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Djalali-Cuevas A, Rettel M, Stein F, Savitski M, Kearns S, Kelly J, Biggs M, Skoufos I, Tzora A, Prassinos N, Diakakis N, Zeugolis DI. Macromolecular crowding in human tenocyte and skin fibroblast cultures: A comparative analysis. Mater Today Bio 2024; 25:100977. [PMID: 38322661 PMCID: PMC10846491 DOI: 10.1016/j.mtbio.2024.100977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/22/2023] [Accepted: 01/24/2024] [Indexed: 02/08/2024] Open
Abstract
Although human tenocytes and dermal fibroblasts have shown promise in tendon engineering, no tissue engineered medicine has been developed due to the prolonged ex vivo time required to develop an implantable device. Considering that macromolecular crowding has the potential to substantially accelerate the development of functional tissue facsimiles, herein we compared human tenocyte and dermal fibroblast behaviour under standard and macromolecular crowding conditions to inform future studies in tendon engineering. Basic cell function analysis made apparent the innocuousness of macromolecular crowding for both cell types. Gene expression analysis of the without macromolecular crowding groups revealed expression of tendon related molecules in human dermal fibroblasts and tenocytes. Protein electrophoresis and immunocytochemistry analyses showed significantly increased and similar deposition of collagen fibres by macromolecular crowding in the two cell types. Proteomics analysis demonstrated great similarities between human tenocyte and dermal fibroblast cultures, as well as the induction of haemostatic, anti-microbial and tissue-protective proteins by macromolecular crowding in both cell populations. Collectively, these data rationalise the use of either human dermal fibroblasts or tenocytes in combination with macromolecular crowding in tendon engineering.
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Affiliation(s)
- Adrian Djalali-Cuevas
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
| | - Mandy Rettel
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Mikhail Savitski
- Proteomics Core Facility, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Jack Kelly
- Galway University Hospital, Galway, Ireland
| | - Manus Biggs
- Science Foundation Ireland (SFI) Centre for Research in Medical Devices (CÚRAM), Biomedical Sciences Building, University of Galway, Galway, Ireland
| | - Ioannis Skoufos
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Athina Tzora
- Laboratory of Animal Science, Nutrition and Biotechnology, School of Agriculture, University of Ioannina, Arta, Greece
| | - Nikitas Prassinos
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Diakakis
- School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios I. Zeugolis
- Regenerative, Modular & Developmental Engineering Laboratory (REMODEL), Charles Institute of Dermatology, Conway Institute of Biomolecular & Biomedical Research and School of Mechanical & Materials Engineering, University College Dublin (UCD), Dublin, Ireland
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2
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Akade E, Jalilian S. The role of high mobility group AT-hook 1 in viral infections: Implications for cancer pathogenesis. Int J Biochem Cell Biol 2024; 169:106532. [PMID: 38278412 DOI: 10.1016/j.biocel.2024.106532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/25/2023] [Accepted: 01/18/2024] [Indexed: 01/28/2024]
Abstract
The crucial role of high mobility group AT-hook 1 (HMGA1) proteins in nuclear processes such as gene transcription, DNA replication, and chromatin remodeling is undeniable. Elevated levels of HMGA1 have been associated with unfavorable clinical outcomes and adverse differentiation status across various cancer types. HMGA1 regulates a diverse array of biological pathways, including tumor necrosis factor-alpha/nuclear factor-kappa B (TNF-α/NF-κB), epidermal growth factor receptor (EGFR), Hippo, Rat sarcoma/extracellular signal-regulated kinase (Ras/ERK), protein kinase B (Akt), wingless-related integration site/beta-catenin (Wnt/beta-catenin), and phosphoinositide 3-kinase/protein kinase B (PI3-K/Akt). While researchers have extensively investigated tumors in the reproductive, digestive, urinary, and hematopoietic systems, mounting evidence suggests that HMGA1 plays a critical role as a tumorigenic factor in tumors across all functional systems. Given its broad interaction network, HMGA1 is an attractive target for viral manipulation. Some viruses, including herpes simplex virus type 1, human herpesvirus 8, human papillomavirus, JC virus, hepatitis B virus, human immunodeficiency virus type 1, severe acute respiratory syndrome Coronavirus 2, and influenza viruses, utilize HMGA1 influence for infection. This interaction, particularly in oncogenesis, is crucial. Apart from the direct oncogenic effect of some of the mentioned viruses, the hit-and-run theory postulates that viruses can instigate cancer even before being completely eradicated from the host cell, implying a potentially greater impact of viruses on cancer development than previously assumed. This review explores the interplay between HMGA1, viruses, and host cellular machinery, aiming to contribute to a deeper understanding of viral-induced oncogenesis, paving the way for innovative strategies in cancer research and treatment.
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Affiliation(s)
- Esma'il Akade
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shahram Jalilian
- Department of Medical Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Achiro JM, Tao Y, Gao F, Lin CH, Watanabe M, Neumann S, Coppola G, Black DL, Martin KC. Aging differentially alters the transcriptome and landscape of chromatin accessibility in the male and female mouse hippocampus. Front Mol Neurosci 2024; 17:1334862. [PMID: 38318533 PMCID: PMC10839115 DOI: 10.3389/fnmol.2024.1334862] [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: 11/07/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Aging-related memory impairment and pathological memory disorders such as Alzheimer's disease differ between males and females, and yet little is known about how aging-related changes in the transcriptome and chromatin environment differ between sexes in the hippocampus. To investigate this question, we compared the chromatin accessibility landscape and gene expression/alternative splicing pattern of young adult and aged mouse hippocampus in both males and females using ATAC-seq and RNA-seq. We detected significant aging-dependent changes in the expression of genes involved in immune response and synaptic function and aging-dependent changes in the alternative splicing of myelin sheath genes. We found significant sex-bias in the expression and alternative splicing of hundreds of genes, including aging-dependent female-biased expression of myelin sheath genes and aging-dependent male-biased expression of genes involved in synaptic function. Aging was associated with increased chromatin accessibility in both male and female hippocampus, especially in repetitive elements, and with an increase in LINE-1 transcription. We detected significant sex-bias in chromatin accessibility in both autosomes and the X chromosome, with male-biased accessibility enriched at promoters and CpG-rich regions. Sex differences in gene expression and chromatin accessibility were amplified with aging, findings that may shed light on sex differences in aging-related and pathological memory loss.
