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Chatterjee O, Jana J, Panda S, Dutta A, Sharma A, Saurav S, Motiani RK, Weisz K, Chatterjee S. Remodeling Ca 2+ dynamics by targeting a promising E-box containing G-quadruplex at ORAI1 promoter in triple-negative breast cancer. Cell Calcium 2024; 123:102944. [PMID: 39191092 PMCID: PMC7616398 DOI: 10.1016/j.ceca.2024.102944] [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: 06/03/2024] [Revised: 07/19/2024] [Accepted: 08/11/2024] [Indexed: 08/29/2024]
Abstract
ORAI1 is an intrinsic component of store-operated calcium entry (SOCE) that strictly regulates Ca2+ influx in most non-excitable cells. ORAI1 is overexpressed in a wide variety of cancers, and its signal transduction has been associated with chemotherapy resistance. There is extensive proteomic interaction of ORAI1 with other channels and effectors, resulting in various altered phenotypes. However, the transcription regulation of ORAI1 is not well understood. We have found a putative G-quadruplex (G4) motif, ORAI1-Pu, in the upstream promoter region of the gene, having regulatory functions. High-resolution 3-D NMR structure elucidation suggests that ORAI1-Pu is a stable parallel-stranded G4, having a long 8-nt loop imparting dynamics without affecting the structural stability. The protruded loop further houses an E-box motif that provides a docking site for transcription factors like Zeb1. The G4 structure was also endogenously observed using Chromatin Immunoprecipitation (ChIP) with anti-G4 antibody (BG4) in the MDA-MB-231 cell line overexpressing ORAI1. Ligand-mediated stabilization suggested that the stabilized G4 represses transcription in cancer cell line MDA-MB-231. Downregulation of transcription further led to decreased Ca2+ entry by the SOCE pathway, as observed by live-cell Fura-2 Ca2+ imaging.
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Affiliation(s)
- Oishika Chatterjee
- Department of Biological Sciences, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Jagannath Jana
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Suman Panda
- Department of Biological Sciences, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biological Sciences, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Akshay Sharma
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad 121001, Delhi NCR, India
| | - Suman Saurav
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad 121001, Delhi NCR, India
| | - Rajender K Motiani
- Laboratory of Calciomics and Systemic Pathophysiology (LCSP), Regional Centre for Biotechnology (RCB), Faridabad 121001, Delhi NCR, India
| | - Klaus Weisz
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany
| | - Subhrangsu Chatterjee
- Department of Biological Sciences, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India.
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Wang J, Bi W, Lv R, Wang Z, Xin Q, Li K, Chen Y, Liu Q, Zhang X. SMEK1 promotes clear cell renal cell carcinoma progression via EGFR tyrosine-kinase dependent pathway. Cancer Lett 2024; 601:217148. [PMID: 39098759 DOI: 10.1016/j.canlet.2024.217148] [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: 12/13/2023] [Revised: 07/21/2024] [Accepted: 07/27/2024] [Indexed: 08/06/2024]
Abstract
Studying the mechanisms underlying clear cell renal cell carcinoma (ccRCC), the most common subtype of kidney cancer, may address an unmet need in ccRCC-targeted drug research. Growing evidences indicate that protein phosphatase 4 (PP4) plays an important role in cancer biology. Here, we characterized the upregulation of PP4 core component SMEK1 in ccRCC using tissue microarrays and revealed that its high expression is closely associated with reduced patient survival. We then conducted cell function experiments and animal experiments to prove the tumor-promoting effect of SMEK1. Next, RNA-seq was performed to explore its underlying mechanism, and the results revealed that SMEK1-regulated genes were extensively involved in cell motility, and the canonical tyrosine kinase receptor EGFR was one of its targets. Moreover, we verified the regulatory effect of SMEK1 on EGFR and its downstream MAPK and AKT pathway through molecular experiments, in which erlotinib, a tyrosine kinase inhibitor, can partially block this regulation, demonstrating that SMEK1 mediates its effects dependent on the tyrosine kinase activity of EGFR. Mechanistically, SMEK1 bond to PRMT5 and facilitated PRMT5-mediated histone methylation to promote the transcription of EGFR. Furthermore, we studied the upstream regulators of SMEK1 and demonstrated that the transcription factor E2F1 could directly bind to the SMEK1 promoter by chromatin immunoprecipitation. Functionally, E2F1 could also induce ccRCC progression by manipulating the expression of SMEK1. Collectively, our findings demonstrate the overexpression of SMEK1 in ccRCC, and reveal a novel E2F1/SMEK1/PRMT5/EGFR-tyrosine-kinase-dependent pathway for ccRCC progression.
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Affiliation(s)
- Jue Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; Institute of Medical Sciences, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Wenhao Bi
- Department of Urology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; Department of Urology, Zibo 148 Hospital, Zibo, Shandong, 255300, China
| | - Renguang Lv
- Department of Urology, Jinan Seventh People's Hospital, Jinan, Shandong, 251400, China
| | - Zekun Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Qian Xin
- Institute of Medical Sciences, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Kailin Li
- Institute of Medical Sciences, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Yuan Chen
- Institute of Medical Sciences, The Second Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China; School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266071, China; NHC Key Laboratory of Birth Defects Prevention, Institute of Reproductive Health, Henan Academy of Innovations in Medical Science, Zhengzhou, 451163, Henan, China.
| | - Xiang Zhang
- Department of Urology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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3
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Yan Z, Xia J, Cao Z, Zhang H, Wang J, Feng T, Shu Y, Zou L. Multi-omics integration reveals potential stage-specific druggable targets in T-cell acute lymphoblastic leukemia. Genes Dis 2024; 11:100949. [PMID: 39071111 PMCID: PMC11282411 DOI: 10.1016/j.gendis.2023.03.022] [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: 10/20/2022] [Accepted: 03/11/2023] [Indexed: 07/30/2024] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL), a heterogeneous hematological malignancy, is caused by the developmental arrest of normal T-cell progenitors. The development of targeted therapeutic regimens is impeded by poor knowledge of the stage-specific aberrances in this disease. In this study, we performed multi-omics integration analysis, which included mRNA expression, chromatin accessibility, and gene-dependency database analyses, to identify potential stage-specific druggable targets and repositioned drugs for this disease. This multi-omics integration helped identify 29 potential pathological genes for T-ALL. These genes exhibited tissue-specific expression profiles and were enriched in the cell cycle, hematopoietic stem cell differentiation, and the AMPK signaling pathway. Of these, four known druggable targets (CDK6, TUBA1A, TUBB, and TYMS) showed dysregulated and stage-specific expression in malignant T cells and may serve as stage-specific targets in T-ALL. The TUBA1A expression level was higher in the early T cell precursor (ETP)-ALL cells, while TUBB and TYMS were mainly highly expressed in malignant T cells arrested at the CD4 and CD8 double-positive or single-positive stage. CDK6 exhibited a U-shaped expression pattern in malignant T cells along the naïve to maturation stages. Furthermore, mebendazole and gemcitabine, which target TUBA1A and TYMS, respectively, exerted stage-specific inhibitory effects on T-ALL cell lines, indicating their potential stage-specific antileukemic role in T-ALL. Collectively, our findings might aid in identifying potential stage-specific druggable targets and are promising for achieving more precise therapeutic strategies for T-ALL.
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Affiliation(s)
- Zijun Yan
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jie Xia
- Bioinformatics and BioMedical Bigdata Mining Laboratory, School of Big Health, Guizhou Medical University, Guiyang, Guizhou 554300, China
| | - Ziyang Cao
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Hongyang Zhang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Jinxia Wang
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
| | - Tienan Feng
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Clinical Research Institute, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi Shu
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
| | - Lin Zou
- Clinical Research Unit, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200062, China
- Center for Clinical Molecular Laboratory Medicine of Children's Hospital of Chongqing Medical University, Chongqing 400014, China
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Shackebaei D, Hesari M, Gorgani S, Vafaeipour Z, Salaramoli S, Yarmohammadi F. The Role of mTOR in the Doxorubicin-Induced Cardiotoxicity: A Systematic Review. Cell Biochem Biophys 2024:10.1007/s12013-024-01475-7. [PMID: 39102090 DOI: 10.1007/s12013-024-01475-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2024] [Indexed: 08/06/2024]
Abstract
Doxorubicin (DOX) is a chemotherapy drug known to induce metabolic changes in the heart, leading to potential heart toxicity. These changes impact various cellular functions and pathways such as disrupting the mechanistic target of rapamycin (mTOR) signaling pathway. The study aimed to investigate the effect of DOX on the mTOR pathway through an in vivo systematic review. Databases were searched on September 11, 2023. We finally included 30 in vivo studies that examined the mTOR expression in cardiac tissue samples. The present study has shown that the PI3K/AKT/mTOR, the AMPK/mTOR, the p53/mTOR signaling, the mTOR/TFEB pathway, the p38 MAPK/mTOR, the sestrins/mTOR, and the KLF15/eNOS/mTORC1 signaling pathways play a crucial role in the development of DOX-induced cardiotoxicity. Inhibition or dysregulation of these pathways can lead to increased oxidative stress, apoptosis, and other adverse effects on the heart. Strategies that target and modulate the mTOR pathways, such as the use of mTOR inhibitors like rapamycin, have the potential to enhance the anticancer effects of DOX while also mitigating its cardiotoxic side effects.
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Affiliation(s)
- Dareuosh Shackebaei
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mahvash Hesari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sara Gorgani
- Tissue Engineering Research Group (TERG), Department of Anatomy and Cell Biology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zeinab Vafaeipour
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sanaz Salaramoli
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Yarmohammadi
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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5
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Huang P, Wen F, Li Q. Current concepts of the crosstalk between lncRNA and E2F1: shedding light on the cancer therapy. Front Pharmacol 2024; 15:1432490. [PMID: 39119602 PMCID: PMC11306149 DOI: 10.3389/fphar.2024.1432490] [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: 05/14/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) constitute a distinctive subset of RNA molecules with limited protein-coding potential, which exert crucial impacts on various biological activities. In the context of cancer, dysregulated lncRNAs function as essential regulators that affect tumor initiation and malignant progression. These lncRNAs serve as competitive endogenous RNAs (ceRNAs) through sponging microRNAs and regulating the expression of targeted genes. Moreover, they also directly bind to RNA-binding proteins, which can be integrated into a complex mechanistic network. E2F1, an extensively studied transcription factor, mediates multiple malignant behaviors by regulating cell cycle progression, tumor metastasis, and therapeutic response. Emerging evidence suggests that lncRNAs play a pivotal role in regulating the E2F1 pathway. This review aims to elucidate the intricate gene regulatory programs between lncRNAs and E2F1 in cancer progression. We elaborate on distinct mechanistic networks involved in cancer progression, emphasizing the potential of the lncRNAs/E2F1 axes as promising targets for cancer therapy. Additionally, we provide novel perspectives on current evidence, limitations, and future directions for targeting lncRNAs in human cancers. Fully deciphering the intricate network of lncRNA/E2F1-mediated regulatory mechanisms in cancer could facilitate the translation of current findings into clinical course, such efforts ultimately significantly improve the clinical prognosis of cancer patients.
