window for RB. Long non-coding RNAs (lncRNAs) presented a potential role as a biomarker for the detection of RB in various stages. CONCLUSION LncRNAs by targeting several miRNA/transcription factors play critical roles in the stimulation or suppression of RB. In this review, we summarized recent progress on the functions of tumor suppressors or oncogenes lncRNAs in RB.
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16
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Yang Z, Xu F, Teschendorff AE, Zhao Y, Yao L, Li J, He Y. Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation. Front Mol Biosci 2022; 9:1067406. [PMID: 36533073 PMCID: PMC9755597 DOI: 10.3389/fmolb.2022.1067406] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 09/12/2023] Open
Abstract
DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.
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Affiliation(s)
- Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Andrew E. Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
| | - Lei Yao
- Experiment Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Jian Li
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yungang He
- Center for Medical Research and Innovation of Pudong Hospital, The Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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17
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Fang D, Ou X, Sun K, Zhou X, Li Y, Shi P, Zhao Z, He Y, Peng J, Xu J. m6A modification-mediated lncRNA TP53TG1 inhibits gastric cancer progression by regulating CIP2A stability. Cancer Sci 2022; 113:4135-4150. [PMID: 36114757 DOI: 10.1111/cas.15581] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 08/27/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are associated with various types of cancer. However, the precise roles of many lncRNAs in tumor progression remain unclear. In this study, we found that the expression of the lncRNA TP53TG1 was downregulated in gastric cancer (GC) and it functioned as a tumor suppressor. In addition, low TP53TG1 expression was significantly associated with poor survival in patients with GC. TP53TG1 inhibited the proliferation, metastasis, and cell cycle progression of GC cells, while it promoted their apoptosis. m6A modification sites are highly abundant on TP53TG1, and demethylase ALKBH5 reduces TP53TG1 stability and downregulates its expression. TP53TG1 interacts with cancerous inhibitor of protein phosphatase 2A (CIP2A) and triggers its ubiquitination-mediated degradation, resulting in the inhibition of the PI3K/AKT pathway. These results suggest that TP53TG1 plays an important role in inhibiting the progression of GC and provides a crucial target for GC treatment.
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Affiliation(s)
- Deliang Fang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xinde Ou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Kaiyu Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zhou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Youpei Li
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Shi
- Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Zirui Zhao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yulong He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianjun Peng
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianbo Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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18
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Cheng Y, Huang N, Yin Q, Cheng C, Chen D, Gong C, Xiong H, Zhao J, Wang J, Li X, Zhang J, Mao S, Qin K. LncRNA TP53TG1 plays an anti-oncogenic role in cervical cancer by synthetically regulating transcriptome profile in HeLa cells. Front Genet 2022; 13:981030. [PMID: 36267418 PMCID: PMC9576931 DOI: 10.3389/fgene.2022.981030] [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: 06/29/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have been extensively studied as important regulators of tumor development in various cancers. Tumor protein 53 target gene 1 (TP53TG1) is a newly identified lncRNA in recent years, and several studies have shown that TP53TG1 may play oncogenic or anti-oncogenic roles in different cancers. Nevertheless, the role of TP53TG1 in the development of cervical cancer is unclear. In our study, pan-cancer analysis showed that high expression of TP53TG1 was significantly associated with a better prognosis. We then constructed a TP53TG1 overexpression model in HeLa cell line to explore its functions and molecular targets. We found that TP53TG1 overexpression significantly inhibited cell proliferation and induced apoptosis, demonstrating that TP53TG1 may be a novel anti-oncogenic factor in cervical cancer. Furthermore, overexpression of TP53TG1 could activate type I interferon signaling pathways and inhibit the expression of genes involved in DNA damage responses. Meanwhile, TP53TG1 could affect alternative splicing of genes involved in cell proliferation or apoptosis by regulating the expression of many RNA-binding protein genes. Competing endogenous RNA (ceRNA) network analysis demonstrated that TP53TG1 could act as the sponge of several miRNAs to regulate the expression level of target genes. In conclusion, our study highlights the essential role of lncRNA TP53TG1 in the development of cervical cancer and suggests the potential regulatory mechanisms.
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Affiliation(s)
- Yi Cheng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Nan Huang
- Department of Allergy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Qingqing Yin
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Chao Cheng
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Dong Chen
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., Wuhan, Hubei, China
| | - Chen Gong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huihua Xiong
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jing Zhao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianhua Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jing Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shuangshuang Mao
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kai Qin
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- *Correspondence: Kai Qin,
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Knockdown of lncRNA TP53TG1 Enhances the Efficacy of Sorafenib in Human Hepatocellular Carcinoma Cells. Noncoding RNA 2022; 8:ncrna8040061. [PMID: 36005829 PMCID: PMC9414591 DOI: 10.3390/ncrna8040061] [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: 06/01/2022] [Revised: 07/19/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
The multikinase inhibitor, sorafenib, is a first-line treatment for hepatocellular carcinoma (HCC), but its limited efficacy, drug resistance and toxicity are a concern. In this study, we investigated the role of lncRNA TP53TG1 in the efficacy of sorafenib in HCC cells. We found that treatment with sorafenib increased the expression of TP53TG1 in HCC cells. Knockdown of TP53TG1 sensitized tumor cells to the antiproliferative effects of sorafenib. Furthermore, TP53TG1 knockdown had an additive inhibitory effect on HCC cell proliferation and migration in the presence of sorafenib. The combination of TP53TG1 knockdown and sorafenib drastically inhibited the activation of the ERK pathway. This work demonstrates that TP53TG1 deficiency enhances the efficacy of sorafenib in HCC. Combining TP53TG1 knockdown with sorafenib may be an optimal form of therapy for HCC treatment.
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20
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Comprehensive analysis of DRAIC and TP53TG1 in breast cancer luminal subtypes through the construction of lncRNAs regulatory model. Breast Cancer 2022; 29:1050-1066. [DOI: 10.1007/s12282-022-01385-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 07/07/2022] [Indexed: 12/23/2022]
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21
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Ruiz-Bañobre J, Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, Alvarez-Castro A, Carreras-Presas M, Brozos-Vazquez E, Vidal-Insua Y, Vazquez-Rivera F, Candamio-Folgar S, Mosquera-Presedo M, Lago-Lestón RM, Muinelo-Romay L, Vázquez-Bueno JÁ, Sanz-Pamplona R, Moreno V, Goel A, Castillo L, Martin AC, Arroyo R, Esteller M, Crujeiras AB, López-López R, Díaz-Lagares A. Noninvasive early detection of colorectal cancer by hypermethylation of the LINC00473 promoter in plasma cell-free DNA. Clin Epigenetics 2022; 14:86. [PMID: 35810318 PMCID: PMC9271259 DOI: 10.1186/s13148-022-01302-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Current noninvasive assays have limitations in the early detection of colorectal cancer. We evaluated the clinical utility of promoter methylation of the long noncoding RNA LINC00473 as a noninvasive biomarker to detect colorectal cancer and associated precancerous lesions. METHODS We evaluated the epigenetic regulation of LINC00473 through promoter hypermethylation in colorectal cancer cell lines using bisulfite genomic sequencing and expression analyses. DNA methylation of LINC00473 was analyzed in primary colorectal tumors using 450K arrays and RNA-seq from The Cancer Genome Atlas (TCGA). Tissue-based findings were validated in several independent cohorts of colorectal cancer and advanced colorectal polyp patients by pyrosequencing. We explored the clinical utility of LINC00473 methylation for the early detection of colorectal cancer in plasma cell-free DNA by quantitative methylation-specific PCR and droplet digital PCR. RESULTS LINC00473 showed transcriptionally silencing due to promoter hypermethylation in colorectal cancer cell lines and primary tumors. Methylation of the LINC00473 promoter accurately detected primary colorectal tumors in two independent clinical cohorts, with areas under the receiver operating characteristic curves (AUCs) of 0.94 and 0.89. This biomarker also identified advanced colorectal polyps from two other tissue-based clinical cohorts with high diagnostic accuracy (AUCs of 0.99 and 0.78). Finally, methylation analysis of the LINC00473 promoter in plasma cell-free DNA accurately identified patients with colorectal cancer and advanced colorectal polyps (AUCs of 0.88 and 0.84, respectively), which was confirmed in an independent cohort of patients. CONCLUSIONS Hypermethylation of the LINC00473 promoter is a new promising biomarker for noninvasive early detection of colorectal cancer and related precancerous lesions.