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Affiliation(s)
- Jennifer M. Achiro
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Yang Tao
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Fuying Gao
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Chia-Ho Lin
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Marika Watanabe
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Sylvia Neumann
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
| | - Douglas L. Black
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA, United States
| | - Kelsey C. Martin
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States
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Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 2023; 14:4682. [PMID: 37542049 PMCID: PMC10403523 DOI: 10.1038/s41467-023-40386-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Solomon Hailu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Arjan Hada
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff A Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yuan-Chi Lin
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- BioAgilytix, Durham, NC, 27713, USA
| | - Kyle Feola
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- Department of Internal Medicine (Nephrology) and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA.
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA.
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Wang S, Zheng Q, Wang J, Chen S, Chen L. Long non-coding RNA MYU promotes ovarian cancer cell proliferation by sponging miR-6827-5p and upregulating HMGA1. Pathol Oncol Res 2023; 29:1610870. [PMID: 36776216 PMCID: PMC9911462 DOI: 10.3389/pore.2023.1610870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/20/2023] [Indexed: 01/28/2023]
Abstract
Background: Long non-coding RNAs (lncRNAs) have been confirmed to play vital roles in tumorigenesis. LncRNA MYU has recently been reported as an oncogene in several kinds of tumors. However, MYU's expression status and potential involvement in ovarian cancer (OC) remain unclear. In this study, we explored the underlying role of MYU in OC. Methods and results: The expression of MYU was upregulated in OC tissues, and MYU's overexpression was significantly correlated with the FIGO stage and lymphatic metastasis. Knockdown of MYU inhibited cell proliferation in SKOV3 and A2780 cells. Mechanistically, MYU directly interacted with miR-6827-5p in OC cells; HMGA1 is a downstream target gene of miR-6827-5p. Furthermore, MYU knockdown increased the expression of miR-6827-5p and decreased the expression of HMGA1. Restoration of HMGA1 expression reversed the influence on cell proliferation caused by MYU knockdown. Conclusion: MYU functions as a ceRNA that positively regulates HMGA1 expression by sponging miR-6827-5p in OC cells, which may provide a potential target and biomarker for the diagnosis or prognosis of OC.
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Affiliation(s)
- Shaoyu Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Qiaomei Zheng
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Jinhua Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Shaozhan Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Lihong Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Department of Obstetrics and Gynecology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, China,Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China,*Correspondence: Lihong Chen,
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Wang Z, Jia R, Wang L, Yang Q, Hu X, Fu Q, Zhang X, Li W, Ren Y. The Emerging Roles of Rad51 in Cancer and Its Potential as a Therapeutic Target. Front Oncol 2022; 12:935593. [PMID: 35875146 PMCID: PMC9300834 DOI: 10.3389/fonc.2022.935593] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 05/26/2022] [Indexed: 12/03/2022] Open
Abstract
Defects in DNA repair pathways are emerging hallmarks of cancer. Accurate DNA repairs and replications are essential for genomic stability. Cancer cells require residual DNA repair capabilities to repair the damage from replication stress and genotoxic anti-tumor agents. Defective DNA repair also promotes the accumulation of genomic changes that eventually lead to tumorigenesis, tumor progression, and therapeutic resistance to DNA-damaging anti-tumor agents. Rad51 recombinase is a critical effector of homologous recombination, which is an essential DNA repair mechanism for double-strand breaks. Rad51 has been found to be upregulated in many malignant solid tumors, and is correlated with poor prognosis. In multiple tumor types, Rad51 is critical for tumor metabolism, metastasis and drug resistance. Herein, we initially introduced the structure, expression pattern of Rad51 and key Rad51 mediators involved in homologous recombination. Additionally, we primarily discussed the role of Rad51 in tumor metabolism, metastasis, resistance to chemotherapeutic agents and poly-ADP ribose polymerase inhibitors.
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Affiliation(s)
- Ziyi Wang
- Department of Thoracic Surgery, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, China
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Renxiang Jia
- Department of Thoracic Surgery, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, China
| | - Linlin Wang
- Department of Thoracic Surgery, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, China
| | - Qiwei Yang
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaohai Hu
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Qiang Fu
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xinyu Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenya Li
- Department of Thoracic Surgery, First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yi Ren, ; Wenya Li,
| | - Yi Ren
- Department of Thoracic Surgery, Shenyang Chest Hospital & Tenth People’s Hospital, Shenyang, China
- *Correspondence: Yi Ren, ; Wenya Li,
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Saed L, Jeleń A, Mirowski M, Sałagacka-Kubiak A. Prognostic Significance of HMGA1 Expression in Lung Cancer Based on Bioinformatics Analysis. Int J Mol Sci 2022; 23:ijms23136933. [PMID: 35805937 PMCID: PMC9266824 DOI: 10.3390/ijms23136933] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/18/2022] [Accepted: 06/18/2022] [Indexed: 12/15/2022] Open
Abstract
High-mobility group protein 1 (HMGA1) participates in the processes of DNA transcription, replication, recombination, and repair. The HMGA1 gene is expressed abundantly during embryogenesis and is reactivated during carcinogenesis. HMGA1 gene expression has been associated with a high degree of malignancy, metastatic tendency, and poor survival in breast, colon, ovary, and pancreatic cancers. However, its prognostic significance in lung cancer remains unclear. Using publicly available data, HMGA1 was shown to be overexpressed in both small and non-small lung tumors, with higher expression compared to both the adjacent non-malignant lung tissues and non-tumor lung tissues of healthy individuals. Elevated HMGA1 expression could result from lowered HMGA1 methylation and was connected with some clinicopathological features like sex, age, and stage of the disease. The high HMGA1 expression level was connected with shorter overall and first progression survival time among lung adenocarcinoma patients, but not lung squamous cell carcinoma patients. HMGA1 could interact with proteins involved in cellular senescence and cell cycle control (TP53, RB1, RPS6KB1, and CDK1), transcription regulation (EP400 and HMGA2), chromatin assembly and remodeling (LMNB1), and cholesterol and isoprene biosynthesis (HMGCR and INSIG1). Taken together, HMGA1 overexpression could be an essential element of lung carcinogenesis and a prognostic feature in lung cancer.
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Shomali N, Marofi F, Tarzi S, Tamjdidfar R, Akbari M, Parvari S, Sadeghvand S, Deljavan M, Moridi O, Javadi M, Shotorbani SS. HSP90 inhibitor modulates HMGA1 and HMGB2 expression along with cell viability via NF-KB signaling pathways in melanoma in-vitro. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Zhang J, Yue W, Zhou Y, Liao M, Chen X, Hua J. Super enhancers-Functional cores under the 3D genome. Cell Prolif 2021; 54:e12970. [PMID: 33336467 PMCID: PMC7848964 DOI: 10.1111/cpr.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Complex biochemical reactions take place in the nucleus all the time. Transcription machines must follow the rules. The chromatin state, especially the three-dimensional structure of the genome, plays an important role in gene regulation and expression. The super enhancers are important for defining cell identity in mammalian developmental processes and human diseases. It has been shown that the major components of transcriptional activation complexes are recruited by super enhancer to form phase-separated condensates. We summarize the current knowledge about super enhancer in the 3D genome. Furthermore, a new related transcriptional regulation model from super enhancer is outlined to explain its role in the mammalian cell progress.