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Affiliation(s)
- Peng Huang
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Wen
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qiu Li
- Division of Abdominal Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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6
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Liu Z, Zhang Y, Yu L, Zhang Z, Li G. A miR-361-5p/ ORC6/ PLK1 axis regulates prostate cancer progression. Exp Cell Res 2024; 440:114130. [PMID: 38885805 DOI: 10.1016/j.yexcr.2024.114130] [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: 04/17/2024] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 06/20/2024]
Abstract
Prostate cancer (PCa) is the most prevalent malignant tumor of the genitourinary system, and metastatic disease has a significant impact on the prognosis of PCa patients. As a result, knowing the processes of PCa development can help patients achieve better outcomes. Here, we investigated the expression and function of ORC6 in PCa. Our findings indicated that ORC6 was elevated in advanced PCa tissues. Patients with PCa who exhibited high levels of ORC6 had a poor prognosis. Following that, we investigated the function of ORC6 in PCa progression using a variety of functional experiments both in vivo and in vitro, and discovered that ORC6 knockdown inhibited PCa cell proliferation, growth, and migration. Furthermore, RNA-seq was employed to examine the molecular mechanism of PCa progression. The results revealed that ORC6 might promote the expression of PLK1, a serine/threonine kinase in PCa cells. We also discovered that ORC6 as a novel miR-361-5p substrate using database analysis, and miR-361-5p was found to lower ORC6 expression. Additionally, RNA immunoprecipitation (RIP) and luciferase reporter tests revealed that the transcription factor E2F1 could regulate ORC6 expression in PCa cells. PLK1 overexpression or miR-361-5p inhibitor treatment effectively removed the inhibitory effects caused by ORC6 silencing. Notably, our data showed that therapeutically targeting the miR-361-5p/ORC6/PLK1 axis may be a viable therapy option for PCa.
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Affiliation(s)
- Zhiqi Liu
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China; Anhui Public Health Clinical Center, Hefei, 230000, China; Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Ying Zhang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230000, China; Department of Urology, Peking University Shenzhen Hospital, Shenzhen, 518000, China
| | - Lin Yu
- Department of Urology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Zhiqiang Zhang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230000, China
| | - Guangyuan Li
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, China; Anhui Public Health Clinical Center, Hefei, 230000, China.
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7
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Bertonnier‐Brouty L, Andersson J, Kaprio T, Hagström J, Bsharat S, Asplund O, Hatem G, Haglund C, Seppänen H, Prasad RB, Artner I. E2F transcription factors promote tumorigenicity in pancreatic ductal adenocarcinoma. Cancer Med 2024; 13:e7187. [PMID: 38686617 PMCID: PMC11058697 DOI: 10.1002/cam4.7187] [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: 09/18/2023] [Revised: 03/14/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with limited treatment options, illustrating an urgent need to identify new drugable targets in PDACs. OBJECTIVE Using the similarities between tumor development and normal embryonic development, which is accompanied by rapid cell expansion, we aimed to identify and characterize embryonic signaling pathways that were reinitiated during tumor formation and expansion. METHODS AND RESULTS Here, we report that the transcription factors E2F1 and E2F8 are potential key regulators in PDAC. E2F1 and E2F8 RNA expression is mainly localized in proliferating cells in the developing pancreas and in malignant ductal cells in PDAC. Silencing of E2F1 and E2F8 in PANC-1 pancreatic tumor cells inhibited cell proliferation and impaired cell spreading and migration. Moreover, loss of E2F1 also affected cell viability and apoptosis with E2F expression in PDAC tissues correlating with expression of apoptosis and mitosis pathway genes, suggesting that E2F factors promote cell cycle regulation and tumorigenesis in PDAC cells. CONCLUSION Our findings illustrate that E2F1 and E2F8 transcription factors are expressed in pancreatic progenitor and PDAC cells, where they contribute to tumor cell expansion by regulation of cell proliferation, viability, and cell migration making these genes attractive therapeutic targets and potential prognostic markers for pancreatic cancer.
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Affiliation(s)
- Ludivine Bertonnier‐Brouty
- Lund Stem Cell CenterLund UniversityLundSweden
- Lund University Diabetes Center, Lund UniversityMalmöSweden
| | | | - Tuomas Kaprio
- Department of SurgeryHelsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- iCAN, Digital Cancer Precision MedicineUniversity of Helsinki and HUS Helsinki University HospitalHelsinkiFinland
| | - Jaana Hagström
- Department of SurgeryHelsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- iCAN, Digital Cancer Precision MedicineUniversity of Helsinki and HUS Helsinki University HospitalHelsinkiFinland
- Department of Oral Pathology and RadiologyUniversity of TurkuTurkuFinland
| | - Sara Bsharat
- Lund Stem Cell CenterLund UniversityLundSweden
- Lund University Diabetes Center, Lund UniversityMalmöSweden
| | - Olof Asplund
- Lund University Diabetes Center, Lund UniversityMalmöSweden
| | - Gad Hatem
- Lund University Diabetes Center, Lund UniversityMalmöSweden
| | - Caj Haglund
- Department of SurgeryHelsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- iCAN, Digital Cancer Precision MedicineUniversity of Helsinki and HUS Helsinki University HospitalHelsinkiFinland
| | - Hanna Seppänen
- Department of SurgeryHelsinki University HospitalHelsinkiFinland
- Translational Cancer Medicine Research Program, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- iCAN, Digital Cancer Precision MedicineUniversity of Helsinki and HUS Helsinki University HospitalHelsinkiFinland
| | | | - Isabella Artner
- Lund Stem Cell CenterLund UniversityLundSweden
- Lund University Diabetes Center, Lund UniversityMalmöSweden
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Iacobini C, Vitale M, Haxhi J, Menini S, Pugliese G. Impaired Remodeling of White Adipose Tissue in Obesity and Aging: From Defective Adipogenesis to Adipose Organ Dysfunction. Cells 2024; 13:763. [PMID: 38727299 PMCID: PMC11083890 DOI: 10.3390/cells13090763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 04/22/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
The adipose organ adapts and responds to internal and environmental stimuli by remodeling both its cellular and extracellular components. Under conditions of energy surplus, the subcutaneous white adipose tissue (WAT) is capable of expanding through the enlargement of existing adipocytes (hypertrophy), followed by de novo adipogenesis (hyperplasia), which is impaired in hypertrophic obesity. However, an impaired hyperplastic response may result from various defects in adipogenesis, leading to different WAT features and metabolic consequences, as discussed here by reviewing the results of the studies in animal models with either overexpression or knockdown of the main molecular regulators of the two steps of the adipogenesis process. Moreover, impaired WAT remodeling with aging has been associated with various age-related conditions and reduced lifespan expectancy. Here, we delve into the latest advancements in comprehending the molecular and cellular processes underlying age-related changes in WAT function, their involvement in common aging pathologies, and their potential as therapeutic targets to influence both the health of elderly people and longevity. Overall, this review aims to encourage research on the mechanisms of WAT maladaptation common to conditions of both excessive and insufficient fat tissue. The goal is to devise adipocyte-targeted therapies that are effective against both obesity- and age-related disorders.
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9
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Jiang YN, Gao Y, Lai X, Li X, Liu G, Ding M, Wang Z, Guo Z, Qin Y, Li X, Sun L, Wang ZQ, Zhou ZW. Microcephaly Gene Mcph1 Deficiency Induces p19ARF-Dependent Cell Cycle Arrest and Senescence. Int J Mol Sci 2024; 25:4597. [PMID: 38731817 PMCID: PMC11083351 DOI: 10.3390/ijms25094597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
MCPH1 has been identified as the causal gene for primary microcephaly type 1, a neurodevelopmental disorder characterized by reduced brain size and delayed growth. As a multifunction protein, MCPH1 has been reported to repress the expression of TERT and interact with transcriptional regulator E2F1. However, it remains unclear whether MCPH1 regulates brain development through its transcriptional regulation function. This study showed that the knockout of Mcph1 in mice leads to delayed growth as early as the embryo stage E11.5. Transcriptome analysis (RNA-seq) revealed that the deletion of Mcph1 resulted in changes in the expression levels of a limited number of genes. Although the expression of some of E2F1 targets, such as Satb2 and Cdkn1c, was affected, the differentially expressed genes (DEGs) were not significantly enriched as E2F1 target genes. Further investigations showed that primary and immortalized Mcph1 knockout mouse embryonic fibroblasts (MEFs) exhibited cell cycle arrest and cellular senescence phenotype. Interestingly, the upregulation of p19ARF was detected in Mcph1 knockout MEFs, and silencing p19Arf restored the cell cycle and growth arrest to wild-type levels. Our findings suggested it is unlikely that MCPH1 regulates neurodevelopment through E2F1-mediated transcriptional regulation, and p19ARF-dependent cell cycle arrest and cellular senescence may contribute to the developmental abnormalities observed in primary microcephaly.
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Affiliation(s)
- Yi-Nan Jiang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Yizhen Gao
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.G.); (L.S.)
| | - Xianxin Lai
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Xinjie Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Gen Liu
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.G.); (L.S.)
| | - Mingmei Ding
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Zhiyi Wang
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Zixiang Guo
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Yinying Qin
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.G.); (L.S.)
| | - Xin Li
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
| | - Litao Sun
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.G.); (L.S.)
| | - Zhao-Qi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China;
| | - Zhong-Wei Zhou
- Shenzhen Key Laboratory for Systems Medicine in Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China; (Y.-N.J.); (X.L.)
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10
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Coleman JC, Tattersall L, Yianni V, Knight L, Yu H, Hallett SR, Johnson P, Caetano AJ, Cosstick C, Ridley AJ, Gartland A, Conte MR, Grigoriadis AE. The RNA binding proteins LARP4A and LARP4B promote sarcoma and carcinoma growth and metastasis. iScience 2024; 27:109288. [PMID: 38532886 PMCID: PMC10963253 DOI: 10.1016/j.isci.2024.109288] [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: 05/01/2023] [Revised: 11/01/2023] [Accepted: 02/16/2024] [Indexed: 03/28/2024] Open
Abstract
RNA-binding proteins (RBPs) are emerging as important regulators of cancer pathogenesis. We reveal that the RBPs LARP4A and LARP4B are differentially overexpressed in osteosarcoma and osteosarcoma lung metastases, as well as in prostate cancer. Depletion of LARP4A and LARP4B reduced tumor growth and metastatic spread in xenografts, as well as inhibiting cell proliferation, motility, and migration. Transcriptomic profiling and high-content multiparametric analyses unveiled a central role for LARP4B, but not LARP4A, in regulating cell cycle progression in osteosarcoma and prostate cancer cells, potentially through modulating key cell cycle proteins such as Cyclins B1 and E2, Aurora B, and E2F1. This first systematic comparison between LARP4A and LARP4B assigns new pro-tumorigenic functions to LARP4A and LARP4B in bone and prostate cancer, highlighting their similarities while also indicating distinct functional differences. Uncovering clear biological roles for these paralogous proteins provides new avenues for identifying tissue-specific targets and potential druggable intervention.