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Affiliation(s)
- Juan Ruiz-Bañobre
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Nicolas Costa-Fraga
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Ana Alvarez-Castro
- Department of Gastroenterology and Hepatology, University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Martín Carreras-Presas
- Department of Gastroenterology and Hepatology, University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Elena Brozos-Vazquez
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Yolanda Vidal-Insua
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Francisca Vazquez-Rivera
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
| | - Sonia Candamio-Folgar
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
| | - Manuel Mosquera-Presedo
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Universidade de Santiago de Compostela (USC), 15782, Santiago de Compostela, Spain
| | - Ramón M Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), 15706, Santiago de Compostela, Spain
| | - José Ángel Vázquez-Bueno
- Department of Pathology, Complejo Hospitalario Universitario de Ferrol (SERGAS), 15405, Ferrol, Spain
| | - Rebeca Sanz-Pamplona
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08907, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08907, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Víctor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), 08907, Barcelona, Spain
- Colorectal Cancer Group, Bellvitge Biomedical Research Institute (IDIBELL), 08907, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Barcelona, 08907, Barcelona, Spain
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott and White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, TX, USA
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA
- City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Ana C Martin
- Advanced Marker Discovery (AMADIX), 47004, Valladolid, Spain
| | - Rocio Arroyo
- Advanced Marker Discovery (AMADIX), 47004, Valladolid, Spain
| | - Manel Esteller
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Ana B Crujeiras
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de La Obesidad y Nutrición (CIBERobn), ISCIII, 28029, Madrid, Spain
| | - Rafael López-López
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain.
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain.
- Roche-Chus Joint Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), 15706, Santiago de Compostela, Spain.
| | - Angel Díaz-Lagares
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), ISCIII, 28029, Madrid, Spain.
- Cancer Epigenomics Laboratory, Epigenomics Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706, Santiago de Compostela, Spain.
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22
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Long non-coding RNAs involved in different steps of cancer metastasis. Clin Transl Oncol 2022; 24:997-1013. [PMID: 35119654 DOI: 10.1007/s12094-021-02761-z] [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: 10/18/2021] [Accepted: 12/14/2021] [Indexed: 11/09/2022]
Abstract
Non-proteincoding transcripts bearing 200 base pairs known as long non-coding RNAs (lncRNAs) play a role in a variety of molecular mechanisms, including cell differentiation, apoptosis and metastasis. Previous studies have suggested that frequently dysregulated lncRNAs play a crucial role in various aspects of cancer metastasis. Metastasis is the main leading cause of death in cancer. The role of lncRNAs in different stages of metastasis is the subject of this review. Based on in vitro and in vivo investigations on metastasis, we categorized lncRNAs into distinct stages of metastasis including angiogenesis, invasion, intravasation, survival in circulation, and extravasation. The involvement of lncRNAs in angiogenesis and invasion has been extensively studied. Here, we comprehensively discuss the role and functions of these lncRNAs with a particular focus on the molecular mechanisms.
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23
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Xu W, Liu C, Deng B, Lin P, Sun Z, Liu A, Xuan J, Li Y, Zhou K, Zhang X, Huang Q, Zhou H, He Q, Li B, Qu L, Yang J. TP53-inducible putative long noncoding RNAs encode functional polypeptides that suppress cell proliferation. Genome Res 2022; 32:1026-1041. [PMID: 35609991 DOI: 10.1101/gr.275831.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 05/06/2022] [Indexed: 01/10/2023]
Abstract
Polypeptides encoded by long non-coding RNAs (lncRNAs) are a novel class of functional molecules. However, whether these hidden polypeptides participate in the TP53 pathway and play a significant biological role is still unclear. Here, we discover that TP53-regulated lncRNAs encode peptides, two of which are functional in various human cell lines. Using ribosome profiling and RNA-seq approaches in HepG2 cells, we systematically identified more than 300 novel TP53-regulated lncRNAs and further confirmed that fifteen of these TP53-regulated lncRNAs encode peptides. Furthermore, several peptides were validated by multiple mass spectrometry measures. Ten of the novel translational lncRNAs were directly inducible by TP53 in response to DNA damage. Notably, we showed that the TP53-inducible peptides TP53LC02 and TP53LC04, but not their lncRNAs, could suppress cell proliferation. TP53LC04 peptide also had a function associated with cell proliferation by regulating the cell cycle in response to DNA damage. This study demonstrates that TP53-inducible lncRNAs encode new functional peptides, leading to the enlargement of the components of TP53 tumor suppressor network and providing novel potential targets for cancer therapy.
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Affiliation(s)
- Wenli Xu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, The Third Affiliated Hospital, Sun Yat-sen University
| | - Chang Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Bing Deng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Penghui Lin
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Zhenghua Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University
| | - Anrui Liu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Jiajia Xuan
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Yuying Li
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University
| | - Keren Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | | | - Qiaojuan Huang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Hui Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Qingyu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University
| | - Bin Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Lianghu Qu
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, Sun Yat-sen University
| | - Jianhua Yang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol,The Fifth Affiliated Hospital, Sun Yat-sen University
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24
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Meza-Sosa KF, Miao R, Navarro F, Zhang Z, Zhang Y, Hu JJ, Hartford CCR, Li XL, Pedraza-Alva G, Pérez-Martínez L, Lal A, Wu H, Lieberman J. SPARCLE, a p53-induced lncRNA, controls apoptosis after genotoxic stress by promoting PARP-1 cleavage. Mol Cell 2022; 82:785-802.e10. [PMID: 35104452 PMCID: PMC10392910 DOI: 10.1016/j.molcel.2022.01.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/01/2023]
Abstract
p53, master transcriptional regulator of the genotoxic stress response, controls cell-cycle arrest and apoptosis following DNA damage. Here, we identify a p53-induced lncRNA suicidal PARP-1 cleavage enhancer (SPARCLE) adjacent to miR-34b/c required for p53-mediated apoptosis. SPARCLE is a ∼770-nt, nuclear lncRNA induced 1 day after DNA damage. Despite low expression (<16 copies/cell), SPARCLE deletion increases DNA repair and reduces DNA-damage-induced apoptosis as much as p53 deficiency, while its overexpression restores apoptosis in p53-deficient cells. SPARCLE does not alter gene expression. SPARCLE binds to PARP-1 with nanomolar affinity and causes apoptosis by acting as a caspase-3 cofactor for PARP-1 cleavage, which separates PARP-1's N-terminal (NT) DNA-binding domain from its catalytic domains. NT-PARP-1 inhibits DNA repair. Expressing NT-PARP-1 in SPARCLE-deficient cells increases unrepaired DNA damage and restores apoptosis after DNA damage. Thus, SPARCLE enhances p53-induced apoptosis by promoting PARP-1 cleavage, which interferes with DNA-damage repair.
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Affiliation(s)
- Karla F Meza-Sosa
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, MOR 62210, México.
| | - Rui Miao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Francisco Navarro
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Bluebird Bio, Cambridge, MA 02142, USA
| | - Zhibin Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Ying Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Jacob Hu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Corrine Corrina R Hartford
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20895, USA
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20895, USA
| | - Gustavo Pedraza-Alva
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, MOR 62210, México
| | - Leonor Pérez-Martínez
- Laboratorio de Neuroinmunobiología, Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, MOR 62210, México
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20895, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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25
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Pangeni RP, Olivaries I, Huen D, Buzatto VC, Dawson TP, Ashton KM, Davis C, Brodbelt AR, Jenkinson MD, Bièche I, Yang L, Latif F, Darling JL, Warr TJ, Morris MR. Genome-wide methylation analyses identifies Non-coding RNA genes dysregulated in breast tumours that metastasise to the brain. Sci Rep 2022; 12:1102. [PMID: 35058523 PMCID: PMC8776809 DOI: 10.1038/s41598-022-05050-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
Brain metastases comprise 40% of all metastatic tumours and breast tumours are among the tumours that most commonly metastasise to the brain, the role that epigenetic gene dysregulation plays in this process is not well understood. We carried out 450 K methylation array analysis to investigate epigenetically dysregulated genes in breast to brain metastases (BBM) compared to normal breast tissues (BN) and primary breast tumours (BP). For this, we referenced 450 K methylation data for BBM tumours prepared in our laboratory with BN and BP from The Cancer Genome Atlas. Experimental validation on our initially identified genes, in an independent cohort of BP and in BBM and their originating primary breast tumours using Combined Bisulphite and Restriction Analysis (CoBRA) and Methylation Specific PCR identified three genes (RP11-713P17.4, MIR124-2, NUS1P3) that are hypermethylated and three genes (MIR3193, CTD-2023M8.1 and MTND6P4) that are hypomethylated in breast to brain metastases. In addition, methylation differences in candidate genes between BBM tumours and originating primary tumours shows dysregulation of DNA methylation occurs either at an early stage of tumour evolution (in the primary tumour) or at a later evolutionary stage (where the epigenetic change is only observed in the brain metastasis). Epigentic changes identified could also be found when analysing tumour free circulating DNA (tfcDNA) in patient’s serum taken during BBM biopsies. Epigenetic dysregulation of RP11-713P17.4, MIR3193, MTND6P4 are early events suggesting a potential use for these genes as prognostic markers.