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Affiliation(s)
- Juqing Zhang
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Wei Yue
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Yaqi Zhou
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Mingzhi Liao
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Xingqi Chen
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Jinlian Hua
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
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Liu H, Zhang X, Jin X, Yang Y, Liang G, Ma Y, Wang B. Long Noncoding RNA VPS9D1-AS1 Sequesters microRNA-525-5p to Promote the Oncogenicity of Colorectal Cancer Cells by Upregulating HMGA1. Cancer Manag Res 2020; 12:9915-9928. [PMID: 33116849 PMCID: PMC7553769 DOI: 10.2147/cmar.s273687] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/03/2020] [Indexed: 12/24/2022] Open
Abstract
Background The long noncoding RNA VPS9D1 antisense RNA 1 (VPS9D1-AS1) has emerged as a critical regulator in non-small-cell lung, gastric, and prostate cancers. In this study, we measured the expression levels of VPS9D1-AS1 in colorectal cancer (CRC) and determined the role of VPS9D1-AS1 in regulating the biological activities of CRC cells. In addition, we thoroughly elucidated the molecular mechanism mediating the oncogenic activities of VPS9D1-AS1 in CRC. Methods The expression levels of VPS9D1-AS1 in CRC tissues and cell lines were detected via quantitative reverse transcription-polymerase chain reaction. Loss-of-function experiments were performed to detect the effects of VPS9D1-AS1 silencing on CRC cell proliferation, apoptosis, migration, and invasion as well as on tumor growth in vivo. Bioinformatics analysis predicted the potential microRNAs (miRNAs) interacting with VPS9D1-AS1, and this prediction was further confirmed via RNA immunoprecipitation and luciferase reporter assays. Results Our results demonstrated the upregulated expression of VPS9D1-AS1 in CRC tissues and cell lines. Functionally, VPS9D1-AS1 interference suppressed CRC cell proliferation, migration, and invasion and promoted cell apoptosis in vitro. In addition, the loss of VPS9D1-AS1 hindered tumor growth in vivo. Mechanistic studies identified VPS9D1-AS1 as a competing endogenous RNA in CRC cells, in which VPS9D1-AS1 acted as a molecular sponge of miR-525-5p and consequently increased the expression of high-mobility group AT-hook 1 (HMGA1). Moreover, rescue experiments revealed that the regulatory effects of VPS9D1-AS1 deficiency on CRC cells were abolished after miR-525-5p inhibition or HMGA1 restoration. Conclusion The newly identified competing endogenous RNA pathway involving VPS9D1-AS1, miR-525-5p, and HMGA1 is implicated in the control of CRC progression and may provide an effective target for CRC diagnosis and therapy.
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Affiliation(s)
- Hairui Liu
- Department of Abdominal Surgery, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
| | - Xueying Zhang
- Department of Oncology Medicine, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
| | - Xianmei Jin
- Department of Childhood Solid Tumor, First Hospital of Jilin University, Changchun, Jilin 130021, People's Republic of China
| | - Yubo Yang
- Department of Abdominal Surgery, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
| | - Guodong Liang
- Department of Abdominal Surgery, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
| | - Yuehan Ma
- Department of Abdominal Surgery, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
| | - Bing Wang
- Department of Radiotherapy, Jilin Cancer Hospital, Changchun, Jilin 130021, People's Republic of China
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11
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Pegoraro S, Ros G, Sgubin M, Petrosino S, Zambelli A, Sgarra R, Manfioletti G. Targeting the intrinsically disordered architectural High Mobility Group A (HMGA) oncoproteins in breast cancer: learning from the past to design future strategies. Expert Opin Ther Targets 2020; 24:953-969. [PMID: 32970506 DOI: 10.1080/14728222.2020.1814738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) is the most difficult breast cancer subtype to treat because of its heterogeneity and lack of specific therapeutic targets. High Mobility Group A (HMGA) proteins are chromatin architectural factors that have multiple oncogenic functions in breast cancer, and they represent promising molecular therapeutic targets for this disease. AREAS COVERED We offer an overview of the strategies that have been exploited to counteract HMGA oncoprotein activities at the transcriptional and post-transcriptional levels. We also present the possibility of targeting cancer-associated factors that lie downstream of HMGA proteins and discuss the contribution of HMGA proteins to chemoresistance. EXPERT OPINION Different strategies have been exploited to counteract HMGA protein activities; these involve interfering with their nucleic acid binding properties and the blocking of HMGA expression. Some approaches have provided promising results. However, some unique characteristics of the HMGA proteins have not been exploited; these include their extensive protein-protein interaction network and their intrinsically disordered status that present the possibility that HMGA proteins could be involved in the formation of proteinaceous membrane-less organelles (PMLO) by liquid-liquid phase separation. These unexplored characteristics could open new pharmacological avenues to counteract the oncogenic contributions of HMGA proteins.
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Affiliation(s)
- Silvia Pegoraro
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Gloria Ros
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Michela Sgubin
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Sara Petrosino
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste , Trieste, Italy
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Wu Z, Wang W, Wang Y, Wang X, Sun S, Yao Y, Zhang Y, Ren Z. Long noncoding RNA LINC00963 promotes breast cancer progression by functioning as a molecular sponge for microRNA-625 and thereby upregulating HMGA1. Cell Cycle 2020; 19:610-624. [PMID: 32052688 PMCID: PMC7100992 DOI: 10.1080/15384101.2020.1728024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Extensive research has shown that LINC00963 is aberrantly expressed in human cancers, and that dysregulation of LINC00963 is implicated in the initiation and progression of human cancers. The expression and functions of LINC00963 in breast cancer are still unclear. Our aims were to measure the expression of LINC00963 in breast cancer, determine its effects on malignant behaviors of tumor cells, and uncover the molecular events underlying the actions of LINC00963 in breast cancer. Herein, LINC00963 was found to be overexpressed in breast cancer samples, and its overexpression was correlated with lymph node metastasis, TNM stage and differentiation grade. Patients with breast cancer harboring higher LINC00963 expression showed shorter overall survival than did the patients with lower LINC00963 expression. Functional experiments revealed that depletion of LINC00963 inhibited breast cancer cell proliferation, migration, and invasion and facilitated apoptosis in vitro and impaired tumor growth in vivo. Mechanism investigation revealed that LINC00963 can interact with microRNA-625 (miR-625). LINC00963 worked as a competitive endogenous RNA for miR-625 to weaken the suppressive effect of miR-625 on high mobility group AT-hook 1 (HMGA1) in breast cancer cells. Furthermore, miR-625 inhibition and HMGA1 restoration both abrogated the effects of LINC00963 silencing on breast cancer cells. Our findings indicate that the LINC00963-miR-625-HMGA1 pathway plays an important role in the malignancy of breast cancer in vitro and in vivo. Hence, targeting this pathway may be a novel strategy against breast cancer.