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Affiliation(s)
- Jennifer C. Coleman
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Val Yianni
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Laura Knight
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Hongqiang Yu
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Sadie R. Hallett
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
| | - Philip Johnson
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Ana J. Caetano
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Charlie Cosstick
- Centre for Craniofacial & Regenerative Biology, King’s College London, London, SE1 9RT UK
| | - Anne J. Ridley
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD UK
| | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, Sheffield, S10 2RX UK
| | - Maria R. Conte
- Randall Centre for Cell and Molecular Biophysics, King’s College London, London, SE1 1UL UK
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11
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Liao B, Wang J, Yuan Y, Luo H, Ouyang X. Biological roles of SLC16A1-AS1 lncRNA and its clinical impacts in tumors. Cancer Cell Int 2024; 24:122. [PMID: 38555465 PMCID: PMC10981830 DOI: 10.1186/s12935-024-03285-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 04/02/2024] Open
Abstract
Recent studies have increasingly highlighted the aberrant expression of SLC16A1-AS1 in a variety of tumor types, where it functions as either an oncogene or a tumor suppressor in the pathogenesis of different cancers. The expression levels of SLC16A1-AS1 have been found to significantly correlate with clinical features and the prognosis of cancer patients. Furthermore, SLC16A1-AS1 modulates a range of cellular functions, including proliferation, migration, and invasion, through its interactions with diverse molecules and signaling pathways. This review examines the latest evidence regarding the role of SLC16A1-AS1 in the progression of various tumors and explores its potential clinical applications as a novel prognostic and diagnostic biomarker. Our comprehensive review aims to deepen the understanding of SLC16A1-AS1's multifaceted role in oncology, underscoring its potential as a significant biomarker and therapeutic target.
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Affiliation(s)
- Bing Liao
- Department of Otorhinolaryngology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China
| | - Jialing Wang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China
| | - Yalin Yuan
- Second School of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China
| | - Hongliang Luo
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China
| | - Xi Ouyang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330008, Jiangxi, China.
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12
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Li L, Zhu G, Gong C, Hu M, Tan K, Jiang L, Li Y, Zhu X, Xie P, Chen X, Yang X. Histone demethylase KDM5D represses the proliferation, migration and invasion of hepatocellular carcinoma through the E2F1/TNNC1 axis. Antioxid Redox Signal 2024. [PMID: 38504588 DOI: 10.1089/ars.2023.0448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
OBJECTIVE This study focused on investigating the mechanism in which the KDM5D/E2F1/TNNC1 axis affected hepatocellular carcinoma (HCC) development. METHODS At first, we determined HCC cell proliferation, migration, invasion, and apoptosis, as well as SOD activity, MDA content, and ROS level. ChIP assay was subsequently conducted to examine H3K4me3 modification in the E2F1 promoter region and the binding of E2F1 to the TNNC1 promoter region after KDM5D overexpression. Meanwhile, we performed western blot for testing KDM5D, H3K4me3, and E2F1 expression after KDM5D overexpression in Huh-7 cells. The binding of transcription factor E2F1 to the TNNC1 promoter region was assessed by dual luciferase reporter gene assay. We further observed the tumor growth ability in nude mice transplanted tumor models. RESULTS Overexpressed KDM5D suppressed HCC proliferation, migration, and invasion, promoted the apoptosis, suppressed SOD activity, elevated MDA content and ROS level, and promoted ferroptosis. KDM5D suppressed H3K4me3 modification in the E2F1 promoter region and suppressed E2F1 expression in HCC cells. Reduced KDM5D, H3K4me3, and E2F1 expression was found after KDM5D overexpression in Huh-7 cells. Overexpressing E2F1 reversed the inhibitory effects of KDM5D on HCC cell proliferative, migratory, and invasive behaviors. KDM5D repressed TNNC1 transcription by inhibiting E2F1 binding to the TNNC1 promoter. In vivo KDM5D overexpression inhibited HCC development via the E2F1/TNNC1 axis. CONCLUSION KDM5D inhibits E2F1 expression by suppressing H3K4me3 modification in the E2F1 promoter region, which in turn suppresses the binding of E2F1 to the TNNC1 promoter region, thus leading to the inhibition of HCC development.
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Affiliation(s)
- Lili Li
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Genbao Zhu
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Chen Gong
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Mengxue Hu
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Kemeng Tan
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - La Jiang
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Yafen Li
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Xiaohong Zhu
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Peng Xie
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
| | - Xilan Chen
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, 125 Huaihe West Road. Yongqiao District, Suzhou, China, 234000;
| | - Xianfen Yang
- Anhui Wanbei Coal Electricity Group General Hospital, 645365, Suzhou, Jiangsu, China;
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Xu X, Charrier A, Congrove S, Buchner DA. Cell-state dependent regulation of PPAR γ signaling by ZBTB9 in adipocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583402. [PMID: 38496622 PMCID: PMC10942320 DOI: 10.1101/2024.03.04.583402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Adipocytes play a critical role in metabolic homeostasis. Peroxisome proliferator-activated receptor- γ (PPAR γ ) is a nuclear hormone receptor that is a master regulator of adipocyte differentiation and function. ZBTB9 was predicted to interact with PPAR γ based on large-scale protein interaction experiments. In addition, GWAS studies in the type 2 diabetes (T2D) Knowledge Portal revealed associations between Z btb9 and both BMI and T2D risk. Here we show that ZBTB9 positively regulates PPAR γ activity in mature adipocytes. Surprisingly Z btb9 knockdown (KD) also increased adipogenesis in 3T3-L1 cells and human preadipocytes. E2F activity was increased and E2F downstream target genes were upregulated in Zbtb9 -KD preadipocytes. Accordingly, RB phosphorylation, which regulates E2F activity, was enhanced in Zbtb9 -KD preadipocytes. Critically, an E2F1 inhibitor blocked the effects of Zbtb9 deficiency on adipogenic gene expression and lipid accumulation. Collectively, these results demonstrate that Zbtb9 inhibits adipogenesis as a negative regulator of Pparg expression via altered RB-E2F1 signaling. Our findings reveal complex cell-state dependent roles of ZBTB9 in adipocytes, identifying a new molecule that regulates adipogenesis and adipocyte biology as both a positive and negative regulator of PPAR γ signaling depending on the cellular context, and thus may be important in the pathogenesis and treatment of obesity and T2D.
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14
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Kole A, Bag AK, Pal AJ, De D. Generic model to unravel the deeper insights of viral infections: an empirical application of evolutionary graph coloring in computational network biology. BMC Bioinformatics 2024; 25:74. [PMID: 38365632 PMCID: PMC10874019 DOI: 10.1186/s12859-024-05690-0] [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: 11/22/2023] [Accepted: 02/02/2024] [Indexed: 02/18/2024] Open
Abstract
PURPOSE Graph coloring approach has emerged as a valuable problem-solving tool for both theoretical and practical aspects across various scientific disciplines, including biology. In this study, we demonstrate the graph coloring's effectiveness in computational network biology, more precisely in analyzing protein-protein interaction (PPI) networks to gain insights about the viral infections and its consequences on human health. Accordingly, we propose a generic model that can highlight important hub proteins of virus-associated disease manifestations, changes in disease-associated biological pathways, potential drug targets and respective drugs. We test our model on SARS-CoV-2 infection, a highly transmissible virus responsible for the COVID-19 pandemic. The pandemic took significant human lives, causing severe respiratory illnesses and exhibiting various symptoms ranging from fever and cough to gastrointestinal, cardiac, renal, neurological, and other manifestations. METHODS To investigate the underlying mechanisms of SARS-CoV-2 infection-induced dysregulation of human pathobiology, we construct a two-level PPI network and employed a differential evolution-based graph coloring (DEGCP) algorithm to identify critical hub proteins that might serve as potential targets for resolving the associated issues. Initially, we concentrate on the direct human interactors of SARS-CoV-2 proteins to construct the first-level PPI network and subsequently applied the DEGCP algorithm to identify essential hub proteins within this network. We then build a second-level PPI network by incorporating the next-level human interactors of the first-level hub proteins and use the DEGCP algorithm to predict the second level of hub proteins. RESULTS We first identify the potential crucial hub proteins associated with SARS-CoV-2 infection at different levels. Through comprehensive analysis, we then investigate the cellular localization, interactions with other viral families, involvement in biological pathways and processes, functional attributes, gene regulation capabilities as transcription factors, and their associations with disease-associated symptoms of these identified hub proteins. Our findings highlight the significance of these hub proteins and their intricate connections with disease pathophysiology. Furthermore, we predict potential drug targets among the hub proteins and identify specific drugs that hold promise in preventing or treating SARS-CoV-2 infection and its consequences. CONCLUSION Our generic model demonstrates the effectiveness of DEGCP algorithm in analyzing biological PPI networks, provides valuable insights into disease biology, and offers a basis for developing novel therapeutic strategies for other viral infections that may cause future pandemic.
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Affiliation(s)
- Arnab Kole
- Department of Computer Application, The Heritage Academy, Kolkata, W.B., 700107, India.
| | - Arup Kumar Bag
- Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | | | - Debashis De
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, Nadia, W.B., 741249, India
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15
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Sito H, Tan SC. Genetic polymorphisms as potential pharmacogenetic biomarkers for platinum-based chemotherapy in non-small cell lung cancer. Mol Biol Rep 2024; 51:102. [PMID: 38217759 DOI: 10.1007/s11033-023-08915-2] [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: 09/04/2023] [Accepted: 11/08/2023] [Indexed: 01/15/2024]
Abstract
Platinum-based chemotherapy (PBC) is a widely used treatment for various solid tumors, including non-small cell lung cancer (NSCLC). However, its efficacy is often compromised by the emergence of drug resistance in patients. There is growing evidence that genetic variations may influence the susceptibility of NSCLC patients to develop resistance to PBC. Here, we provide a comprehensive overview of the mechanisms underlying platinum drug resistance and highlight the important role that genetic polymorphisms play in this process. This paper discussed the genetic variants that regulate DNA repair, cellular movement, drug transport, metabolic processing, and immune response, with a focus on their effects on response to PBC. The potential applications of these genetic polymorphisms as predictive indicators in clinical practice are explored, as are the challenges associated with their implementation.
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Affiliation(s)
- Hilary Sito
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Shing Cheng Tan
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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16
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Darvish M. LncRNA FTH1P3: A New Biomarker for Cancer-Related Therapeutic Development. Curr Mol Med 2024; 24:576-584. [PMID: 37491858 DOI: 10.2174/1566524023666230724141353] [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: 04/15/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/27/2023]
Abstract
Cancer is a persistent and urgent health problem that affects the entire world. Not long ago, regulatory biomolecules referred to as long noncoding RNAs (lncRNAs) might have value for their innate abundance and stability. These single-stranded RNAs potentially interfere with several physiological and biochemical cellular processes involved in many human pathological situations, particularly cancer diseases. Ferritin heavy chain1 pseudogene 3 (FTH1P3), a lncRNA that is ubiquitously transcribed and belongs to the ferritin heavy chain (FHC) family, represents a novel class of lncRNAs primarily found in oral squamous cell carcinoma. Further research has shown that FTH1P3 is involved in other malignancies such as uveal melanoma, glioma, esophageal squamous cell carcinoma, non-small cell lung cancer, breast cancer, laryngeal squamous cell carcinoma, and cervical cancer. Accordingly, FTH1P3 significantly enhances cancer symptoms, including cell proliferation, invasion, metastasis, chemoresistance, and inhibition of apoptosis through many specific mechanisms. Notably, the clinical data significantly demonstrated the association of FTH1P3 overexpression with poor prognosis and poor overall survival within the examined samples. Here, we summarize all the research published to date (13 articles) on FTH1P3, focusing on the biological function underlying the regulatory mechanism and its possible clinical relevance.