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26
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Ou X, Zhou X, Li J, Ye J, Liu H, Fang D, Cai Q, Cai S, He Y, Xu J. p53-Induced LINC00893 Regulates RBFOX2 Stability to Suppress Gastric Cancer Progression. Front Cell Dev Biol 2022; 9:796451. [PMID: 35127712 PMCID: PMC8807521 DOI: 10.3389/fcell.2021.796451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/29/2021] [Indexed: 01/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to regulate diverse tumorigenic processes. However, little is known about long intergenic non-protein coding RNA 00893 (LINC00893) and its role in gastric cancer (GC). Herein we investigated its biological functions and molecular mechanism in GC. LINC00893 was decreased in GC tissues but significantly elevated in AGS cells after treatment with Nutlin-3. In GC patients, it was found that low expression of LINC00893 was correlated with tumor growth, metastasis and poor survival. Functionally, overexpression of LINC00893 suppressed the proliferation, migration and invasion of GC cells. Mechanistically, LINC00893 regulated the expression of epithelial-mesenchymal transition (EMT)-related proteins by binding to RNA binding fox-1 homolog 2 (RBFOX2) and promoting its ubiquitin-mediated degradation, thus suppressing the EMT and related functions of GC. In addition, the transcription factor p53 can regulate the expression of LINC00893 in an indirect way. Taken together, these results suggested that LINC00893 regulated by p53 repressed GC proliferation, migration and invasion by functioning as a binding site for RBFOX2 to regulate its stability and the expression of EMT-related proteins. LINC00893 acts as a tumor-inhibiting lncRNA that is induced by p53 in GC and regulates EMT by binding to RBFOX2, thus providing a novel experimental basis for the clinical treatment of GC.
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Affiliation(s)
- Xinde Ou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zhou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jin Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jinning Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haohan Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Deliang Fang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinbo Cai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shirong Cai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yulong He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yulong He, ; Jianbo Xu,
| | - Jianbo Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yulong He, ; Jianbo Xu,
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27
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Wang C, Yang Y, Wu X, Li J, Liu K, Fang D, Li B, Shan G, Mei X, Wang F, Mei Y. Reciprocal modulation of long noncoding RNA EMS and p53 regulates tumorigenesis. Proc Natl Acad Sci U S A 2022; 119:e2111409119. [PMID: 35022235 PMCID: PMC8784137 DOI: 10.1073/pnas.2111409119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
p53 plays a central role in tumor suppression. Emerging evidence suggests long noncoding RNA (lncRNA) as an important class of regulatory molecules that control the p53 signaling. Here, we report that the oncogenic lncRNA E2F1 messenger RNA (mRNA) stabilizing factor (EMS) and p53 mutually repress each other's expression. EMS is negatively regulated by p53. As a direct transcriptional repression target of p53, EMS is surprisingly shown to inhibit p53 expression. EMS associates with cytoplasmic polyadenylation element-binding protein 2 (CPEB2) and thus, disrupts the CPEB2-p53 mRNA interaction. This disassociation attenuates CPEB2-mediated p53 mRNA polyadenylation and suppresses p53 translation. Functionally, EMS is able to exert its oncogenic activities, at least partially, via the CPEB2-p53 axis. Together, these findings reveal a double-negative feedback loop between p53 and EMS, through which p53 is finely controlled. Our study also demonstrates a critical role for EMS in promoting tumorigenesis via the negative regulation of p53.
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Affiliation(s)
- Chenfeng Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yang Yang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xianning Wu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Jingxin Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Kaiyue Liu
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Debao Fang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Bingyan Li
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xinyu Mei
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
| | - Fang Wang
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
| | - Yide Mei
- The First Affiliated Hospital of University of Science and Technology of China (USTC), Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China;
- The Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei 230027, China
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Yang LR, Lin ZY, Hao QG, Li TT, Zhu Y, Teng ZW, Zhang J. The prognosis biomarkers based on m6A-related lncRNAs for myeloid leukemia patients. Cancer Cell Int 2022; 22:10. [PMID: 34996458 PMCID: PMC8739709 DOI: 10.1186/s12935-021-02428-3] [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] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/15/2022] Open
Abstract
Background Chronic myeloid leukemia (CML) and acute myeloid leukemia (AML) are two common malignant disorders in leukemia. Although potent drugs are emerging, CML and AML may still relapse after the drug treatment is stopped. N6-methyladenosine (m6A) and lncRNAs play certain roles in the occurrence and development of tumors, but m6A-modified LncRNAs in ML remain to be further investigated. Methods In this study, we extracted and analyzed the TCGA gene expression profile of 151 ML patients and the clinical data. On this basis, we then evaluated the immune infiltration capacity of ML and LASSO-penalized Cox analysis was applied to construct the prognostic model based on m6A related lncRNAs to verify the prognostic risk in clinical features of ML. Quantitative reverse transcription PCR was used to detect the expression level of LncRNA in in ML cell lines K562, MOLM13 and acute monocytic leukemia cell line THP-1. Results We found 70 m6A-related lncRNAs that were related to prognosis, and speculated that the content of stromal cells and immune cells would correlate with the survival of patients with ML. Next, Prognostic risk model of m6A-related lncRNAs was validated to have excellent consistency in clinical features of ML. Finally, we verified the expression levels of CRNDE, CHROMR and NARF-IT1 in ML cell lines K562, MOLM13 and acute monocytic leukemia cell line THP-1, which were significant. Conclusions The research provides clues for the prognosis prediction of ML patients by using the m6A-related lncRNAs model we have created, and clarifies the accuracy and authenticity of it. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02428-3.
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Affiliation(s)
- Li-Rong Yang
- Department of Oncology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, 82 Qinglong Road, Chengdu, 610031, Sichuan, China
| | - Zhu-Ying Lin
- Kunming Medical University, Kunming, 650000, Yunnan, China
| | - Qing-Gang Hao
- Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, 650000, China
| | - Tian-Tian Li
- Kunming Medical University, Kunming, 650000, Yunnan, China
| | - Yun Zhu
- The Sixth Affiliated Hospital of Kunming Medical University, The People's Hospital of Yuxi City, Yunnan, 653100, Yuxi, China
| | - Zhao-Wei Teng
- Yunnan Key Laboratory of Digital Orthopedics, Department of Orthopedic, The First People's Hospital of Yunnan Province, Kunming, 650000, Yunnan, China.
| | - Jun Zhang
- Department of Oncology, The Third People's Hospital of Chengdu, The Affiliated Hospital of Southwest Jiaotong University, 82 Qinglong Road, Chengdu, 610031, Sichuan, China.
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Eliseeva IA, Sogorina EM, Smolin EA, Kulakovskiy IV, Lyabin DN. Diverse Regulation of YB-1 and YB-3 Abundance in Mammals. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S48-S167. [PMID: 35501986 DOI: 10.1134/s000629792214005x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
YB proteins are DNA/RNA binding proteins, members of the family of proteins with cold shock domain. Role of YB proteins in the life of cells, tissues, and whole organisms is extremely important. They are involved in transcription regulation, pre-mRNA splicing, mRNA translation and stability, mRNA packaging into mRNPs, including stress granules, DNA repair, and many other cellular events. Many processes, from embryonic development to aging, depend on when and how much of these proteins have been synthesized. Here we discuss regulation of the levels of YB-1 and, in part, of its homologs in the cell. Because the amount of YB-1 is immediately associated with its functioning, understanding the mechanisms of regulation of the protein amount invariably reveals the events where YB-1 is involved. Control over the YB-1 abundance may allow using this gene/protein as a therapeutic target in cancers, where an increased expression of the YBX1 gene often correlates with the disease severity and poor prognosis.