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Affiliation(s)
- Zhen Wu
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Wei Wang
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Yongkun Wang
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Xin Wang
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Shanping Sun
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Yumin Yao
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Yang Zhang
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
| | - Zhongxi Ren
- Department of Breast and Thyroid Surgery, Liaocheng People’s Hospital, Liaocheng, Shandong, P.R. China
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HMGA Genes and Proteins in Development and Evolution. Int J Mol Sci 2020; 21:ijms21020654. [PMID: 31963852 PMCID: PMC7013770 DOI: 10.3390/ijms21020654] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 12/16/2022] Open
Abstract
HMGA (high mobility group A) (HMGA1 and HMGA2) are small non-histone proteins that can bind DNA and modify chromatin state, thus modulating the accessibility of regulatory factors to the DNA and contributing to the overall panorama of gene expression tuning. In general, they are abundantly expressed during embryogenesis, but are downregulated in the adult differentiated tissues. In the present review, we summarize some aspects of their role during development, also dealing with relevant studies that have shed light on their functioning in cell biology and with emerging possible involvement of HMGA1 and HMGA2 in evolutionary biology.
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Huang B, Chang C, Wang BL, Li H. ELK1-induced upregulation of lncRNA TRPM2-AS promotes tumor progression in gastric cancer by regulating miR-195/ HMGA1 axis. J Cell Biochem 2019; 120:16921-16933. [PMID: 31104318 DOI: 10.1002/jcb.28951] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/24/2019] [Accepted: 04/29/2019] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) have been confirmed to be aberrantly expressed in various diseases including tumors. Recently, a new tumor-related lncRNA, lncRNA TRPM2 antisense RNA (TRPM2-AS), was shown to be involved in many tumors, such as lung cancer and breast cancer. However, the expression and role of TRPM2-AS in the development of gastric cancer (GC) have not been elucidated. In the current study, we provided evidence that the expression levels of TRPM2-AS were increased in both GC tissues and cell lines. We also showed that overexpression of TRPM2-AS was modulated by ELK1, a transcription factor. The results of clinical assays showed that higher expressions of TRPM2-AS were significantly related with invasion depth, TNM stage, lymphatic metastasis, and shorter overall survival. Further clinical assays using multivariate analysis suggested that TRPM2-AS expression was an independent prognostic factor in patients with GC. Functional experiments illustrated that depression of TRPM2-AS suppressed proliferation, migration, and invasion in GC cells. In terms of mechanism, we found that TRPM2-AS directly inhibited miR-195, which targeted the 3'-untranslated region of high-mobility group AT-hook 1 (HMGA1) messenger RNA. Overall, these findings revealed that ELK1-induced overexpression of TRPM2-AS promoted the development and progression of GC in part through miR-195/HMGA1 signaling axis, and established its candidacy as a new cancer biomarker for GC patients.
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Affiliation(s)
- Bo Huang
- Department of General Surgery, Guangzhou Red Cross Hospital, Guangzhou, Guangdong, China
| | - Cheng Chang
- Department of General Surgery, Guangzhou Red Cross Hospital, Guangzhou, Guangdong, China
| | - Bai-Lin Wang
- Department of General Surgery, Guangzhou Red Cross Hospital, Guangzhou, Guangdong, China
| | - Huiwen Li
- Department of Gastroenterology, Guangzhou Women and Children Medical Center, Guangzhou, Guangdong, China
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A novel DNA-binding motif in prostate tumor overexpressed-1 (PTOV1) required for the expression of ALDH1A1 and CCNG2 in cancer cells. Cancer Lett 2019; 452:158-167. [PMID: 30922918 DOI: 10.1016/j.canlet.2019.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 03/01/2019] [Accepted: 03/08/2019] [Indexed: 12/26/2022]
Abstract
PTOV1 is a transcription and translation regulator and a promoter of cancer progression. Its overexpression in prostate cancer induces transcription of drug resistance and self-renewal genes, and docetaxel resistance. Here we studied PTOV1 ability to directly activate the transcription of ALDH1A1 and CCNG2 by binding to specific promoter sequences. Chromatin immunoprecipitation and electrophoretic mobility shift assays identified a DNA-binding motif inside the PTOV-A domain with similarities to known AT-hooks that specifically interacts with ALDH1A1 and CCNG2 promoters. Mutation of this AT-hook-like sequence significantly decreased the expression of ALDH1A1 and CCNG2 promoted by PTOV1. Immunohistochemistry revealed the association of PTOV1 with mitotic chromosomes in high grade prostate, colon, bladder, and breast carcinomas. Overexpression of PTOV1, ALDH1A1, and CCNG2 significantly correlated with poor prognosis in prostate carcinomas and with shorter relapse-free survival in colon carcinoma. The previously described interaction with translation complexes and its direct binding to ALDH1A1 and CCNG2 promoters found here reveal the PTOV1 capacity to modulate the expression of critical genes at multiple levels in aggressive cancers. Remarkably, the AT-hook motifs in PTOV1 open possibilities for selective targeting its nuclear and/or cytoplasmic activities.