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Affiliation(s)
- Maryam Darvish
- Department of Medical Biotechnology, School of Medicine, Arak University of Medical Sciences, Arak, Iran
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17
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Zhu L, Dou Z, Wu W, Hou Q, Wang S, Yuan Z, Li B, Liu J. Ghrelin/GHSR Axis Induced M2 Macrophage and Alleviated Intestinal Barrier Dysfunction in a Sepsis Rat Model by Inactivating E2F1/NF- κB Signaling. Can J Gastroenterol Hepatol 2023; 2023:1629777. [PMID: 38187112 PMCID: PMC10769719 DOI: 10.1155/2023/1629777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 10/20/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Sepsis is an inflammatory reaction disorder state that is induced by infection. The activation and regulation of the immune system play an essential role in the development of sepsis. Our previous studies have shown that ghrelin ameliorates intestinal dysfunction in sepsis. Very little is known about the mechanism of ghrelin and its receptor (GHSR) on the intestinal barrier and the immune function of macrophage regulation. Our research is to investigate the regulatory effect and molecular mechanism of the ghrelin/GHSR axis on intestinal dysfunction and macrophage polarization in septic rats. A rat model of sepsis was established by cecal ligation and puncture (CLP) operation. Then, the sepsis rats were treated with a ghrelin receptor agonist (TZP-101) or ghrelin inhibitor (obestatin). The results suggested that TZP-101 further enhanced ghrelin and GHSR expressions in the colon and spleen of septic rats and obestatin showed the opposite results. Ghrelin/GHSR axis ameliorated colonic structural destruction and intestinal epithelial tight junction injury in septic rats. In addition, the ghrelin/GHSR axis promoted M2-type polarization of macrophages, which was characterized by the decreases of IL-1β, IL-6, and TNF-α, as well as the increase of IL-10. Mechanistically, the ghrelin/GHSR axis promoted E2F2 expression and suppressed the activation of the NF-κB signaling pathway in septic rats. Collectively, targeting ghrelin/GHSR during sepsis may represent a novel therapeutic approach for the treatment of intestinal barrier injury.
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Affiliation(s)
- Lei Zhu
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Zhimin Dou
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Wei Wu
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Qiliang Hou
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Sen Wang
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Ziqian Yuan
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Bin Li
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Jian Liu
- Department of Intensive Care Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
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18
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Mondal T, Smith CI, Loffredo CA, Quartey R, Moses G, Howell CD, Korba B, Kwabi-Addo B, Nunlee-Bland G, R. Rucker L, Johnson J, Ghosh S. Transcriptomics of MASLD Pathobiology in African American Patients in the Washington DC Area †. Int J Mol Sci 2023; 24:16654. [PMID: 38068980 PMCID: PMC10706626 DOI: 10.3390/ijms242316654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/18/2023] Open
Abstract
Metabolic-dysfunction-associated steatotic liver disease (MASLD) is becoming the most common chronic liver disease worldwide and is of concern among African Americans (AA) in the United States. This pilot study evaluated the differential gene expressions and identified the signature genes in the disease pathways of AA individuals with MASLD. Blood samples were obtained from MASLD patients (n = 23) and non-MASLD controls (n = 24) along with their sociodemographic and medical details. Whole-blood transcriptomic analysis was carried out using Affymetrix Clarion-S Assay. A validation study was performed utilizing TaqMan Arrays coupled with Ingenuity Pathway Analysis (IPA) to identify the major disease pathways. Out of 21,448 genes in total, 535 genes (2.5%) were significantly (p < 0.05) and differentially expressed when we compared the cases and controls. A significant overlap in the predominant differentially expressed genes and pathways identified in previous studies using hepatic tissue was observed. Of note, TGFB1 and E2F1 genes were upregulated, and HMBS was downregulated significantly. Hepatic fibrosis signaling is the top canonical pathway, and its corresponding biofunction contributes to the development of hepatocellular carcinoma. The findings address the knowledge gaps regarding how signature genes and functional pathways can be detected in blood samples ('liquid biopsy') in AA MASLD patients, demonstrating the potential of the blood samples as an alternative non-invasive source of material for future studies.
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Affiliation(s)
- Tanmoy Mondal
- Department of Biology, Howard University, Washington, DC 20059, USA; (T.M.); (G.M.); (J.J.)
| | - Coleman I. Smith
- MedStar-Georgetown Transplantation Institute, Georgetown University School of Medicine, Washington, DC 20007, USA;
| | | | - Ruth Quartey
- Department of Internal Medicine, College of Medicine, Howard University, Washington, DC 20007, USA; (R.Q.); (C.D.H.)
| | - Gemeyel Moses
- Department of Biology, Howard University, Washington, DC 20059, USA; (T.M.); (G.M.); (J.J.)
| | - Charles D. Howell
- Department of Internal Medicine, College of Medicine, Howard University, Washington, DC 20007, USA; (R.Q.); (C.D.H.)
| | - Brent Korba
- Department of Microbiology & Immunology, Georgetown University, Washington, DC 20007, USA;
| | - Bernard Kwabi-Addo
- Department of Biochemistry, College of Medicine, Howard University, Washington, DC 20059, USA;
| | - Gail Nunlee-Bland
- Departments of Pediatrics and Child Health, College of Medicine, Howard University, Washington, DC 20059, USA;
| | - Leanna R. Rucker
- Department of Internal Medicine, MedStar Georgetown University Hospital, Washington, DC 20007, USA;
| | - Jheannelle Johnson
- Department of Biology, Howard University, Washington, DC 20059, USA; (T.M.); (G.M.); (J.J.)
| | - Somiranjan Ghosh
- Department of Biology, Howard University, Washington, DC 20059, USA; (T.M.); (G.M.); (J.J.)
- Departments of Pediatrics and Child Health, College of Medicine, Howard University, Washington, DC 20059, USA;
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Tao ZG, Yuan YX, Wang GW. Long non-coding RNA CDKN2B-AS1 promotes hepatocellular carcinoma progression via E2F transcription factor 1/G protein subunit alpha Z axis. World J Gastrointest Oncol 2023; 15:1974-1987. [DOI: 10.4251/wjgo.v15.i11.1974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/12/2023] [Accepted: 10/11/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND A series of long non-coding RNAs (lncRNAs) have been reported to play a crucial role in cancer biology. Some previous studies report that lncRNA CDKN2B-AS1 is involved in some human malignancies. However, its role in hepatocellular carcinoma (HCC) has not been fully deciphered.
AIM To decipher the role of CDKN2B-AS1 in the progression of HCC.
METHODS CDKN2B-AS1 expression in HCC was detected by quantitative real-time polymerase chain reaction. The malignant phenotypes of Li-7 and SNU-182 cells were detected by the CCK-8 method, EdU method, and flow cytometry, respectively. RNA immunoprecipitation was executed to confirm the interaction between CDKN2B-AS1 and E2F transcription factor 1 (E2F1). Luciferase reporter assay and chromatin immunoprecipitation were performed to verify the binding of E2F1 to the promoter of G protein subunit alpha Z (GNAZ). E2F1 and GNAZ were detected by western blot in HCC cells.
RESULTS In HCC tissues, CDKN2B-AS1 was upregulated. Depletion of CDKN2B-AS1 inhibited the proliferation of HCC cells, and the depletion of CDKN2B-AS1 also induced cell cycle arrest and apoptosis. CDKN2B-AS1 could interact with E2F1. Depletion of CDKN2B-AS1 inhibited the binding of E2F1 to the GNAZ promoter region. Overexpression of E2F1 reversed the biological effects of depletion of CDKN2B-AS1 on the malignant behaviors of HCC cells.
CONCLUSION CDKN2B-AS1 recruits E2F1 to facilitate GNAZ transcription to promote HCC progression.
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Affiliation(s)
- Zhi-Gang Tao
- Department of Radiology, Hangzhou Cancer Hospital, Hangzhou 310000, Zhejiang Province, China
| | - Yu-Xiao Yuan
- Department of Radiology, Hangzhou Xixi Hospital, Hangzhou 310012, Zhejiang Province, China
| | - Guo-Wei Wang
- Department of Radiology, Hangzhou Xixi Hospital, Hangzhou 310012, Zhejiang Province, China
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20
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Hanlon MA, Gulati R, Johnston M, Fleifil Y, Rivas M, Timchenko NA. Genetic Ablation of C/EBPα-p300 Pathway Blocks Development of Obese Pregnancy Associated Liver Disorders in Offspring. Cell Mol Gastroenterol Hepatol 2023; 17:347-360. [PMID: 37967813 PMCID: PMC10821535 DOI: 10.1016/j.jcmgh.2023.11.006] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND & AIMS The obesity-associated nonalcoholic fatty liver disease represents a common cause of pediatric liver diseases, including the pediatric liver cancer hepatoblastoma. The mechanisms behind the development of fatty liver in children are not yet known. We examined the role of the C/EBPα-p300 pathway in the development of maternal obesity-associated fatty liver phenotype in offspring. METHODS Because the ability of C/EBPα to promote fatty liver phenotype is enhanced by CDK4-mediated phosphorylation of C/EBPα at Ser193 and subsequent formation of C/EBPα-p300 complexes, we used wild-type (WT) and C/EBPα-S193D and C/EBPα-S193A mutant mice to study the effects of maternal high-fat diet (HFD) on the liver health of offspring. The females of these mouse lines were fed an HFD before mating, and the pups were further subjected to either an HFD or a normal diet for 12 weeks. RESULTS WT female mice on the HFD before and during pregnancy and their subsequent offspring on the HFD had severe fatty liver, fibrosis, and an increased rate of liver proliferation. However, the HFD in C/EBPα-S193A mice did not cause development of these disorders. In HFD-HFD treated WT mice, C/EBPα is phosphorylated at Ser193 and forms complexes with p300, which activate expression of genes involved in development of fatty liver, fibrosis, and proliferation. However, S193A-C/EBPα mice do not have complexes of C/EBPα-S193A with p300, leading to a lack of activation of genes of fatty liver, fibrosis, and proliferation. The mutant C/EBPα-S193D mice have accelerated cdk4-dependent pathway and have developed steatosis at early stages. CONCLUSIONS These studies identified the epigenetic cause of obese pregnancy-associated liver diseases and suggest a potential therapy based on inhibition of cdk4-ph-S193-C/EBPα-p300 pathway.