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Affiliation(s)
- Irina A Eliseeva
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | | | - Egor A Smolin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
| | - Ivan V Kulakovskiy
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, 119991, Russia
| | - Dmitry N Lyabin
- Institute of Protein Research, Pushchino, Moscow Region, 142290, Russia.
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Sogorina EM, Kim ER, Sorokin AV, Lyabin DN, Ovchinnikov LP, Mordovkina DA, Eliseeva IA. YB-1 Phosphorylation at Serine 209 Inhibits Its Nuclear Translocation. Int J Mol Sci 2021; 23:ijms23010428. [PMID: 35008856 PMCID: PMC8745666 DOI: 10.3390/ijms23010428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/09/2021] [Accepted: 12/18/2021] [Indexed: 01/18/2023] Open
Abstract
YB-1 is a multifunctional DNA- and RNA-binding protein involved in cell proliferation, differentiation, and migration. YB-1 is a predominantly cytoplasmic protein that is transported to the nucleus in certain conditions, including DNA-damaging stress, transcription inhibition, and viral infection. In tumors, YB-1 nuclear localization correlates with high aggressiveness, multidrug resistance, and a poor prognosis. It is known that posttranslational modifications can regulate the nuclear translocation of YB-1. In particular, well-studied phosphorylation at serine 102 (S102) activates YB-1 nuclear import. Here, we report that Akt kinase phosphorylates YB-1 in vitro at serine 209 (S209), which is located in the vicinity of the YB-1 nuclear localization signal. Using phosphomimetic substitutions, we showed that S209 phosphorylation inhibits YB-1 nuclear translocation and prevents p-S102-mediated YB-1 nuclear import.
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Affiliation(s)
- Ekaterina M. Sogorina
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
| | - Ekaterina R. Kim
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexey V. Sorokin
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
- Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dmitry N. Lyabin
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
| | - Lev P. Ovchinnikov
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
| | - Daria A. Mordovkina
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
- Correspondence: (D.A.M.); (I.A.E.)
| | - Irina A. Eliseeva
- Group of Protein Biosynthesis Regulation, Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (E.M.S.); (E.R.K.); (A.V.S.); (D.N.L.)
- Correspondence: (D.A.M.); (I.A.E.)
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Zhao X, Li J, Liu Z, Powers S. Combinatorial CRISPR/Cas9 Screening Reveals Epistatic Networks of Interacting Tumor Suppressor Genes and Therapeutic Targets in Human Breast Cancer. Cancer Res 2021; 81:6090-6105. [PMID: 34561273 PMCID: PMC9762330 DOI: 10.1158/0008-5472.can-21-2555] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/22/2021] [Indexed: 01/07/2023]
Abstract
The majority of cancers are driven by multiple genetic alterations, but how these changes collaborate during tumorigenesis remains largely unknown. To gain mechanistic insights into tumor-promoting genetic interactions among tumor suppressor genes (TSG), we conducted combinatorial CRISPR screening coupled with single-cell transcriptomic profiling in human mammary epithelial cells. As expected, different driver gene alterations in mammary epithelial cells influenced the repertoire of tumor suppressor alterations capable of inducing tumor formation. More surprisingly, TSG interaction networks were comprised of numerous cliques-sets of three or four genes such that each TSG within the clique showed oncogenic cooperation with all other genes in the clique. Genetic interaction profiling indicated that the predominant cooperating TSGs shared overlapping functions rather than distinct or complementary functions. Single-cell transcriptomic profiling of CRISPR double knockouts revealed that cooperating TSGs that synergized in promoting tumorigenesis and growth factor independence showed transcriptional epistasis, whereas noncooperating TSGs did not. These epistatic transcriptional changes, both buffering and synergistic, affected expression of oncogenic mediators and therapeutic targets, including CDK4, SRPK1, and DNMT1. Importantly, the epistatic expression alterations caused by dual inactivation of TSGs in this system, such as PTEN and TP53, were also observed in patient tumors, establishing the relevance of these findings to human breast cancer. An estimated 50% of differentially expressed genes in breast cancer are controlled by epistatic interactions. Overall, our study indicates that transcriptional epistasis is a central aspect of multigenic breast cancer progression and outlines methodologies to uncover driver gene epistatic networks in other human cancers. SIGNIFICANCE: This study provides a roadmap for moving beyond discovery and development of therapeutic strategies based on single driver gene analysis to discovery based on interactions between multiple driver genes.See related commentary by Fong et al., p. 6078.
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Affiliation(s)
- Xiaoyu Zhao
- Department of Pathology and Cancer Center, Renaissance School of Medicine, Stony Brook, New York
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York
| | - Jinyu Li
- Department of Pathology and Cancer Center, Renaissance School of Medicine, Stony Brook, New York
| | - Zhimin Liu
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York
- Department of Biochemistry, Stony Brook University, Stony Brook, New York
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
- Janssen Research & Development Data Science, Titusville, New Jersey
| | - Scott Powers
- Department of Pathology and Cancer Center, Renaissance School of Medicine, Stony Brook, New York.
- Molecular and Cellular Biology Graduate Program, Stony Brook University, Stony Brook, New York
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York
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Elango R, Vishnubalaji R, Shaath H, Alajez NM. Transcriptional alterations of protein coding and noncoding RNAs in triple negative breast cancer in response to DNA methyltransferases inhibition. Cancer Cell Int 2021; 21:515. [PMID: 34565361 PMCID: PMC8474815 DOI: 10.1186/s12935-021-02213-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022] Open
Abstract
Background DNA methylation plays a crucial role in multiple cellular processes such as gene regulation, chromatin stability, and genetic imprinting. In mammals, DNA methylation is achieved by DNA methyltransferases (DNMTs). A number of studies have associated alterations in DNMT activity to tumorigenesis; however, the exact role of DNMTs in shaping the genome in triple negative breast cancer (TNBC) is still being unraveled. Methods In the current study, we employed two DNMT inhibitors (Decitabine and 5-Azacytidine), two TNBC models (MDA-MB-231 and BT-549) and whole transcriptome RNA-Seq and characterized the transcriptional alterations associated with DNMT inhibition. Colony forming unit (CFU), flow cytometry, and fluorescent microscopy were used to assess cell proliferation, cell cycle distribution, and cell death, respectively. Ingenuity pathway analysis (IPA) was used for network and pathway analyses. Results Remarkably, DNMT inhibition induced the expression of genes involved in endoplasmic reticulum response to stress, response to unfolder protein, as well as cobalamin metabolic processes. In contrast, suppression of cellular processes related to cell cycle and mitosis were hallmarks of DNMT inhibition. Concordantly, DNMT inhibition led to significant inhibition of TNBC cell proliferation, G2-M cell cycle arrest and induction of cell death. Mechanistically, DNMT inhibition activated TP53, NUPR1, and NFkB (complex) networks, while RARA, RABL6, ESR1, FOXM1, and ERBB2 networks were suppressed. Our data also identified the long noncoding RNA (lncRNA) transcriptional portrait associated with DNMT inhibition and identified 25 commonly upregulated and 60 commonly downregulated lncRNAs in response to Decitabine and 5-Azacytidinec treatment in both TNBC models. TPT1-AS1 was the most highly induced (6.3 FC), while MALAT1 was the most highly suppressed (− 7.0 FC) lncRNA in response to DNMT inhibition. Conclusions Taken together, our data provides a comprehensive view of transcriptome alterations in the coding and noncoding transcriptome in TNBC in response to DNMT inhibition. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02213-2.
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Affiliation(s)
- Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Hibah Shaath
- Translational Cancer and Immunity Center (TCIC), Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.,College of Health & Life Sciences, Qatar Foundation (QF), Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Nehad M Alajez
- Translational Cancer and Immunity Center (TCIC), Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar. .,College of Health & Life Sciences, Qatar Foundation (QF), Hamad Bin Khalifa University (HBKU), Doha, Qatar.