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Ren J, Yang M, Xu F, Chen J. microRNA-758 inhibits the malignant phenotype of osteosarcoma cells by directly targeting HMGA1 and deactivating the Wnt/β-catenin pathway. Am J Cancer Res 2019; 9:36-52. [PMID: 30755810 PMCID: PMC6356927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 12/28/2018] [Indexed: 06/09/2023] Open
Abstract
microRNAs (miRNAs) are frequently aberrantly expressed in osteosarcoma (OS) and are implicated in its development. Dysregulation of miR-758 has been reported in various human malignancies. However, whether miR-758 is involved in the oncogenesis and progression of OS remains unclear. In this study, reverse transcription-quantitative polymerase chain reaction was performed to detect miR-758 expression in OS tissues and cell lines. A series of functional experiments were employed to explore the regulatory effects of miR-758 on the malignant behaviors of OS cells both in vitro and in vivo. The molecular mechanisms underlying the activity of miR-758 in OS cells were also investigated. miR-758 was significantly downregulated in OS tissues and cell lines, and a low miR-758 level was correlated with tumor size, clinical stage, and distant metastasis of patients with OS. OS patients with low miR-758 level exhibited poorer overall survival and worse disease-free survival rates compared to patients with high miR-758 level. In addition, functional assays revealed that miR-758 overexpression led to a significant decrease in OS cell growth and metastasis in vitro, whereas miR-758 inhibition had the opposite effect on OS cells. miR-758 reduced the tumorous growth of OS cells in vivo. Furthermore, high mobility group AT-hook 1 (HMGA1) was identified as a direct target of miR-758 in OS cells. HMGA1 was highly expressed in OS tissues, and its expression was inversely correlated with miR-758 expression. HMGA1 silencing exerted an effect similar to that induced by miR-758 upregulation in OS cells. Restored HMGA1 expression abolished the effects of miR-758 on the malignant phenotypes of OS cells. Moreover, miR-758 regulated the Wnt/β-catenin pathway in OS cells in vitro and in vivo. To the best of our knowledge, this is the first study to demonstrate that miR-758 may inhibit the aggressive behavior of OS cells in vitro and in vivo by directly targeting HMGA1 and regulating the Wnt/β-catenin pathway. These results will aid in elucidating the roles of miR-758 and suggest that the miR-758/HMGA1/Wnt/β-catenin pathway represents a potential therapeutic target in OS.
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Affiliation(s)
- Jia Ren
- Department of Emergency, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Mengjie Yang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and PreventionBeijing 102206, P. R. China
| | - Fengyang Xu
- Department of Emergency, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Juwu Chen
- Department of Emergency, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
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Modes of Interaction of KMT2 Histone H3 Lysine 4 Methyltransferase/COMPASS Complexes with Chromatin. Cells 2018; 7:cells7030017. [PMID: 29498679 PMCID: PMC5870349 DOI: 10.3390/cells7030017] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/22/2018] [Accepted: 02/27/2018] [Indexed: 02/07/2023] Open
Abstract
Regulation of gene expression is achieved by sequence-specific transcriptional regulators, which convey the information that is contained in the sequence of DNA into RNA polymerase activity. This is achieved by the recruitment of transcriptional co-factors. One of the consequences of co-factor recruitment is the control of specific properties of nucleosomes, the basic units of chromatin, and their protein components, the core histones. The main principles are to regulate the position and the characteristics of nucleosomes. The latter includes modulating the composition of core histones and their variants that are integrated into nucleosomes, and the post-translational modification of these histones referred to as histone marks. One of these marks is the methylation of lysine 4 of the core histone H3 (H3K4). While mono-methylation of H3K4 (H3K4me1) is located preferentially at active enhancers, tri-methylation (H3K4me3) is a mark found at open and potentially active promoters. Thus, H3K4 methylation is typically associated with gene transcription. The class 2 lysine methyltransferases (KMTs) are the main enzymes that methylate H3K4. KMT2 enzymes function in complexes that contain a necessary core complex composed of WDR5, RBBP5, ASH2L, and DPY30, the so-called WRAD complex. Here we discuss recent findings that try to elucidate the important question of how KMT2 complexes are recruited to specific sites on chromatin. This is embedded into short overviews of the biological functions of KMT2 complexes and the consequences of H3K4 methylation.
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Zhang H, Yang J, Walters MS, Staudt MR, Strulovici-Barel Y, Salit J, Mezey JG, Leopold PL, Crystal RG. Mandatory role of HMGA1 in human airway epithelial normal differentiation and post-injury regeneration. Oncotarget 2018; 9:14324-14337. [PMID: 29581847 PMCID: PMC5865673 DOI: 10.18632/oncotarget.24511] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/20/2018] [Indexed: 12/11/2022] Open
Abstract
Due to high levels of expression in aggressive tumors, high mobility group AT-hook 1 (HMGA1) has recently attracted attention as a potential anti-tumor target. However, HMGA1 is also expressed in normal somatic progenitor cells, raising the question: how might systemic anti-HMGA1 therapies affect the structure and function of normal tissue differentiation? In the present study, RNA sequencing data demonstrated HMGA1 is highly expressed in human airway basal stem/progenitor cells (BC), but decreases with BC differentiation in air-liquid interface cultures (ALI). BC collected from nonsmokers, healthy smokers, and smokers with chronic obstructive pulmonary disease (COPD) displayed a range of HMGA1 expression levels. Low initial expression levels of HMGA1 in BC were associated with decreased ability to maintain a differentiated ALI epithelium. HMGA1 down-regulation in BC diminished BC proliferation, suppressed gene expression related to normal proliferation and differentiation, decreased airway epithelial resistance, suppressed junctional and cell polarity gene expression, and delayed wound closure of airway epithelium following injury. Furthermore, silencing of HMGA1 in airway BC in ALI increased the expression of genes associated with airway remodeling in COPD including squamous, epithelial-mesenchymal transition (EMT), and inflammatory genes. Together, the data suggests HMGA1 plays a central role in normal airway differentiation, and thus caution should be used to monitor airway epithelial structure and function in the context of systemic HMGA1-targeted therapies.
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Affiliation(s)
- Haijun Zhang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jing Yang
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Matthew S Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Michelle R Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY, USA
| | - Philip L Leopold
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, NY, USA
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Chiefari E, Foti DP, Sgarra R, Pegoraro S, Arcidiacono B, Brunetti FS, Greco M, Manfioletti G, Brunetti A. Transcriptional Regulation of Glucose Metabolism: The Emerging Role of the HMGA1 Chromatin Factor. Front Endocrinol (Lausanne) 2018; 9:357. [PMID: 30034366 PMCID: PMC6043803 DOI: 10.3389/fendo.2018.00357] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/13/2018] [Indexed: 02/06/2023] Open
Abstract
HMGA1 (high mobility group A1) is a nonhistone architectural chromosomal protein that functions mainly as a dynamic regulator of chromatin structure and gene transcription. As such, HMGA1 is involved in a variety of fundamental cellular processes, including gene expression, epigenetic regulation, cell differentiation and proliferation, as well as DNA repair. In the last years, many reports have demonstrated a role of HMGA1 in the transcriptional regulation of several genes implicated in glucose homeostasis. Initially, it was proved that HMGA1 is essential for normal expression of the insulin receptor (INSR), a critical link in insulin action and glucose homeostasis. Later, it was demonstrated that HMGA1 is also a downstream nuclear target of the INSR signaling pathway, representing a novel mediator of insulin action and function at this level. Moreover, other observations have indicated the role of HMGA1 as a positive modulator of the Forkhead box protein O1 (FoxO1), a master regulatory factor for gluconeogenesis and glycogenolysis, as well as a positive regulator of the expression of insulin and of a series of circulating proteins that are involved in glucose counterregulation, such as the insulin growth factor binding protein 1 (IGFBP1), and the retinol binding protein 4 (RBP4). Thus, several lines of evidence underscore the importance of HMGA1 in the regulation of glucose production and disposal. Consistently, lack of HMGA1 causes insulin resistance and diabetes in humans and mice, while variations in the HMGA1 gene are associated with the risk of type 2 diabetes and metabolic syndrome, two highly prevalent diseases that share insulin resistance as a common pathogenetic mechanism. This review intends to give an overview about our current knowledge on the role of HMGA1 in glucose metabolism. Although research in this field is ongoing, many aspects still remain elusive. Future directions to improve our insights into the pathophysiology of glucose homeostasis may include epigenetic studies and the use of "omics" strategies. We believe that a more comprehensive understanding of HMGA1 and its networks may reveal interesting molecular links between glucose metabolism and other biological processes, such as cell proliferation and differentiation.