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Affiliation(s)
- Margaret A Hanlon
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Ruhi Gulati
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Michael Johnston
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Surgery, University of Cincinnati, Cincinnati, Ohio
| | - Yasmeen Fleifil
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Maria Rivas
- Institute of Biosciences, University of São Paulo (USP) Cidade Universitária, Butantã, São Paulo, Brazil
| | - Nikolai A Timchenko
- Division of General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Surgery, University of Cincinnati, Cincinnati, Ohio.
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21
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-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: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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22
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Ning J, Ding J, Wang S, Jiang Y, Wang D, Jiang S. GPC3 Promotes Lung Squamous Cell Carcinoma Progression and HLA-A2-Restricted GPC3 Antigenic Peptide-Modified Dendritic Cell-Induced Cytotoxic T Lymphocytes to Kill Lung Squamous Cell Carcinoma Cells. J Immunol Res 2023; 2023:5532617. [PMID: 37965271 PMCID: PMC10643027 DOI: 10.1155/2023/5532617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 09/01/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023] Open
Abstract
Lung squamous cell carcinoma (LUSC) is associated with poor clinical prognosis and lacks available targeted agents. GPC3 is upregulated in LUSC. Our study aimed to explore the roles of GPC3 in LUSC and the antitumor effects of HLA-A2-restricted GPC3 antigenic peptide-sensitized dendritic cell (DC)-induced cytotoxic T lymphocytes (CTLs) on LUSC. LUSC cells with GPC3 knockdown and overexpression were built using lentivirus packaging, and cell viability, clone formation, apoptosis, cycle, migration, and invasion were determined. Western blotting was used to detect the expression of cell cycle-related proteins and PI3K-AKT pathway-associated proteins. Subsequently, HLA-A2-restricted GPC3 antigenic peptides were predicted and synthesized by bioinformatic databases, and DCs were induced and cultured in vitro. Finally, HLA-A2-restricted GPC3 antigenic peptide-modified DCs were co-cultured with T cells to generate specific CTLs, and the killing effects of different CTLs on LUSC cells were studied. A series of cell function experiments showed that GPC3 overexpression promoted the proliferation, migration, and invasion of LUSC cells, inhibited their apoptosis, increased the number of cells in S phase, and reduced the cells in G2/M phase. GPC3 knockdown downregulated cyclin A, c-Myc, and PI3K, upregulated E2F1, and decreased the pAKT/AKT level. Three HLA-A2-restricted GPC3 antigenic peptides were synthesized, with GPC3522-530 FLAELAYDL and GPC3102-110 FLIIQNAAV antigenic peptide-modified DCs inducing CTL production, and exhibiting strong targeted killing ability in LUSC cells at 80 : 1 multiplicity of infection. GPC3 may advance the onset and progression of LUSC, and GPC3522-530 FLAELAYDL and GPC3102-110 FLIIQNAAV antigenic peptide-loaded DC-induced CTLs have a superior killing ability against LUSC cells.
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Affiliation(s)
- Jing Ning
- Department of General Medicine, Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, China
- Molecular Oncology Department of Cancer Research Institution, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Jianqiao Ding
- Department of Thoracic Surgery (2), Cancer Hospital of Dalian University of Technology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang 110042, China
| | - Shu Wang
- Department of Radiotherapy, The Second Hospital of Jilin University, Changchun 130000, China
| | - Youhong Jiang
- Molecular Oncology Department of Cancer Research Institution, The First Affiliated Hospital of China Medical University, Shenyang 110001, China
| | - Daqing Wang
- Hope Plaza Children's Hospital District of Dalian Municipal Women and Children's Medical Center, Dalian 116000, China
| | - Shenyi Jiang
- Department of General Practice, The First Affiliated Hospital of China Medical University, Shengyang 110001, China
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23
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Perez-Estrada JR, Tangeman JA, Proto-Newton M, Sanaka H, Smucker B, Del Rio-Tsonis K. DISTINCT METABOLIC STATES DIRECT RETINAL PIGMENT EPITHELIUM CELL FATE DECISIONS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.26.559631. [PMID: 37808829 PMCID: PMC10557760 DOI: 10.1101/2023.09.26.559631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
During tissue regeneration, proliferation, dedifferentiation, and reprogramming are necessary to restore lost structures. However, it is not fully understood how metabolism intersects with these processes. Chicken embryos can regenerate their retina through retinal pigment epithelium (RPE) reprogramming when treated with fibroblast factor 2 (FGF2). Using transcriptome profiling, we uncovered extensive regulation of gene sets pertaining to proliferation, neurogenesis, and glycolysis throughout RPE-to-neural retina reprogramming. By manipulating cell media composition, we determined that glucose, glutamine, or pyruvate are sufficient to support RPE reprogramming identifying glycolysis as a requisite. Conversely, the induction of oxidative metabolism by activation of pyruvate dehydrogenase induces Epithelial-to-mesenchymal transition (EMT), while simultaneously blocking the activation of neural retina fate. We also identify that EMT is partially driven by an oxidative environment. Our findings provide evidence that metabolism controls RPE cell fate decisions and provide insights into the metabolic state of RPE cells, which are prone to fate changes in regeneration and pathologies, such as proliferative vitreoretinopathy.
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24
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Wruck W, Genfi AKA, Adjaye J. Natural Products in Renal-Associated Drug Discovery. Antioxidants (Basel) 2023; 12:1599. [PMID: 37627594 PMCID: PMC10451693 DOI: 10.3390/antiox12081599] [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: 07/21/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The global increase in the incidence of kidney failure constitutes a major public health problem. Kidney disease is classified into acute and chronic: acute kidney injury (AKI) is associated with an abrupt decline in kidney function and chronic kidney disease (CKD) with chronic renal failure for more than three months. Although both kidney syndromes are multifactorial, inflammation and oxidative stress play major roles in the diversity of processes leading to these kidney malfunctions. Here, we reviewed various publications on medicinal plants with antioxidant and anti-inflammatory properties with the potential to treat and manage kidney-associated diseases in rodent models. Additionally, we conducted a meta-analysis to identify gene signatures and associated biological processes perturbed in human and mouse cells treated with antioxidants such as epigallocatechin gallate (EGCG), the active ingredient in green tea, and the mushroom Ganoderma lucidum (GL) and in kidney disease rodent models. We identified EGCG- and GL-regulated gene signatures linked to metabolism; inflammation (NRG1, E2F1, NFKB1 and JUN); ion signalling; transport; renal processes (SLC12A1 and LOX) and VEGF, ERBB and BDNF signalling. Medicinal plant extracts are proving to be effective for the prevention, management and treatment of kidney-associated diseases; however, more detailed characterisations of their targets are needed to enable more trust in their application in the management of kidney-associated diseases.
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Affiliation(s)
- Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Afua Kobi Ampem Genfi
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, University for Development Studies, Nyankpala P.O. Box TL 1882, Ghana
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
- EGA Institute for Women's Health, Zayed Centre for Research into Rare Diseases in Children (ZCR), University College London (UCL), 20 Guilford Street, London WC1N 1DZ, UK
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25
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Oger F, Bourouh C, Friano ME, Courty E, Rolland L, Gromada X, Moreno M, Carney C, Rabhi N, Durand E, Amanzougarene S, Berberian L, Derhourhi M, Blanc E, Hannou SA, Denechaud PD, Benfodda Z, Meffre P, Fajas L, Kerr-Conte J, Pattou F, Froguel P, Pourcet B, Bonnefond A, Collombat P, Annicotte JS. β-Cell-Specific E2f1 Deficiency Impairs Glucose Homeostasis, β-Cell Identity, and Insulin Secretion. Diabetes 2023; 72:1112-1126. [PMID: 37216637 DOI: 10.2337/db22-0604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 05/01/2023] [Indexed: 05/24/2023]
Abstract
The loss of pancreatic β-cell identity has emerged as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cell-autonomous role of the cell-cycle regulator and transcription factor E2F1 in the maintenance of β-cell identity, insulin secretion, and glucose homeostasis. We show that the β-cell-specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, altered endocrine cell mass, downregulation of many β-cell genes, and concomitant increase of non-β-cell markers. Mechanistically, epigenomic profiling of the promoters of these non-β-cell upregulated genes identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, promoters of downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that specific E2f1 transcriptional, cistromic, and epigenomic signatures are associated with these β-cell dysfunctions, with E2F1 directly regulating several β-cell genes at the chromatin level. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of β-cell identity genes. Our data suggest that E2F1 is critical for maintaining β-cell identity and function through sustained control of β-cell and non-β-cell transcriptional programs. ARTICLE HIGHLIGHTS β-Cell-specific E2f1 deficiency in mice impairs glucose tolerance. Loss of E2f1 function alters the ratio of α- to β-cells but does not trigger β-cell conversion into α-cells. Pharmacological inhibition of E2F activity inhibits glucose-stimulated insulin secretion and alters β- and α-cell gene expression in human islets. E2F1 maintains β-cell function and identity through control of transcriptomic and epigenetic programs.
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Affiliation(s)
- Frédérik Oger
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Cyril Bourouh
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Marika Elsa Friano
- INSERM, CNRS, Institut de Biologie Valrose, Université Côte d'Azur, Nice, France
| | - Emilie Courty
- INSERM, U1167 - RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Laure Rolland
- INSERM, U1167 - RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Xavier Gromada
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Maeva Moreno
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Charlène Carney
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Nabil Rabhi
- Department of Biochemistry, Boston University School of Medicine, Boston, MA
| | - Emmanuelle Durand
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Souhila Amanzougarene
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Lionel Berberian
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Mehdi Derhourhi
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Etienne Blanc
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Sarah Anissa Hannou
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | | | | | | | - Lluis Fajas
- Center for Integrative Genomics, Université de Lausanne, Lausanne, Switzerland
| | - Julie Kerr-Conte
- INSERM, U1190 - EGID, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - François Pattou
- INSERM, U1190 - EGID, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Philippe Froguel
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
- Department of Metabolism, Hammersmith Hospital, Imperial College London, London, U.K
| | - Benoit Pourcet
- INSERM, U1011 - EGID, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
| | - Amélie Bonnefond
- INSERM, U1283 - UMR8199 - European Genomic Institute for Diabetes (EGID), CNRS, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
- Department of Metabolism, Hammersmith Hospital, Imperial College London, London, U.K
| | - Patrick Collombat
- INSERM, CNRS, Institut de Biologie Valrose, Université Côte d'Azur, Nice, France
| | - Jean-Sébastien Annicotte
- INSERM, U1167 - RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies Liées au Vieillissement, Institut Pasteur de Lille, CHU Lille, Université de Lille, Lille, France
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26
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Xiong X, Jian G. E2F1‑mediated RAB34 upregulation accelerates the proliferation and inhibits the cell cycle arrest and apoptosis of acute myeloid leukemia cells. Exp Ther Med 2023; 26:389. [PMID: 37456160 PMCID: PMC10347365 DOI: 10.3892/etm.2023.12088] [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: 09/15/2022] [Accepted: 12/21/2022] [Indexed: 07/18/2023] Open
Abstract
Acute myeloid leukemia (AML) is a malignant disease that is mainly arisen from myeloid stem/progenitor cells. The pathogenesis of AML is complex. Ras-related protein member RAS oncogene GTPases (RAB) 34 protein has been reported to serve an important role in the development of cancer. However, to the best of our knowledge, the role of RAB34 in AML has not been previously reported. The GEPIA database was used to predict the expression levels of RAB34 in patients with AML. Reverse transcription-quantitative PCR and western blotting were used to detect the expression of RAB34 in AML cell lines. Cell transfection with short hairpin (sh)RNAs targeting RAB34 was used to interfere with RAB34 expression. Cell Counting Kit-8 and 5-ethynyl-2'-deoxyuridine staining were used to measure cell proliferation. Flow cytometry was used to investigate cell cycle distribution and apoptosis. Western blotting was used to assess the protein expression levels of RAB34 and E2F transcription factor 1 (E2F1), and cell cycle- and apoptosis-associated proteins, including Bcl-2, Bax, CDK4, CDK8 and cyclin D1. The potential binding between E2F1 and RAB34 was then verified by luciferase reporter and chromatin immunoprecipitation assays. Subsequently, cells were co-transfected with RAB34 shRNA and the E2F1 overexpression plasmid before cell proliferation, cell cycle and apoptosis were analyzed further. The expression of RAB34 was found to be significantly increased in AML cell lines. Knocking down RAB34 expression in AML cells was found to significantly inhibit cell proliferation, induce cell cycle arrest and promote apoptosis. E2F1 activated the transcription of RAB34 and E2F1 elevation reversed the impacts of RAB34 silencing on cell proliferation, cell cycle and apoptosis in AML. Therefore, these findings suggest that E2F1-mediated RAB34 upregulation may accelerate the malignant progression of AML.