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Masoumi F, Saraiva SM, Bouzo BL, López-López R, Esteller M, Díaz-Lagares Á, de la Fuente M. Modulation of Colorectal Tumor Behavior via lncRNA TP53TG1-Lipidic Nanosystem. Pharmaceutics 2021; 13:pharmaceutics13091507. [PMID: 34575588 PMCID: PMC8470159 DOI: 10.3390/pharmaceutics13091507] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 01/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an emerging group of RNAs with a crucial role in cancer pathogenesis. In gastrointestinal cancers, TP53 target 1 (TP53TG1) is an epigenetically regulated lncRNA that represents a promising therapeutic target due to its tumor suppressor properties regulating the p53-mediated DNA damage and the intracellular localization of the oncogenic YBX1 protein. However, to translate this finding into the clinic as a gene therapy, it is important to develop effective carriers able to deliver exogenous lncRNAs to the targeted cancer cells. Here, we propose the use of biocompatible sphingomyelin nanosystems comprising DOTAP (DSNs) to carry and deliver a plasmid vector encoding for TP53TG1 (pc(TP53TG1)-DSNs) to a colorectal cancer cell line (HCT-116). DSNs presented a high association capacity and convenient physicochemical properties. In addition, pc(TP53TG1)-DSNs showed anti-tumor activities in vitro, specifically a decrease in the proliferation rate, a diminished colony-forming capacity, and hampered migration and invasiveness of the treated cancer cells. Consequently, the proposed strategy displays a high potential as a therapeutic approach for colorectal cancer.
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Affiliation(s)
- Farimah Masoumi
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Immunology Department, School of Medicine, Tehran University of Medical Sciences, Tehran 14176-13151, Iran
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon 46841-61167, Iran
| | - Sofia M. Saraiva
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
| | - Belén L. Bouzo
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
| | - Rafael López-López
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain
| | - Manel Esteller
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08907 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Ángel Díaz-Lagares
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago (CHUS), SERGAS, 15706 Santiago de Compostela, Spain
- Correspondence: (A.D.-L.); (M.d.l.F.)
| | - María de la Fuente
- Nano-Oncology and Translational Therapeutics Unit, Health Research Institute of Santiago de Compostela (IDIS), SERGAS, 15706 Santiago de Compostela, Spain; (F.M.); (S.M.S.); (B.L.B.)
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), 28029 Madrid, Spain; (R.L.-L.); (M.E.)
- Correspondence: (A.D.-L.); (M.d.l.F.)
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Price RL, Bhan A, Mandal SS. HOTAIR beyond repression: In protein degradation, inflammation, DNA damage response, and cell signaling. DNA Repair (Amst) 2021; 105:103141. [PMID: 34183273 PMCID: PMC10426209 DOI: 10.1016/j.dnarep.2021.103141] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 05/13/2021] [Accepted: 05/21/2021] [Indexed: 01/17/2023]
Abstract
Long noncoding RNAs (lncRNAs) are pervasively transcribed from the mammalian genome as transcripts that are usually >200 nucleotides long. LncRNAs generally do not encode proteins but are involved in a variety of physiological processes, principally as epigenetic regulators. HOX transcript antisense intergenic RNA (HOTAIR) is a well-characterized lncRNA that has been implicated in several cancers and in various other diseases. HOTAIR is a repressor lncRNA and regulates various repressive chromatin modifications. However, recent studies have revealed additional functions of HOTAIR in regulation of protein degradation, microRNA (miRNA) sponging, NF-κB activation, inflammation, immune signaling, and DNA damage response. Herein, we have summarized the diverse functions and modes of action of HOTAIR in protein degradation, inflammation, DNA repair, and diseases, beyond its established functions in gene silencing.
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Affiliation(s)
- Rachel L Price
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States
| | - Arunoday Bhan
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States
| | - Subhrangsu S Mandal
- Gene Regulation and Epigenetics Research Laboratory, Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, United States.
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Yang JW, Sun C, Jin QY, Qiao XH, Guo XL. Potential therapeutic strategies for targeting Y-box-binding protein 1 in cancers. Curr Cancer Drug Targets 2021; 21:897-906. [PMID: 34465278 DOI: 10.2174/1568009621666210831125001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/22/2022]
Abstract
As one of the most conservative proteins in evolution, Y-box-binding protein 1 (YB-1) has long been considered as a potential cancer target. YB-1 is usually poorly expressed in normal cells and exerts cellular physiological functions such as DNA repair, pre-mRNA splicing and mRNA stabilizing. In cancer cells, the expression of YB-1 is up-regulated and undergoes nuclear translocation and contributes to tumorigenesis, angiogenesis, tumor proliferation, invasion, migration and chemotherapy drug resistance. During the past decades, a variety of pharmacological tools such as siRNA, shRNA, microRNA, circular RNA, lncRNA and various compounds have been developed to target YB-1 for cancer therapy. In this review, we describe the physiological characteristics of YB-1 in detail, highlight the role of YB-1 in tumors and summarize the current therapeutic methods for targeting YB-1 in cancer.
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Affiliation(s)
- Jia-Wei Yang
- Department of Pharmacology, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012. China
| | - Chao Sun
- Department of Pharmacology, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012. China
| | - Qiu-Yang Jin
- Department of Pharmacology, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012. China
| | - Xing-Hui Qiao
- Department of Pharmacology, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012. China
| | - Xiu-Li Guo
- Department of Pharmacology, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Jinan 250012. China
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Lu Q, Guo Q, Xin M, Lim C, Gamero AM, Gerhard GS, Yang L. LncRNA TP53TG1 Promotes the Growth and Migration of Hepatocellular Carcinoma Cells via Activation of ERK Signaling. Noncoding RNA 2021; 7:ncrna7030052. [PMID: 34564314 PMCID: PMC8482154 DOI: 10.3390/ncrna7030052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNA (lncRNA) TP53 target 1 (TP53TG1) was discovered as a TP53 target gene. TP53TG1 has been reported as having dual roles by exerting tumor-suppressive and oncogenic activities that vary depending on the cancer type. Yet, the role of TP53TG1 in hepatocellular carcinoma (HCC) is not fully understood. In this study, we performed both gain- and loss-of-function studies to determine the biological role of TP53TG1 in HCC. We found that the knockdown of TP53 in HCC cells caused the upregulation of TP53TG1. Furthermore, we found that the knockdown of TP53TG1 not only suppressed HCC cell proliferation and migration, but also reduced intrinsic ERK signaling. In contrast, the overexpression of TP53TG1 increased ERK activation and enhanced HCC proliferation. In conclusion, our study reveals an oncogenic role of TP53TG1 in HCC, which provides a novel insight into the cell-type-specific function of TP53TG1 in HCC.
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Affiliation(s)
| | | | | | | | | | | | - Ling Yang
- Correspondence: ; Tel.: +1-215-707-3779
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37
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Liu B, Liu Y, Zou J, Zou M, Cheng Z. Smoking is Associated with Lung Adenocarcinoma and Lung Squamous Cell Carcinoma Progression through Inducing Distinguishing lncRNA Alterations in Different Genders. Anticancer Agents Med Chem 2021; 22:1541-1550. [PMID: 34315392 DOI: 10.2174/1871520621666210727115147] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/08/2021] [Accepted: 06/21/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Smoking participates in pathogenesis of lung cancer. Long non-coding RNAs (lncRNAs) play some specific roles during development of lung cancers. OBJECTIVE To investigate effects of smoking on lncRNA alterations in lung cancer. METHODS There are 522 lung adenocarcinoma (LUAD) and 504 lung squamous cell carcinoma (LUSC) participants. Clinical and lncRNA genetic data were downloaded from The Cancer Genome Atlas (TCGA) database. LncRNA alterations were analyzed in lung cancer patients. Smoking category and packs were evaluated. Correlations between smoking and LncRNA alterations were analyzed. Kaplan-Meier analysis was performed to determine overall survival and disease free survival. RESULTS There are more non-smokers in LUSC than in LUAD. In both LUAD and LUSC, smoking could increase total mutation counts and fraction of copy number alterations. Smoking index positively correlated with total mutations in LUAD, but not in LUSC. Smoking could trigger lncRNA alterations both in LUAD and LUSC. Smoking regulated different lncRNA between male and female. EXOC3-AS1 and LINC00603 alterations were positively correlated with smoking index in male LUAD smokers. In female LUAD smokers, smoking index was positively correlated with SNHG15, TP53TG1 and LINC01600 and negatively with LINC00609 and PTCSC3. In both male and female LUSC patients, smoking increased or decreased several lncRNA alterations. DGCR5 alteration increased in male LUSC than in female LUSC patients. In female LUSC patients, LOH12CR2 alteration was positively correlated with smoking index. CONCLUSIONS Smoking promoted LUAD and LUSC development by affecting different lncRNA alterations in different genders.