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Affiliation(s)
- Eusebio Chiefari
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Daniela P. Foti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Silvia Pegoraro
- Department of Life Sciences, University of Trieste, Trieste, Italy
| | - Biagio Arcidiacono
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Francesco S. Brunetti
- Department of Medical and Surgical Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | - Manfredi Greco
- Department of Clinical and Experimental Medicine, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
| | | | - Antonio Brunetti
- Department of Health Sciences, University “Magna Græcia” of Catanzaro, Catanzaro, Italy
- *Correspondence: Antonio Brunetti
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Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-content. PLoS Genet 2017; 13:e1007102. [PMID: 29267285 PMCID: PMC5756049 DOI: 10.1371/journal.pgen.1007102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 01/05/2018] [Accepted: 11/04/2017] [Indexed: 11/26/2022] Open
Abstract
Genomic location can inform on potential function and recruitment signals for chromatin-associated proteins. High mobility group (Hmg) proteins are of similar size as histones with Hmga1 and Hmga2 being particularly abundant in replicating normal tissues and in cancerous cells. While several roles for Hmga proteins have been proposed we lack a comprehensive description of their genomic location as a function of chromatin, DNA sequence and functional domains. Here we report such a characterization in mouse embryonic stem cells in which we introduce biotin-tagged constructs of wild-type and DNA-binding domain mutants. Comparative analysis of the genome-wide distribution of Hmga proteins reveals pervasive binding, a feature that critically depends on a functional DNA-binding domain and which is shared by both Hmga proteins. Assessment of the underlying queues instructive for this binding modality identifies AT richness, defined as high frequency of A or T bases, as the major criterion for local binding. Additionally, we show that other chromatin states such as those linked to cis-regulatory regions have little impact on Hmga binding both in stem and differentiated cells. As a consequence, Hmga proteins are preferentially found at AT-rich regions such as constitutively heterochromatic regions but are absent from enhancers and promoters arguing for a limited role in regulating individual genes. In line with this model, we show that genetic deletion of Hmga proteins in stem cells causes limited transcriptional effects and that binding is conserved in neuronal progenitors. Overall our comparative study describing the in vivo binding modality of Hmga1 and Hmga2 identifies the proteins’ preference for AT-rich DNA genome-wide and argues against a suggested function of Hmga at regulatory regions. Instead we discover pervasive binding with enrichment at regions of higher AT content irrespective of local variation in chromatin modifications. We investigated the chromosomal location of a group of highly abundant nuclear proteins. Our genome-wide results for Hmga1 and Hmga2 reveal a unique binding modality indicating preference for DNA rich in A or T bases in vivo. Importantly this preferential binding to AT-rich sequences occurs throughout the genome irrespectively of other local chromatin features. Genomic location and loss of function experiments challenge the view that Hmga proteins act as local modulators of transcriptional regulation but rather argue for a role as structural components of chromatin.
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Eilebrecht S, Benecke BJ, Benecke AG. Latent HIV-1 TAR Regulates 7SK-responsive P-TEFb Target Genes and Targets Cellular Immune Responses in the Absence of Tat. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:313-323. [PMID: 29037489 PMCID: PMC5673678 DOI: 10.1016/j.gpb.2017.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/10/2017] [Accepted: 05/24/2017] [Indexed: 01/04/2023]
Abstract
The transactivating response element (TAR) structure of the nascent HIV-1 transcript is critically involved in the recruitment of inactive positive transcription elongation factor b (P-TEFb) to the promoter proximal paused RNA polymerase II. The viral transactivator Tat is responsible for subsequent P-TEFb activation in order to start efficient viral transcription elongation. In the absence of the viral transactivator of transcription (Tat), e.g., during latency or in early stages of HIV transcription, TAR mediates an interaction of P-TEFb with its inhibitor hexamethylene bis-acetamide-inducible protein 1 (HEXIM1), keeping P-TEFb in its inactive form. In this study, we address the function of HIV-1 TAR in the absence of Tat by analyzing consequences of HIV-1 TAR overexpression on host cellular gene expression. An RNA chimera consisting of Epstein-Barr virus-expressed RNA 2 (EBER2) and HIV-1 TAR was developed to assure robust overexpression of TAR in HEK293 cells. The overexpression results in differential expression of more than 800 human genes. A significant proportion of these genes is involved in the suppression of cellular immune responses, including a significant set of 7SK-responsive P-TEFb target genes. Our findings identify a novel role for HIV-1 TAR in the absence of Tat, involving the interference with host cellular immune responses by targeting 7SK RNA-mediated gene expression and P-TEFb inactivation.
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Affiliation(s)
- Sebastian Eilebrecht
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; ACSIOMA GmbH, Technologiezentrum Ruhr, Bochum 44799, Germany.
| | | | - Arndt G Benecke
- CNRS UMR8246, Université Pierre et Marie Curie, Paris 75005, France; Center for Innate Immunity and Immune Disease, University of Washington School of Medicine, Seattle, WA 98195, USA.