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Affiliation(s)
- Xiaojie Xiong
- Clinical Laboratory, The First Affiliated Hospital of HaiNan Medical University, Haikou, Hainan 570102, P.R. China
| | - Gang Jian
- Department of Pharmacy, The First Affiliated Hospital of HaiNan Medical University, Haikou, Hainan 570102, P.R. China
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27
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Wörthmüller J, Disler S, Pradervand S, Richard F, Haerri L, Ruiz Buendía GA, Fournier N, Desmedt C, Rüegg C. MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER + Breast Cancer. Cells 2023; 12:1929. [PMID: 37566008 PMCID: PMC10417439 DOI: 10.3390/cells12151929] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
MAGI1 acts as a tumor suppressor in estrogen receptor-positive (ER+) breast cancer (BC), and its loss correlates with a more aggressive phenotype. To identify the pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, the cell cycle, and DNA damage responses affected by MAGI1 loss. Upon exposure to TNF-α/IFN-γ, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence compared with MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition using olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored the expression of DNA repair proteins and sensitized cells to fulvestrant. An analysis of human BC patients' transcriptomic data revealed that patients with low MAGI1 levels had a higher tumor mutational burden and homologous recombination deficiency. Moreover, MAGI1 expression levels negatively correlated with PI3K/AKT and MAPK signaling, which confirmed our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.
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Affiliation(s)
- Janine Wörthmüller
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Simona Disler
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Pradervand
- Lausanne Genomic Technologies Facility (LGTF), University of Lausanne, 1015 Lausanne, Switzerland
| | - François Richard
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Lisa Haerri
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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28
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Wang Y, Chen L, Wang L, Pei G, Cheng H, Zhang Q, Wang S, Hu D, He Y, He C, Fu C, Wei Q. Pulsed Electromagnetic Fields Combined With Adipose-Derived Stem Cells Protect Ischemic Myocardium by Regulating miR-20a-5p/E2F1/p73 Signaling. Stem Cells 2023; 41:724-737. [PMID: 37207995 DOI: 10.1093/stmcls/sxad037] [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: 01/07/2023] [Accepted: 05/03/2023] [Indexed: 05/21/2023]
Abstract
Myocardial infarction (MI) is a serious threat to human health. Although monotherapy with pulsed electromagnetic fields (PEMFs) or adipose-derived stem cells (ADSCs) has been reported to have positive effect on the treatment of MI, a satisfactory outcome has not yet been achieved. In recent years, combination therapy has attracted widespread interest. Herein, we explored the synergistic therapeutic effect of combination therapy with PEMFs and ADSCs on MI and found that the combination of PEMFs and ADSCs effectively reduced infarct size, inhibited cardiomyocyte apoptosis and protected the cardiac function in mice with MI. In addition, bioinformatics analysis and RT-qPCR showed that the combination therapy could affect apoptosis by regulating the expression of miR-20a-5p. A dual-luciferase reporter gene assay also confirmed that the miR-20a-5p could target E2F transcription factor 1 (E2F1) and inhibit cardiomyocyte apoptosis by regulating the E2F1/p73 signaling pathway. Therefore, our study systematically demonstrated the effectiveness of combination therapy on the inhibition of cardiomyocyte apoptosis by regulating the miR-20a-5p/E2F1/p73 signaling pathway in mice with MI. Thus, our study underscored the effectiveness of the combination of PEMFs and ADSCs and identified miR-20a-5p as a promising therapeutic target for the treatment of MI in the future.
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Affiliation(s)
- Yang Wang
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Li Chen
- Department of Rehabilitation Medicine, The Fifth Affiliated People's Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, People's Republic of China
| | - Lu Wang
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Gaiqin Pei
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Hongxin Cheng
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Qing Zhang
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Shiqi Wang
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Danrong Hu
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Yong He
- Department of Cardiology, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Chengqi He
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
| | - Chenying Fu
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Aging and Geriatric Mechanism Laboratory, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Quan Wei
- Department of Rehabilitation Medicine and Institute of Rehabilitation Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
- Key Laboratory of Rehabilitation Medicine in Sichuan Province, Chengdu, People's Republic of China
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29
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Sadhu N, He Y, Yao Y, Wilkie DJ, Molokie RE, Wang ZJ. Candidate gene association study suggests potential role of dopamine beta-hydroxylase in pain heterogeneity in sickle cell disease. Front Genet 2023; 14:1193603. [PMID: 37384335 PMCID: PMC10296203 DOI: 10.3389/fgene.2023.1193603] [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: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: Pain is a lifelong companion of individuals with sickle cell disease (SCD) and has a severe impact on their quality of life. Both acute crisis pain and chronic non-crisis pain exhibit high variability between individuals, making it difficult to effectively manage sickle cell-related pain. We investigated the role of dopamine beta-hydroxylase (DBH) gene polymorphisms on pain variability in SCD. DBH is a key enzyme in the catecholamine biosynthesis pathway that catalyzes the conversion of dopamine to norepinephrine, both of which are known mediators of pain and pain-related behaviors. Methods: Acute crisis pain-related utilization and non-crisis chronic pain scores of 131 African Americans with SCD were obtained. Results and discussion: Association analyses revealed that the T allele of upstream variant rs1611115 and downstream variant rs129882 correlated with higher severity of chronic pain in an additive model. On the other hand, the A allele of missense variant rs5324 associated with lower risk of both acute crisis pain and chronic pain. Similarly, the C allele of intronic variant rs2797849 was associated with lower incidence of acute crisis pain in the additive model. In addition, tissue-specific eQTL revealed that the T allele of rs1611115 correlated with decreased expression of DBH in the frontal cortex and anterior cingulate cortex (GTEx), and decreased expression of DBH-AS1 in blood (eQTLGen). Bioinformatic approaches predicted that rs1611115 may be altering a transcription factor binding site, thereby, contributing to its potential effect. Taken together, findings from this study suggest that potential functional polymorphisms of DBH may modulate pain perception in SCD.
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Affiliation(s)
- Nilanjana Sadhu
- Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, IL, United States
| | - Ying He
- Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, IL, United States
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL, United States
| | - Yingwei Yao
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainesville, FL, United States
| | - Diana J. Wilkie
- Department of Biobehavioral Nursing Science, University of Florida College of Nursing, Gainesville, FL, United States
| | - Robert E. Molokie
- Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, IL, United States
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL, United States
- Jesse Brown Veteran’s Administration Medical Center, Chicago, IL, United States
- Division of Hematology/Oncology, University of Illinois Chicago College of Medicine, Chicago, IL, United States
| | - Zaijie Jim Wang
- Department of Pharmaceutical Sciences, University of Illinois Chicago College of Pharmacy, Chicago, IL, United States
- Comprehensive Sickle Cell Center, University of Illinois Chicago, Chicago, IL, United States
- Department of Neurology and Rehabilitation, University of Illinois Chicago College of Medicine, Chicago, IL, United States
- Department of Biomedical Engineering, University of Illinois Chicago College of Engineering, Chicago, IL, United States
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Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540401. [PMID: 37214836 PMCID: PMC10197627 DOI: 10.1101/2023.05.11.540401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Transcription factors (TF) are proteins that bind DNA in a sequence-specific manner to regulate gene transcription. Despite their unique intrinsic sequence preferences, in vivo genomic occupancy profiles of TFs differ across cellular contexts. Hence, deciphering the sequence determinants of TF binding, both intrinsic and context-specific, is essential to understand gene regulation and the impact of regulatory, non-coding genetic variation. Biophysical models trained on in vitro TF binding assays can estimate intrinsic affinity landscapes and predict occupancy based on TF concentration and affinity. However, these models cannot adequately explain context-specific, in vivo binding profiles. Conversely, deep learning models, trained on in vivo TF binding assays, effectively predict and explain genomic occupancy profiles as a function of complex regulatory sequence syntax, albeit without a clear biophysical interpretation. To reconcile these complementary models of in vitro and in vivo TF binding, we developed Affinity Distillation (AD), a method that extracts thermodynamic affinities de-novo from deep learning models of TF chromatin immunoprecipitation (ChIP) experiments by marginalizing away the influence of genomic sequence context. Applied to neural networks modeling diverse classes of yeast and mammalian TFs, AD predicts energetic impacts of sequence variation within and surrounding motifs on TF binding as measured by diverse in vitro assays with superior dynamic range and accuracy compared to motif-based methods. Furthermore, AD can accurately discern affinities of TF paralogs. Our results highlight thermodynamic affinity as a key determinant of in vivo binding, suggest that deep learning models of in vivo binding implicitly learn high-resolution affinity landscapes, and show that these affinities can be successfully distilled using AD. This new biophysical interpretation of deep learning models enables high-throughput in silico experiments to explore the influence of sequence context and variation on both intrinsic affinity and in vivo occupancy.