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Affiliation(s)
- Bing Liu
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yuan Liu
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jingfeng Zou
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Menglin Zou
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Zhenshun Cheng
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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38
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Li S, Xiong Q, Chen M, Wang B, Yang X, Yang M, Wang Q, Cui Z, Ge F. Long noncoding RNA HOTAIR interacts with Y-Box Protein-1 (YBX1) to regulate cell proliferation. Life Sci Alliance 2021; 4:4/9/e202101139. [PMID: 34266873 PMCID: PMC8321693 DOI: 10.26508/lsa.202101139] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
The authors determined that HOTAIR specifically bind to YBX1 and promote its nuclear translocation, and then regulating cell proliferation by stimulating the PI3K/Akt and ERK/RSK signaling pathways. HOTAIR is a long noncoding RNA (lncRNA) which serves as an important factor regulating diverse processes linked with cancer development. Here, we used comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP-MS) to explore the HOTAIR-protein interactome. We were able to identify 348 proteins interacting with HOTAIR, allowing us to establish a heavily interconnected HOTAIR-protein interaction network. We further developed a novel near-infrared fluorescent protein (iRFP)-trimolecular fluorescence complementation (TriFC) system to assess the interaction between HOTAIR and its interacting proteins. Then, we determined that HOTAIR specifically binds to YBX1, promotes YBX1 nuclear translocation, and stimulates the PI3K/Akt and ERK/RSK signaling pathways. We further demonstrated that HOTAIR exerts its effects on cell proliferation, at least in part, through the regulation of two YBX1 downstream targets phosphoenolpyruvate carboxykinase 2 (PCK2) and platelet derived growth factor receptor β. Our findings revealed a novel mechanism, whereby an lncRNA is able to regulate cell proliferation via altering intracellular protein localization. Moreover, the imaging tools developed herein have excellent potential for future in vivo imaging of lncRNA–protein interaction.
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Affiliation(s)
- Siting Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qian Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Minghai Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xue Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mingkun Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China .,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Ge
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China .,Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
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39
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Wang H, Zhang Z, Zhang Y, Liu S, Li L. Long Non-Coding RNA TP53TG1 Upregulates SHCBP1 to Promote Retinoblastoma Progression by Sponging miR-33b. Cell Transplant 2021; 30:9636897211025223. [PMID: 34247545 PMCID: PMC8278459 DOI: 10.1177/09636897211025223] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNA (lncRNA) TP53 target 1 (TP53TG1) is known to be strongly associated with tumor and cancer progression. However, its expression profile, unique role, and regulatory pathways in retinoblastoma (RB) are not known. Here, we revealed a large expression of TP53TG1 in RB tissues and cell lines. Conversely, we showed marked suppression of cell proliferation, migration, and invasion in TP53TG1 knocked down RB cells. Mechanistically, we established that TP53TG1 directly interacted with microRNA (miR)-33b in RB cells. Furthermore, TP53TG1 transcripts were found to be inversely correlated with miR-33b in RB tissues. We also showed that miR-33b suppression partly reversed the TP53TG1 knockdown mediated effects on tumor biology. Finally, TP53TG1 was shown to modulate the levels of SHC Binding and Spindle Associated 1 (SHCBP1), a direct target of miR-33b in RB cells. Based on the above data, we propose that TP53TG1 regulates RB progression via its modulation of the miR-33b/SHCBP1 pathway.
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Affiliation(s)
- Hongyi Wang
- Department of Thoracic Surgery, 162798The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710000, China
| | - Zhen Zhang
- Department of Ophthalmology, 162798The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710000, China
| | - Yue Zhang
- Department of Ophthalmology, 162798The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710000, China
| | - Shihai Liu
- Center laboratory, 74657The first Hospital of Qingdao University, Qingdao 266000, China
| | - Li Li
- Department of Ophthalmology, 162798The First Affiliated Hospital of Xian Jiaotong University, Xi'an 710000, China
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40
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Talib WH, Mahmod AI, Kamal A, Rashid HM, Alashqar AMD, Khater S, Jamal D, Waly M. Ketogenic Diet in Cancer Prevention and Therapy: Molecular Targets and Therapeutic Opportunities. Curr Issues Mol Biol 2021; 43:558-589. [PMID: 34287243 PMCID: PMC8928964 DOI: 10.3390/cimb43020042] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/19/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Although cancer is still one of the most significant global challenges facing public health, the world still lacks complementary approaches that would significantly enhance the efficacy of standard anticancer therapies. One of the essential strategies during cancer treatment is following a healthy diet program. The ketogenic diet (KD) has recently emerged as a metabolic therapy in cancer treatment, targeting cancer cell metabolism rather than a conventional dietary approach. The ketogenic diet (KD), a high-fat and very-low-carbohydrate with adequate amounts of protein, has shown antitumor effects by reducing energy supplies to cells. This low energy supply inhibits tumor growth, explaining the ketogenic diet's therapeutic mechanisms in cancer treatment. This review highlights the crucial mechanisms that explain the ketogenic diet's potential antitumor effects, which probably produces an unfavorable metabolic environment for cancer cells and can be used as a promising adjuvant in cancer therapy. Studies discussed in this review provide a solid background for researchers and physicians to design new combination therapies based on KD and conventional therapies.
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Affiliation(s)
- Wamidh H. Talib
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Asma Ismail Mahmod
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Ayah Kamal
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Hasan M. Rashid
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Aya M. D. Alashqar
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Samar Khater
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Duaa Jamal
- Department of Clinical Pharmacy and Therapeutics, Applied Science Private University, Amman 11931, Jordan; (A.I.M.); (A.K.); (H.M.R.); (A.M.D.A.); (S.K.); (D.J.)
| | - Mostafa Waly
- Department of Food Science and Nutrition, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al-Khoud 34-123, Oman;
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41
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Chatterjee M, Viswanathan P. Long noncoding RNAs in the regulation of p53-mediated apoptosis in human cancers. Cell Biol Int 2021; 45:1364-1382. [PMID: 33760332 DOI: 10.1002/cbin.11597] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/02/2021] [Accepted: 03/21/2021] [Indexed: 02/05/2023]
Abstract
Long noncoding RNAs (lncRNAs) are widely known for their regulatory function in transcriptional and posttranscriptional processes. The involvement of such non-protein-coding RNAs in nuclear organization and chromatin remodeling is often associated with an increased risk of human malignancies. In cancer, lncRNAs either promote cell survival or may act as a growth suppressor, thus conferring a key regulatory function other than their established role in fundamental cellular processes. Interestingly, lncRNAs interfere with the stages of apoptosis and related pathways involving p53. Many of these molecules either regulate or are regulated by p53 while mounting oncogenic events. Consequently, they may confer both prosurvival or proapoptotic functions depending upon the tissue type. Since the mechanism of cell death is bypassed in many human cancers, it has emerged that the lncRNAs are either overexpressed or knocked down to sensitize cells to apoptotic stimuli. Nonetheless, the abundant expression of lncRNAs in tumor cells renders them suitable targets for anticancer therapies. Although the role of lncRNAs in the p53 network and apoptosis has been independently defined, their interplay in activating p53-target genes during cell cycle arrest remains unexplored. Thus, we have specifically reviewed the possible involvement of lncRNAs in the p53-mediated apoptosis of human cancer cells. In particular, we summarize the growing evidence from individual studies and analyze whether lncRNAs are essential to facilitate apoptosis in a p53-dependent manner. This may lead to the identification of p53-associated lncRNAs that are suitable therapeutic targets or diagnostic/prognostic markers.
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Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Pragasam Viswanathan
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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42
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Wang Y, Zhu Y, Pu Z, Li Z, Deng Y, Li N, Peng F. Soluble resistance-related calcium-binding protein participates in multiple diseases via protein-protein interactions. Biochimie 2021; 189:76-86. [PMID: 34153376 DOI: 10.1016/j.biochi.2021.06.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/21/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022]
Abstract
Soluble resistance-related calcium-binding protein (sorcin), a 22 kDa penta-EF-hand protein, has been intensively studied in cancers and multidrug resistance over a prolonged period. Sorcin is widely distributed in tissues and participates in the regulation of Ca2+ homeostasis and Ca2+-dependent signaling. Protein-protein interactions (PPIs) are essential for regulating protein functions in almost all biological processes. Sorcin interaction partners tend to vary in type, including Ca2+ receptors, Ca2+ transporters, endoplasmic reticulum stress markers, transcriptional regulatory elements, immunomodulation-related factors, and viral proteins. Recent studies have shown that sorcin is involved in a broad range of pathological conditions, such as cardiomyopathy, type 2 diabetes mellitus, neurodegenerative diseases, liver diseases, and viral infections. As a multifunctional cellular protein, in these diseases, sorcin has a role by interacting with or regulating the expression of other proteins, such as sarcoplasmic reticulum/endoplasmic reticulum Ca2+ ATPase, ryanodine receptors, presenilin 2, L-type Ca2+ channels, carbohydrate-responsive element-binding protein, tau, α-synuclein, signal transducer and activator of transcription 3, HCV nonstructural 5A protein, and viral capsid protein 1. This review summarizes the roles that sorcin plays in various diseases, mainly via different PPIs, and focuses principally on non-neoplastic diseases to help acquire a more comprehensive understanding of sorcin's multifunctional characteristics.