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Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug-Resistant Target in Non-Small Cell Lung Cancer. Sci Rep 2017; 7:44021. [PMID: 28290473 PMCID: PMC5349541 DOI: 10.1038/srep44021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 02/03/2017] [Indexed: 12/13/2022] Open
Abstract
Although EGFR tyrosine kinase inhibitors (TKIs) have demonstrated good efficacy in non-small-cell lung cancer (NSCLC) patients harboring EGFR mutations, most patients develop intrinsic and acquired resistance. We quantitatively profiled the phosphoproteome and proteome of drug-sensitive and drug-resistant NSCLC cells under gefitinib treatment. The construction of a dose-dependent responsive kinase-substrate network of 1548 phosphoproteins and 3834 proteins revealed CK2-centric modules as the dominant core network for the potential gefitinib resistance-associated proteins. CK2 knockdown decreased cell survival in gefitinib-resistant NSCLCs. Using motif analysis to identify the CK2 core sub-network, we verified that elevated phosphorylation level of a CK2 substrate, HMGA1 was a critical node contributing to EGFR-TKI resistance in NSCLC cell. Both HMGA1 knockdown or mutation of the CK2 phosphorylation site, S102, of HMGA1 reinforced the efficacy of gefitinib in resistant NSCLC cells through reactivation of the downstream signaling of EGFR. Our results delineate the TKI resistance-associated kinase-substrate network, suggesting a potential therapeutic strategy for overcoming TKI-induced resistance in NSCLC.
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Sekimoto N, Suzuki A, Suzuki Y, Sugano S. Expression of miR‑26a exhibits a negative correlation with HMGA1 and regulates cancer progression by targeting HMGA1 in lung adenocarcinoma cells. Mol Med Rep 2016; 15:534-542. [PMID: 28000891 PMCID: PMC5364888 DOI: 10.3892/mmr.2016.6053] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 09/23/2016] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the most common cause of cancer-associated mortality worldwide, and the number of cases is increasing annually. Several studies have shown that microRNAs (miRNAs) control proliferation, differentiation, and apoptosis in various cell types, and increasing evidence indicates the presence of aberrant miRNA expression profiles and unique miRNA signaling pathways in several types of cancer. The present study aimed to identify miRNAs, which correlated specifically with the progression of lung cancer through the analysis of 57,100 transcripts and 1,341 small RNA expression profiles in 26 lung adenocarcinoma cell lines using next-generation sequencing. The most marked negative correlation was found between the expression of hsa-miR-26a-1 and messenger RNA (mRNA), and a list of mRNAs, which exhibited negative correlation with hsa-miR-26a-1 were investigated. The most marked negative correlation was observed between the expression levels of hsa-miR-26a-1 and high mobility group A1 (HMGA1). Using a lung adenocarcinoma cell line, the present study analyzed the effect of the overexpression of miR-26a on the expression of HMGA1 and found that miR-26a repressed the expression of HMGA1 by reducing the mRNA levels of HMGA1. Furthermore, it was demonstrated that the overexpression of miR-26a in a lung adenocarcinoma cell line repressed cell migration, invasion and growth by targeting HMGA1. Taken together, the present study showed a significant negative correlation between the expression of miR-26a and HMGA1 in 26 lung adenocarcinoma cell lines, and provided evidence that the suppression of miR-26a supports the progression of cancer by stimulating the expression of HMGA1.
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Affiliation(s)
- Noboru Sekimoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108‑8639, Japan
| | - Ayako Suzuki
- Division of Translational Research, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba 277‑8577, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277‑8562, Japan
| | - Sumio Sugano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 108‑8639, Japan
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DeLaughter DM, Bick AG, Wakimoto H, McKean D, Gorham JM, Kathiriya IS, Hinson JT, Homsy J, Gray J, Pu W, Bruneau BG, Seidman JG, Seidman CE. Single-Cell Resolution of Temporal Gene Expression during Heart Development. Dev Cell 2016; 39:480-490. [PMID: 27840107 PMCID: PMC5198784 DOI: 10.1016/j.devcel.2016.10.001] [Citation(s) in RCA: 293] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 03/30/2016] [Accepted: 09/30/2016] [Indexed: 12/29/2022]
Abstract
Activation of complex molecular programs in specific cell lineages governs mammalian heart development, from a primordial linear tube to a four-chamber organ. To characterize lineage-specific, spatiotemporal developmental programs, we performed single-cell RNA sequencing of >1,200 murine cells isolated at seven time points spanning embryonic day 9.5 (primordial heart tube) to postnatal day 21 (mature heart). Using unbiased transcriptional data, we classified cardiomyocytes, endothelial cells, and fibroblast-enriched cells, thus identifying markers for temporal and chamber-specific developmental programs. By harnessing these datasets, we defined developmental ages of human and mouse pluripotent stem-cell-derived cardiomyocytes and characterized lineage-specific maturation defects in hearts of mice with heterozygous mutations in Nkx2.5 that cause human heart malformations. This spatiotemporal transcriptome analysis of heart development reveals lineage-specific gene programs underlying normal cardiac development and congenital heart disease.
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Affiliation(s)
| | - Alexander G. Bick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroko Wakimoto
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - David McKean
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Joshua M. Gorham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Irfan S. Kathiriya
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Department of Anesthesia and Perioperative Care, University of California, San Francisco
| | - John T. Hinson
- Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jesse Gray
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - William Pu
- Department of Cardiology, Harvard Medical School, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Benoit G. Bruneau
- Gladstone Institute of Cardiovascular Disease, San Francisco, CA
- Cardiovascular Research Institute and Department of Pediatrics, University of California, San Francisco
| | - J. G. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute and Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
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25
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Wang J, Xu X, Mo S, Tian Y, Wu J, Zhang J, Zhao J. Involvement of microRNA-1297, a new regulator of HMGA1, in the regulation of glioma cell growth in vivo and in vitro. Am J Transl Res 2016; 8:2149-58. [PMID: 27347322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/19/2016] [Indexed: 09/28/2022]
Abstract
MicroRNAs (miRNAs) are a class of versatile gene expression regulators, participating in the regulation of gene expression at the post-transcriptional level in both physiological and pathological conditions. Gliomas are the most common brain malignancy in adults, and deregulation of microRNAs takes part in the gliomagenesis process. Here, we found that the expression of miR-1297 is significantly reduced in both glioma cell lines and clinical glioma tissues. Using the MTT assay, soft agar colony formation assay and xenograft tumor formation assay, we show that miR-1297 is a tumor suppressor microRNA in gliomas. We demonstrate that the high mobility group protein A1 (HMGA1) is the functional target of miR-1297 in glioma cells. HMGA1 significantly promotes the growth of glioma cells both in vitro and in vivo. Together, we unveil a new molecular mechanism in gliomas that may shed new light on understanding this brain malignancy.