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Affiliation(s)
- Amr M. Alexandari
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | | | - Avanti Shrikumar
- Department of Earth System Science, Stanford University, Stanford, CA 94305
| | - Nilay Shah
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eileen Li
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Miles A. Pufall
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
| | - Polly M. Fordyce
- Department of Genetics, Stanford University, Stanford, CA 94305
- Department of Bioengineering, Stanford University, Stanford, CA 94305
- ChEM-H Institute, Stanford University, Stanford, CA 94305
- Chan Zuckerberg Biohub, San Francisco, CA 94110
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
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Ghafouri-Fard S, Askari A, Behzad Moghadam K, Hussen BM, Taheri M, Samadian M. A review on the role of ZEB1-AS1 in human disorders. Pathol Res Pract 2023; 245:154486. [PMID: 37120907 DOI: 10.1016/j.prp.2023.154486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/02/2023]
Abstract
ZEB1 Antisense RNA 1 (ZEB1-AS1) is a type of RNA characterized as long non-coding RNA (lncRNA). This lncRNA has important regulatory roles on its related gene, Zinc Finger E-Box Binding Homeobox 1 (ZEB1). In addition, role of ZEB1-AS1 has been approved in diverse malignancies such as colorectal cancer, breast cancer, glioma, hepatocellular carcinoma and gastric cancer. ZEB1-AS1 serves as a sponge for a number of microRNAs, namely miR-577, miR-335-5p, miR-101, miR-505-3p, miR-455-3p, miR-205, miR-23a, miR-365a-3p, miR-302b, miR-299-3p, miR-133a-3p, miR-200a, miR-200c, miR-342-3p, miR-214, miR-149-3p and miR-1224-5p. In addition to malignant conditions, ZEB1-AS1 has functional role in non-malignant conditions like diabetic nephropathy, diabetic lung, arthrosclerosis, Chlamydia trachomatis infection, pulmonary fibrosis and ischemic stroke. This review outlines different molecular mechanisms of ZEB1-AS1 in a variety of disorders and highlights its importance in their pathogenesis.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arian Askari
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Institue of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Samadian
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ou ZY, Wang K, Shen WW, Deng G, Xu YY, Wang LF, Zai ZY, Ling YA, Zhang T, Peng XQ, Chen FH. Oncogenic FLT3 internal tandem duplication activates E2F1 to regulate purine metabolism in acute myeloid leukaemia. Biochem Pharmacol 2023; 210:115458. [PMID: 36803956 DOI: 10.1016/j.bcp.2023.115458] [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: 11/09/2022] [Revised: 01/28/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Oncogene FLT3 internal tandem duplication (FLT3-ITD) mutation accounts for 30 % of acute myeloid leukaemia (AML) cases and induces transformation. Previously, we found that E2F transcription factor 1 (E2F1) was involved in AML cell differentiation. Here, we reported that E2F1 expression was aberrantly upregulated in AML patients, especially in AML patients carrying FLT3-ITD. E2F1 knockdown inhibited cell proliferation and increased cell sensitivity to chemotherapy in cultured FLT3-ITD-positive AML cells. E2F1-depleted FLT3-ITD+ AML cells lost their malignancy as shown by the reduced leukaemia burden and prolonged survival in NOD-PrkdcscidIl2rgem1/Smoc mice receiving xenografts. Additionally, FLT3-ITD-driven transformation of human CD34+ hematopoietic stem and progenitor cells was counteracted by E2F1 knockdown. Mechanistically, FLT3-ITD enhanced the expression and nuclear accumulation of E2F1 in AML cells. Further study using chromatin immunoprecipitation-sequencing and metabolomics analyses revealed that ectopic FLT3-ITD promoted the recruitment of E2F1 on genes encoding key enzymatic regulators of purine metabolism and thus supported AML cell proliferation. Together, this study demonstrates that E2F1-activated purine metabolism is a critical downstream process of FLT3-ITD in AML and a potential target for FLT3-ITD+ AML patients.
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Affiliation(s)
- Zi-Yao Ou
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Ke Wang
- Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Wen-Wen Shen
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Ge Deng
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Ya-Yun Xu
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Long-Fei Wang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Zhuo-Yan Zai
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Yi-An Ling
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Tao Zhang
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China
| | - Xiao-Qing Peng
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Fei-Hu Chen
- School of Pharmacy, Anhui Medical University, Hefei, Anhui, China; Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, Hefei, Anhui, China; Anhui Laboratory of Inflammatory and Immune Disease, Anhui Medical University, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, Anhui, China.
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Golubev DA, Zemskaya NV, Gorbunova AA, Kukuman DV, Moskalev A, Shaposhnikov MV. Studying the Geroprotective Properties of YAP/TAZ Signaling Inhibitors on Drosophila melanogaster Model. Int J Mol Sci 2023; 24:ijms24066006. [PMID: 36983079 PMCID: PMC10058302 DOI: 10.3390/ijms24066006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/28/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
The transcriptional coactivators Yes-associated protein (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ) are the main downstream effectors of the evolutionarily conserved Hippo signaling pathway. YAP/TAZ are implicated in the transcriptional regulation of target genes that are involved in a wide range of key biological processes affecting tissue homeostasis and play dual roles in the aging process, depending on the cellular and tissue context. The aim of the present study was to investigate whether pharmacological inhibitors of Yap/Taz increase the lifespan of Drosophila melanogaster. Real-time qRT-PCR was performed to measure the changes in the expression of Yki (Yorkie, the Drosophila homolog of YAP/TAZ) target genes. We have revealed a lifespan-increasing effect of YAP/TAZ inhibitors that was mostly associated with decreased expression levels of the wg and E2f1 genes. However, further analysis is required to understand the link between the YAP/TAZ pathway and aging.
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Affiliation(s)
- Denis A Golubev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Nadezhda V Zemskaya
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Anastasia A Gorbunova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Daria V Kukuman
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
| | - Mikhail V Shaposhnikov
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 167982 Syktyvkar, Russia
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Role of E2F transcription factor in Oral cancer: Recent Insight and Advancements. Semin Cancer Biol 2023; 92:28-41. [PMID: 36924812 DOI: 10.1016/j.semcancer.2023.03.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023]
Abstract
The family of mammalian E2F transcription factors (E2Fs) comprise of 8 members (E2F1-E2F8) classified as activators (E2F1-E2F3) and repressors (E2F4-E2F8) primarily regulating the expression of several genes related to cell proliferation, apoptosis and differentiation, mainly in a cell cycle-dependent manner. E2F activity is frequently controlled via the retinoblastoma protein (pRb), cyclins, p53 and the ubiquitin-proteasome pathway. Additionally, genetic or epigenetic changes result in the deregulation of E2F family genes expression altering S phase entry and apoptosis, an important hallmark for the onset and development of cancer. Although studies reveal E2Fs to be involved in several human malignancies, the mechanisms underlying the role of E2Fs in oral cancer lies nascent and needs further investigations. This review focuses on the role of E2Fs in oral cancer and the etiological factors regulating E2Fs activity, which in turn transcriptionally control the expression of their target genes, thus contributing to cell proliferation, metastasis, and drug/therapy resistance. Further, we will discuss therapeutic strategies for E2Fs, which may prevent oral tumor growth, metastasis, and drug resistance.
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Yildiz E, El Alam G, Perino A, Jalil A, Denechaud PD, Huber K, Fajas L, Auwerx J, Sorrentino G, Schoonjans K. Hepatic lipid overload triggers biliary epithelial cell activation via E2Fs. eLife 2023; 12:81926. [PMID: 36876915 PMCID: PMC10030116 DOI: 10.7554/elife.81926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 03/03/2023] [Indexed: 03/07/2023] Open
Abstract
During severe or chronic hepatic injury, biliary epithelial cells (BECs) undergo rapid activation into proliferating progenitors, a crucial step required to establish a regenerative process known as ductular reaction (DR). While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Here, we demonstrate that BECs readily accumulate lipids during high-fat diet feeding in mice and upon fatty acid treatment in BEC-derived organoids. Lipid overload induces metabolic rewiring to support the conversion of adult cholangiocytes into reactive BECs. Mechanistically, we found that lipid overload activates the E2F transcription factors in BECs, which drive cell cycle progression while promoting glycolytic metabolism. These findings demonstrate that fat overload is sufficient to reprogram BECs into progenitor cells in the early stages of NAFLD and provide new insights into the mechanistic basis of this process, revealing unexpected connections between lipid metabolism, stemness, and regeneration.
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Affiliation(s)
- Ece Yildiz
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alessia Perino
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Antoine Jalil
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Katharina Huber
- Center for Integrative Genomics, Université de Lausanne, Lausanne, Switzerland
| | - Lluis Fajas
- Center for Integrative Genomics, Université de Lausanne, Lausanne, Switzerland
- INSERM, Occitanie, Montpellier, France
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Giovanni Sorrentino
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Li Y, Huang HQ, Huang ZH, Yu ND, Ye XL, Jiang MC, Chen LM. SNHG15 enhances cisplatin resistance in lung adenocarcinoma by affecting the DNA repair capacity of cancer cells. Diagn Pathol 2023; 18:33. [PMID: 36864456 PMCID: PMC9979449 DOI: 10.1186/s13000-023-01291-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 01/12/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a prevalent malignancy. SNHG15 has been demonstrated to be oncogenic in many kinds of cancers, however the mechanism of SNHG15 in LUAD cisplatin (DDP) resistance remains unclear. In this study, we demonstrated the effect of SNHG15 on DDP resistance in LUAD and its related mechanism. METHODS Bioinformatics analysis was adopted to assess SNHG15 expression in LUAD tissues and predict the downstream genes of SNHG15. The binding relationship between SNHG15 and downstream regulatory genes was proved through RNA immunoprecipitation, chromatin immunoprecipitation and dual-luciferase reporter assays. Cell counting kit-8 assay was adopted to evaluate LUAD cell viability, and gene expression was determined by Western blot and quantitative real-time polymerase chain reaction. We then performed comet assay to assess DNA damage. Cell apoptosis was detected by Tunnel assay. Xenograft animal models were created to test the function of SNHG15 in vivo. RESULTS SNHG15 was up-regulated in LUAD cells. Moreover, SNHG15 was also highly expressed in drug-resistant LUAD cells. Down-regulated SNHG15 strengthened the sensitivity of LUAD cells to DDP and induced DNA damage. SNHG15 could elevate ECE2 expression through binding with E2F1, and it could induce DDP resistance by modulating the E2F1/ECE2 axis. In vivo experiments verified that the SNHG15 could enhance DDP resistance in LUAD tissue. CONCLUSION The results suggested that SNHG15 could up-regulate ECE2 expression by recruiting E2F1, thereby enhancing the DDP resistance of LUAD.
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Affiliation(s)
- Yong Li
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Hui-Qin Huang
- grid.488150.0Fujian Provincial Key Laboratory of Medical Testing, Fujian Academy of Medical Sciences, Fuzhou, 350000 Fujian China
| | - Zheng-Hui Huang
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Nan-Ding Yu
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Xiang-Li Ye
- grid.411176.40000 0004 1758 0478Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000 Fujian China
| | - Mei-Chen Jiang
- grid.411176.40000 0004 1758 0478Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, 350000 Fujian China
| | - Li-Min Chen
- Department of Respiration Medicine, Fujian Medical University Union Hospital, No.29 Xin Quan Road, Fuzhou, 350000, Fujian, China.