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Affiliation(s)
- Yinmiao Wang
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China; NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China
| | - Yuanyuan Zhu
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China; NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China
| | - Zhangya Pu
- Department of Infectious Diseases and Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China
| | - Zhenfen Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China; NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China
| | - Ying Deng
- People's Hospital of Ningxiang, Changsha, Hunan Province 410600, China
| | - Ning Li
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China
| | - Fang Peng
- Department of Blood Transfusion, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China; NHC Key Laboratory of Cancer Proteomics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan Province 410008, China.
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Sanegre S, Eritja N, de Andrea C, Diaz-Martin J, Diaz-Lagares Á, Jácome MA, Salguero-Aranda C, García Ros D, Davidson B, Lopez R, Melero I, Navarro S, Ramon Y Cajal S, de Alava E, Matias-Guiu X, Noguera R. Characterizing the Invasive Tumor Front of Aggressive Uterine Adenocarcinoma and Leiomyosarcoma. Front Cell Dev Biol 2021; 9:670185. [PMID: 34150764 PMCID: PMC8209546 DOI: 10.3389/fcell.2021.670185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
The invasive tumor front (the tumor–host interface) is vitally important in malignant cell progression and metastasis. Tumor cell interactions with resident and infiltrating host cells and with the surrounding extracellular matrix and secreted factors ultimately determine the fate of the tumor. Herein we focus on the invasive tumor front, making an in-depth characterization of reticular fiber scaffolding, infiltrating immune cells, gene expression, and epigenetic profiles of classified aggressive primary uterine adenocarcinomas (24 patients) and leiomyosarcomas (11 patients). Sections of formalin-fixed samples before and after microdissection were scanned and studied. Reticular fiber architecture and immune cell infiltration were analyzed by automatized algorithms in colocalized regions of interest. Despite morphometric resemblance between reticular fibers and high presence of macrophages, we found some variance in other immune cell populations and distinctive gene expression and cell adhesion-related methylation signatures. Although no evident overall differences in immune response were detected at the gene expression and methylation level, impaired antimicrobial humoral response might be involved in uterine leiomyosarcoma spread. Similarities found at the invasive tumor front of uterine adenocarcinomas and leiomyosarcomas could facilitate the use of common biomarkers and therapies. Furthermore, molecular and architectural characterization of the invasive front of uterine malignancies may provide additional prognostic information beyond established prognostic factors.
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Affiliation(s)
- Sabina Sanegre
- Cancer CIBER (CIBERONC), Madrid, Spain.,Department of Pathology, School of Medical, University of Valencia-INCLIVA, Valencia, Spain
| | - Núria Eritja
- Cancer CIBER (CIBERONC), Madrid, Spain.,Institut de Recerca Biomèdica de LLeida (IRBLLEIDA), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Department of Pathology, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida - University of Barcelona, Barcelona, Spain
| | - Carlos de Andrea
- Cancer CIBER (CIBERONC), Madrid, Spain.,Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Juan Diaz-Martin
- Cancer CIBER (CIBERONC), Madrid, Spain.,Institute of Biomedicine of Sevilla, Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, Seville, Spain
| | - Ángel Diaz-Lagares
- Cancer CIBER (CIBERONC), Madrid, Spain.,Cancer Epigenomics, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - María Amalia Jácome
- Department of Mathematics, MODES Group, CITIC, Faculty of Science, Universidade da Coruña, A Coruña, Spain
| | - Carmen Salguero-Aranda
- Cancer CIBER (CIBERONC), Madrid, Spain.,Institute of Biomedicine of Sevilla, Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, Seville, Spain
| | - David García Ros
- Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Ben Davidson
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Rafel Lopez
- Cancer CIBER (CIBERONC), Madrid, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Ignacio Melero
- Cancer CIBER (CIBERONC), Madrid, Spain.,Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
| | - Samuel Navarro
- Cancer CIBER (CIBERONC), Madrid, Spain.,Department of Pathology, School of Medical, University of Valencia-INCLIVA, Valencia, Spain
| | - Santiago Ramon Y Cajal
- Cancer CIBER (CIBERONC), Madrid, Spain.,Department of Pathology, Vall d'Hebron University Hospital, Autonomous University of Barcelona, Barcelona, Spain
| | - Enrique de Alava
- Cancer CIBER (CIBERONC), Madrid, Spain.,Institute of Biomedicine of Sevilla, Virgen del Rocio University Hospital/CSIC/University of Sevilla/CIBERONC, Seville, Spain
| | - Xavier Matias-Guiu
- Cancer CIBER (CIBERONC), Madrid, Spain.,Institut de Recerca Biomèdica de LLeida (IRBLLEIDA), Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Department of Pathology, Hospital U Arnau de Vilanova and Hospital U de Bellvitge, University of Lleida - University of Barcelona, Barcelona, Spain
| | - Rosa Noguera
- Cancer CIBER (CIBERONC), Madrid, Spain.,Department of Pathology, School of Medical, University of Valencia-INCLIVA, Valencia, Spain
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Chen B, Lan J, Xiao Y, Liu P, Guo D, Gu Y, Song Y, Zhong Q, Ma D, Lei P, Liu Q. Long noncoding RNA TP53TG1 suppresses the growth and metastasis of hepatocellular carcinoma by regulating the PRDX4/β-catenin pathway. Cancer Lett 2021; 513:75-89. [PMID: 33957185 DOI: 10.1016/j.canlet.2021.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023]
Abstract
Emerging evidence has shown that aberrant expression of lncRNA-TP53TG1 plays important roles in various malignancies. However, the biological functions of lncRNA-TP53TG1 in hepatocarcinogenesis, as well as the underlying mechanisms, remain largely unknown. Here, we assessed whether lncRNA-TP53TG1 plays a key role in the progression of hepatocellular carcinoma (HCC). The expression of lncRNA-TP53TG1 was significantly decreased in HCC tissues and cells. Decreased expression of lncRNA-TP53TG1 was associated with aggressive clinical phenotypes and a poor prognosis. Ectopic expression of lncRNA-TP53TG1 inhibited hepatoma cell proliferation and migration in vitro and in vivo, whereas lncRNA-TP53TG1 knockdown exerted the opposite effects. Furthermore, lncRNA-TP53TG1 played an important role in slowing the epithelial-mesenchymal transition (EMT) process in HCC. Mechanistically, lncRNA-TP53TG1 physically interacted with PRDX4 and promoted its ubiquitin-mediated degradation, resulting in the inactivation of the WNT/β-catenin signaling pathway in hepatoma cells. Our findings demonstrate a novel mechanism by which lncRNA-TP53TG1 exerts its tumor-suppressive effects through the WNT/β-catenin signaling pathway in a PRDX4-mediated manner in HCC. Based on these results, lncRNA-TP53TG1 potentially represents a prognostic indicator and therapeutic target for patients with HCC.
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Affiliation(s)
- Baiyang Chen
- Department of General Surgery, Xiangyang Central Hospital, Affiliated with Hubei University of Arts and Science, Xiangyang, Hubei, PR China; Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Jianwei Lan
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Yusha Xiao
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Pengpeng Liu
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Deliang Guo
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Yang Gu
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Youai Song
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Qiu Zhong
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Dong Ma
- Department of General Surgery, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Ping Lei
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, 300052, PR China.
| | - Quanyan Liu
- Department of Hepatobiliary Surgery, Tianjin Medical University General Hospital, Tianjin, 300052, PR China.