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Affiliation(s)
- Jiachong Wang
- Tianjin Neurological Institute, Department of Neurosurgery, General Hospital, Tianjin Medical UniversityTianjin 300052, China; Department of Neurosurgery, The People's Hospital of Hainan ProvinceHaikou 570311, Hainan, China
| | - Xiaoyun Xu
- Department of Neurosurgery, The People's Hospital of Hainan Province Haikou 570311, Hainan, China
| | - Shaowei Mo
- Department of Neurosurgery, The People's Hospital of Hainan Province Haikou 570311, Hainan, China
| | - Ye Tian
- Tianjin Neurological Institute, Department of Neurosurgery, General Hospital, Tianjin Medical University Tianjin 300052, China
| | - Jian Wu
- Department of Laboratory Medicine, The First People's Hospital of Yancheng City Yancheng 224005, Jiangsu, China
| | - Jianning Zhang
- Tianjin Neurological Institute, Department of Neurosurgery, General Hospital, Tianjin Medical University Tianjin 300052, China
| | - Jiannong Zhao
- Department of Neurosurgery, The People's Hospital of Hainan Province Haikou 570311, Hainan, China
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26
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Järvelin AI, Noerenberg M, Davis I, Castello A. The new (dis)order in RNA regulation. Cell Commun Signal 2016; 14:9. [PMID: 27048167 PMCID: PMC4822317 DOI: 10.1186/s12964-016-0132-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 03/21/2016] [Indexed: 02/03/2023] Open
Abstract
RNA-binding proteins play a key role in the regulation of all aspects of RNA metabolism, from the synthesis of RNA to its decay. Protein-RNA interactions have been thought to be mostly mediated by canonical RNA-binding domains that form stable secondary and tertiary structures. However, a number of pioneering studies over the past decades, together with recent proteome-wide data, have challenged this view, revealing surprising roles for intrinsically disordered protein regions in RNA binding. Here, we discuss how disordered protein regions can mediate protein-RNA interactions, conceptually grouping these regions into RS-rich, RG-rich, and other basic sequences, that can mediate both specific and non-specific interactions with RNA. Disordered regions can also influence RNA metabolism through protein aggregation and hydrogel formation. Importantly, protein-RNA interactions mediated by disordered regions can influence nearly all aspects of co- and post-transcriptional RNA processes and, consequently, their disruption can cause disease. Despite growing interest in disordered protein regions and their roles in RNA biology, their mechanisms of binding, regulation, and physiological consequences remain poorly understood. In the coming years, the study of these unorthodox interactions will yield important insights into RNA regulation in cellular homeostasis and disease.
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Affiliation(s)
- Aino I. Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Marko Noerenberg
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU UK
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27
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Kumar Mishra S, Kumar A. NALDB: nucleic acid ligand database for small molecules targeting nucleic acid. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw002. [PMID: 26896846 PMCID: PMC4761111 DOI: 10.1093/database/baw002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022]
Abstract
Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL:http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php
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Affiliation(s)
- Subodh Kumar Mishra
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 452017, Madhya Pradesh, India
| | - Amit Kumar
- Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 452017, Madhya Pradesh, India
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28
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Panagopoulos I, Gorunova L, Bjerkehagen B, Lobmaier I, Heim S. Fusion of the TBL1XR1 and HMGA1 genes in splenic hemangioma with t(3;6)(q26;p21). Int J Oncol 2015; 48:1242-50. [PMID: 26708416 PMCID: PMC4750536 DOI: 10.3892/ijo.2015.3310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/26/2015] [Indexed: 11/06/2022] Open
Abstract
RNA-sequencing of a splenic hemangioma with the karyotype 45~47,XX,t(3;6)(q26;p21) showed that this translocation generated a chimeric TBL1XR1-HMGA1 gene. This is the first time that this tumor has been subjected to genetic analysis, but the finding of an acquired clonal chromosome abnormality in cells cultured from the lesion and the presence of the TBL1XR1-HMGA1 fusion in them strongly favor the conclusion that splenic hemangiomas are of a neoplastic nature. Genomic PCR confirmed the presence of the TBL1XR1-HMGA1 fusion gene, and RT-PCR together with Sanger sequencing verified the presence of the fusion transcripts. The molecular consequences of the t(3;6) would be substantial. The cells carrying the translocation would retain only one functional copy of the wild-type TBL1XR1 gene while the other, rearranged allele could produce a putative truncated form of TBL1XR1 protein containing the LiSH and F-box-like domains. In the TBL1XR1-HMGA1 fusion transcript, furthermore, untranslated exons of HMGA1 are replaced by the first 5 exons of the TBL1XR1 gene. The result is that the entire coding region of HMGA1 comes under the control of the TBL1XR1 promoter, bringing about dysregulation of HMGA1. This is reminiscent of similar pathogenetic mechanisms involving high mobility genes in benign connective tissue tumors such as lipomas and leiomyomas.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Bodil Bjerkehagen
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ingvild Lobmaier
- Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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29
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Mondragón E, Maher LJ. Anti-Transcription Factor RNA Aptamers as Potential Therapeutics. Nucleic Acid Ther 2015; 26:29-43. [PMID: 26509637 PMCID: PMC4753637 DOI: 10.1089/nat.2015.0566] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Transcription factors (TFs) are DNA-binding proteins that play critical roles in regulating gene expression. These proteins control all major cellular processes, including growth, development, and homeostasis. Because of their pivotal role, cells depend on proper TF function. It is, therefore, not surprising that TF deregulation is linked to disease. The therapeutic drug targeting of TFs has been proposed as a frontier in medicine. RNA aptamers make interesting candidates for TF modulation because of their unique characteristics. The products of in vitro selection, aptamers are short nucleic acids (DNA or RNA) that bind their targets with high affinity and specificity. Aptamers can be expressed on demand from transgenes and are intrinsically amenable to recognition by nucleic acid-binding proteins such as TFs. In this study, we review several natural prokaryotic and eukaryotic examples of RNAs that modulate the activity of TFs. These examples include 5S RNA, 6S RNA, 7SK, hepatitis delta virus-RNA (HDV-RNA), neuron restrictive silencer element (NRSE)-RNA, growth arrest-specific 5 (Gas5), steroid receptor RNA activator (SRA), trophoblast STAT utron (TSU), the 3' untranslated region of caudal mRNA, and heat shock RNA-1 (HSR1). We then review examples of unnatural RNA aptamers selected to inhibit TFs nuclear factor-kappaB (NF-κB), TATA-binding protein (TBP), heat shock factor 1 (HSF1), and runt-related transcription factor 1 (RUNX1). The field of RNA aptamers for DNA-binding proteins continues to show promise.
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Affiliation(s)
- Estefanía Mondragón
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine , Rochester, Minnesota
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