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45
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Chatterjee M, Viswanathan P. Long noncoding RNAs in the regulation of p53‐mediated apoptosis in human cancers. Cell Biol Int 2021. [DOI: https://doi.org/10.1002/cbin.11597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Manjima Chatterjee
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
| | - Pragasam Viswanathan
- School of Bio Sciences and Technology, Vellore Institute of Technology Vellore Tamil Nadu India
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Jones R, Wijesinghe S, Wilson C, Halsall J, Liloglou T, Kanhere A. A long intergenic non-coding RNA regulates nuclear localization of DNA methyl transferase-1. iScience 2021; 24:102273. [PMID: 33851096 PMCID: PMC8022221 DOI: 10.1016/j.isci.2021.102273] [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: 06/16/2020] [Revised: 12/21/2020] [Accepted: 03/02/2021] [Indexed: 01/10/2023] Open
Abstract
DNA methyl transferase-1 or DNMT1 maintains DNA methylation in the genome and is important for regulating gene expression in cells. Aberrant changes in DNMT1 activity and DNA methylation are commonly observed in cancers and many other diseases. Recently, a number of long intergenic non-protein-coding RNAs or lincRNAs have been shown to play a role in regulating DNMT1 activity. CCDC26 is a nuclear lincRNA that is frequently mutated in cancers and is a hotbed for disease-associated single nucleotide changes. However, the functional mechanism of CCDC26 is not understood. Here, we show that this lincRNA is concentrated on the nuclear periphery. Strikingly, in the absence of CCDC26 lincRNA, DNMT1 is mis-located in the cytoplasm, and the genomic DNA is significantly hypomethylated. This is accompanied by double-stranded DNA breaks and increased cell death. These results point to a previously unrecognized mechanism of lincRNA-mediated subcellular localization of DNMT1 and regulation of DNA methylation.
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Affiliation(s)
- Rhian Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Susanne Wijesinghe
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, UK
| | - Claire Wilson
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John Halsall
- Institute of Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Triantafillos Liloglou
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Aditi Kanhere
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.,Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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Lorenzo PM, Crujeiras AB. Potential effects of nutrition-based weight loss therapies in reversing obesity-related breast cancer epigenetic marks. Food Funct 2021; 12:1402-1414. [PMID: 33480953 DOI: 10.1039/d0fo01984d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Obesity is a modifiable risk factor of breast cancer and epigenetic marks were proposed as a relevant mechanistic link. These mechanisms can be remodelled by modifying lifestyle factors and this fact could be useful in the treatment of obesity-related breast cancer. This review aimed to reveal the current evidence on the effects of differences in body composition and lifestyle factors on the risk, treatment, and survival of breast cancer with a focus on the effects of weight loss therapies based on different nutrients, bioactive compounds, and Mediterranean and ketogenic diets to counteract obesity-related breast cancer epigenetic marks. This review was framed on the most relevant and recently published articles and abstracts selected in PubMed using key words related to epigenetics, lifestyle, dietary habits, nutrients, bioactive compounds, ketone bodies, and weight loss treatments in obesity and breast cancer. Several studies have demonstrated that lifestyle interventions, including dietary modifications towards a healthy diet pattern, are effective therapies to prevent the onset of breast cancer and to improve the survival after treatment. These therapies reduce the main factors associated with obesity that are links between adiposity and cancer, including oxidative stress, inflammation and epigenetic mechanisms. However, although sufficient evidence exists regarding the effects of nutrients, dietary patterns, and weight loss therapies to prevent breast cancer or to improve survival, the effects of these strategies on the oncological treatment response were less studied. This review summarises the current scientific evidence regarding these nutritional strategies as adjuvant therapies in the management of obesity-related breast cancer by remodelling epigenetic marks related to carcinogenesis.
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Affiliation(s)
- Paula M Lorenzo
- Epigenomics in Endocrinology and Nutrition Group, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.
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48
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Rodriguez-Casanova A, Costa-Fraga N, Bao-Caamano A, López-López R, Muinelo-Romay L, Diaz-Lagares A. Epigenetic Landscape of Liquid Biopsy in Colorectal Cancer. Front Cell Dev Biol 2021; 9:622459. [PMID: 33614651 PMCID: PMC7892964 DOI: 10.3389/fcell.2021.622459] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/05/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignancies and is a major cause of cancer-related deaths worldwide. Thus, there is a clinical need to improve early detection of CRC and personalize therapy for patients with this disease. In the era of precision oncology, liquid biopsy has emerged as a major approach to characterize the circulating tumor elements present in body fluids, including cell-free DNA and RNA, circulating tumor cells, and extracellular vesicles. This non-invasive tool has allowed the identification of relevant molecular alterations in CRC patients, including some indicating the disruption of epigenetic mechanisms. Epigenetic alterations found in solid and liquid biopsies have shown great utility as biomarkers for early detection, prognosis, monitoring, and evaluation of therapeutic response in CRC patients. Here, we summarize current knowledge of the most relevant epigenetic mechanisms associated with cancer development and progression, and the implications of their deregulation in cancer cells and liquid biopsy of CRC patients. In particular, we describe the methodologies used to analyze these epigenetic alterations in circulating tumor material, and we focus on the clinical utility of epigenetic marks in liquid biopsy as tumor biomarkers for CRC patients. We also discuss the great challenges and emerging opportunities of this field for the diagnosis and personalized management of CRC patients.
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Affiliation(s)
- Aitor Rodriguez-Casanova
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Nicolás Costa-Fraga
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aida Bao-Caamano
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rafael López-López
- Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.,Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
| | - Laura Muinelo-Romay
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics Laboratory, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
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49
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Statello L, Ali MM, Reischl S, Mahale S, Kosalai ST, Huarte M, Kanduri C. The DNA damage inducible lncRNA SCAT7 regulates genomic integrity and topoisomerase 1 turnover in lung adenocarcinoma. NAR Cancer 2021; 3:zcab002. [PMID: 34316698 PMCID: PMC8209975 DOI: 10.1093/narcan/zcab002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/26/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
Despite the rapid improvements in unveiling the importance of lncRNAs in all aspects of cancer biology, there is still a void in mechanistic understanding of their role in the DNA damage response. Here we explored the potential role of the oncogenic lncRNA SCAT7 (ELF3-AS1) in the maintenance of genome integrity. We show that SCAT7 is upregulated in response to DNA-damaging drugs like cisplatin and camptothecin, where SCAT7 expression is required to promote cell survival. SCAT7 silencing leads to decreased proliferation of cisplatin-resistant cells in vitro and in vivo through interfering with cell cycle checkpoints and DNA repair molecular pathways. SCAT7 regulates ATR signaling, promoting homologous recombination. Importantly, SCAT7 also takes part in proteasome-mediated topoisomerase I (TOP1) degradation, and its depletion causes an accumulation of TOP1–cc structures responsible for the high levels of intrinsic DNA damage. Thus, our data demonstrate that SCAT7 is an important constituent of the DNA damage response pathway and serves as a potential therapeutic target for hard-to-treat drug resistant cancers.
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Affiliation(s)
- Luisa Statello
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Mohamad M Ali
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Silke Reischl
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Sagar Mahale
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Subazini Thankaswamy Kosalai
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona 31008, Spain
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, The Sahlgrenska Academy, Institute of Biomedicine, University of Gothenburg, SE-40530 Gothenburg, Sweden
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50
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Li G, Deng L, Huang N, Sun F. The Biological Roles of lncRNAs and Future Prospects in Clinical Application. Diseases 2021; 9:diseases9010008. [PMID: 33450825 PMCID: PMC7838801 DOI: 10.3390/diseases9010008] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/08/2021] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
Chemo and radiation therapies are the most commonly used therapies for cancer, but they can induce DNA damage, resulting in the apoptosis of host cells. DNA double-stranded breaks (DSBs) are the most lethal form of DNA damage in cells, which are constantly caused by a wide variety of genotoxic agents, both environmentally and endogenously. To maintain genomic integrity, eukaryotic organisms have developed a complex mechanism for the repair of DNA damage. Researches reported that many cellular long noncoding RNAs (lncRNAs) were involved in the response of DNA damage. The roles of lncRNAs in DNA damage response can be regulated by the dynamic modification of N6-adenosine methylation (m6A). The cellular accumulation of DNA damage can result in various diseases, including cancers. Additionally, lncRNAs also play roles in controlling the gene expression and regulation of autophagy, which are indirectly involved with individual development. The dysregulation of these functions can facilitate human tumorigenesis. In this review, we summarized the origin and overview function of lncRNAs and highlighted the roles of lncRNAs involved in the repair of DNA damage.
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Affiliation(s)
- Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
| | - Liang Deng
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China; (G.L.); (L.D.)
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
| | - Fenyong Sun
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai 200072, China;
- Correspondence: ; Tel.: +86-021-6630-6909
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