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Ma Z, Ma J, Lang B, Xu F, Zhang B, Wang X. Circ_0001982 Up-regulates the Expression of E2F1 by Adsorbing miR-1205 to Facilitate the Progression of Glioma. Mol Biotechnol 2023; 65:466-476. [PMID: 35994229 DOI: 10.1007/s12033-022-00540-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/14/2022] [Indexed: 11/25/2022]
Abstract
This study was aimed at probing into the regulatory effects of circular RNA (circRNA)_0001982 on glioma cell proliferation, migration, invasion, and cell cycle, and its underlying mechanism. CircRNA expression profile of glioma tissues/normal brain tissues was downloaded from the Gene Expression Omnibus (GEO) database and analyzed. Circ_0001982, microRNA (miRNA, miR)-1205, and E2F transcription factor 1 (E2F1) expressions in glioma tissues and cell lines were quantified using quantitative real-time polymerase chain reaction (qRT-PCR) and/or Western blot. Glioma cell proliferation, migration, invasion, and cell cycle were detected employing cell counting kit-8 (CCK-8), 5-Ethynyl-2'-deoxyuridine (EdU), scratch-healing, Transwell, and flow cytometry assays, respectively. The targeting relationships between miR-1205 and circ_0001982, and miR-1205 and E2F1 3'UTR were verified using bioinformatics, dual-luciferase reporter experiments, and RNA immunoprecipitation (RIP) assay. Pearson's correlation analysis was applied to detect the correlations among circ_0001982, miR-1205, and E2F1 expression levels. Circ_0001982 expression level was increased in glioma tissues and correlated with larger tumor size. Circ_0001982 overexpression enhanced glioma cell proliferation, migration, and invasion, and accelerated cell cycle progression while knocking down circ_0001982 exerted opposite effects. Circ_0001982 directly targeted miR-1205, and miR-1205 directly targeted E2F1. Besides, circ_0001982 could up-regulate E2F1 expression via repressing miR-1205 expression. Circ_0001982 accelerates glioma progression by modulating the miR-1205/E2F1 axis.
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Affiliation(s)
- Zhihui Ma
- Department of Neurosurgery, The First Hospital of Qinhuangdao, The First Hospital of Qinhuangdao, Qinhuangdao, Hebei, China
| | - Jinyang Ma
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, Hubei, China
| | - Bojuan Lang
- Department of Neurology, The First College of Clinical Medical Sciences, China Three Gorges University & Yichang Central People's Hospital, Yichang, Hubei, China.
| | - Fei Xu
- Department of Neurosurgery, Shenzhen People's Hospital, The 2nd Clinical Medical College of Jinan University, Shenzhen, 518020, Guangdong, China
| | - Bo Zhang
- Department of Neurosurgery, Shenzhen People's Hospital, The 2nd Clinical Medical College of Jinan University, Shenzhen, 518020, Guangdong, China
| | - Xiangyu Wang
- Department of Neurosurgery, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, Guangdong, China
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Oubounyt M, Elkjaer ML, Laske T, Grønning AB, Moeller M, Baumbach J. De-novo reconstruction and identification of transcriptional gene regulatory network modules differentiating single-cell clusters. NAR Genom Bioinform 2023; 5:lqad018. [PMID: 36879901 PMCID: PMC9985332 DOI: 10.1093/nargab/lqad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 01/16/2023] [Accepted: 02/09/2023] [Indexed: 03/07/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technology provides an unprecedented opportunity to understand gene functions and interactions at single-cell resolution. While computational tools for scRNA-seq data analysis to decipher differential gene expression profiles and differential pathway expression exist, we still lack methods to learn differential regulatory disease mechanisms directly from the single-cell data. Here, we provide a new methodology, named DiNiro, to unravel such mechanisms de novo and report them as small, easily interpretable transcriptional regulatory network modules. We demonstrate that DiNiro is able to uncover novel, relevant, and deep mechanistic models that not just predict but explain differential cellular gene expression programs. DiNiro is available at https://exbio.wzw.tum.de/diniro/.
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Affiliation(s)
- Mhaned Oubounyt
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Chair of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Maria L Elkjaer
- Department of Neurology, Odense University Hospital, Odense, Denmark
- Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Tanja Laske
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
| | - Alexander G B Grønning
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marcus J Moeller
- Heisenberg Chair of Preventive and Translational Nephrology, Department of Nephrology, Rheumatology and Clinical Immunology, RWTH Aachen University, Aachen, Germany
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, Hamburg, Germany
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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Dede M, Hart T. Recovering false negatives in CRISPR fitness screens with JLOE. Nucleic Acids Res 2023; 51:1637-1651. [PMID: 36727483 PMCID: PMC9976895 DOI: 10.1093/nar/gkad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 02/03/2023] Open
Abstract
It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared to false negatives. Cumulative analyses across tissues improves our understanding of core essential genes and suggest only a small number of lineage-specific essential genes, enriched for transcription factors that define pathways of tissue differentiation. To recover false negatives, we introduce a method, Joint Log Odds of Essentiality (JLOE), which builds on our prior work with BAGEL to selectively rescue the false negatives without an increased false discovery rate.
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Affiliation(s)
- Merve Dede
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Traver Hart
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Turki T, Taguchi YH. A new machine learning based computational framework identifies therapeutic targets and unveils influential genes in pancreatic islet cells. Gene 2023; 853:147038. [PMID: 36503891 DOI: 10.1016/j.gene.2022.147038] [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: 09/16/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022]
Abstract
Pancreatic islets comprise a group of cells that produce hormones regulating blood glucose levels. Particularly, the alpha and beta islet cells produce glucagon and insulin to stabilize blood glucose. When beta islet cells are dysfunctional, insulin is not secreted, inducing a glucose metabolic disorder. Identifying effective therapeutic targets against the disease is a complicated task and is not yet conclusive. To close the wide gap between understanding the molecular mechanism of pancreatic islet cells and providing effective therapeutic targets, we present a computational framework to identify potential therapeutic targets against pancreatic disorders. First, we downloaded three transcriptome expression profiling datasets pertaining to pancreatic islet cells (GSE87375, GSE79457, GSE110154) from the Gene Expression Omnibus database. For each dataset, we extracted expression profiles for two cell types. We then provided these expression profiles along with the cell types to our proposed constrained optimization problem of a support vector machine and to other existing methods, selecting important genes from the expression profiles. Finally, we performed (1) an evaluation from a classification perspective which showed the superiority of our methods against the baseline; and (2) an enrichment analysis which indicated that our methods achieved better outcomes. Results for the three datasets included 44 unique genes and 10 unique transcription factors (SP1, HDAC1, EGR1, E2F1, AR, STAT6, RELA, SP3, NFKB1, and ESR1) which are reportedly related to pancreatic islet functions, diseases, and therapeutic targets.
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Affiliation(s)
- Turki Turki
- King Abdulaziz University, Department of Computer Science, Jeddah 21589, Saudi Arabia.
| | - Y-H Taguchi
- Chuo University, Department of Physics, Tokyo 112-8551, Japan.
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Wang P, Wang HY, Gao XJ, Zhu HX, Zhang XP, Liu F, Wang W. Encoding and Decoding of p53 Dynamics in Cellular Response to Stresses. Cells 2023; 12:cells12030490. [PMID: 36766831 PMCID: PMC9914463 DOI: 10.3390/cells12030490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/20/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
In the cellular response to stresses, the tumor suppressor p53 is activated to maintain genomic integrity and fidelity. As a transcription factor, p53 exhibits rich dynamics to allow for discrimination of the type and intensity of stresses and to direct the selective activation of target genes involved in different processes including cell cycle arrest and apoptosis. In this review, we focused on how stresses are encoded into p53 dynamics and how the dynamics are decoded into cellular outcomes. Theoretical modeling may provide a global view of signaling in the p53 network by coupling the encoding and decoding processes. We discussed the significance of modeling in revealing the mechanisms of the transition between p53 dynamic modes. Moreover, we shed light on the crosstalk between the p53 network and other signaling networks. This review may advance the understanding of operating principles of the p53 signaling network comprehensively and provide insights into p53 dynamics-based cancer therapy.
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Affiliation(s)
- Ping Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- Key Laboratory of High Performance Scientific Computation, School of Science, Xihua University, Chengdu 610039, China
| | - Hang-Yu Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Xing-Jie Gao
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Hua-Xia Zhu
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Xiao-Peng Zhang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- Correspondence: (X.-P.Z.); (W.W.)
| | - Feng Liu
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
- Department of Physics, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- Institute of Brain Sciences, Nanjing University, Nanjing 210093, China
- National Laboratory of Solid State Microstructure, Nanjing University, Nanjing 210093, China
- Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (X.-P.Z.); (W.W.)
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Dehydrovomifoliol Alleviates Nonalcoholic Fatty Liver Disease via the E2F1/AKT/mTOR Axis: Pharmacophore Modeling and Molecular Docking Study. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2023; 2023:9107598. [PMID: 36777627 PMCID: PMC9908351 DOI: 10.1155/2023/9107598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023]
Abstract
Objective Herbal medicine discovery is a complex and time-consuming process, while pharmacophore modeling and molecular docking methods enable simple and economic studies. The pharmacophore model provides an abstract description of essential intermolecular interactions between chemical structures, and the molecular docking technology can identify novel compounds of therapeutic interests and predict the ligand-target interaction at the molecular level. This study was based on the two methods to elucidate the mechanism of dehydrovomifoliol, an active ingredient extracted from Artemisia frigida willd, in nonalcoholic fatty liver disease (NAFLD). Methods Bioinformatics analysis was performed to screen target genes of dehydrovomifoliol in NAFLD treatment, which were thus intersected with NAFLD-related differentially expressed genes (DEGs) and NAFLD-related genes. Venn diagram was used to identify candidate DEGs. A pharmacophore model was then generated, and molecular docking was performed. A protein-protein interaction (PPI) network was constructed to identify core genes, which were evaluated using GO and the KEGG enrichment analyses. Results Seven target genes of dehydrovomifoliol in NAFLD treatment were screened out, namely E2F1, MERTK, SOX17, MMP9, SULT2A1, VEGFA, and BLVRA. The pharmacophore model and molecular docking of candidate DEGs and dehydrovomifoliol were successfully constructed. E2F1 was identified as a core gene of dehydrovomifoliol in NAFLD treatment. Further enrichment analysis indicated the regulatory role of E2F1 in fat metabolism was associated with the regulation of the AKT/mTOR signaling pathway. Conclusion Overall, this study illustrates the anti-NAFLD mechanism of dehydrovomifoliol, which could be a useful compound for developing novel drugs in the treatment of NAFLD.
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İlhan A, Golestani S, Shafagh SG, Asadi F, Daneshdoust D, Al-Naqeeb BZT, Nemati MM, Khalatbari F, Yaseri AF. The dual role of microRNA (miR)-20b in cancers: Friend or foe? Cell Commun Signal 2023; 21:26. [PMID: 36717861 PMCID: PMC9885628 DOI: 10.1186/s12964-022-01019-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/14/2022] [Indexed: 01/31/2023] Open
Abstract
MicroRNAs, as non-coding transcripts, modulate gene expression through RNA silencing under normal physiological conditions. Their aberrant expression has strongly associated with tumorigenesis and cancer development. MiR-20b is one of the crucial miRNAs that regulate essential biological processes such as cell proliferation, apoptosis, autophagy, and migration. Deregulated levels of miR-20b contribute to the early- and advanced stages of cancer. On the other hand, investigations emphasize the tumor suppressor ability of miR-20b. High-throughput strategies are developed to identify miR-20b potential targets, providing the proper insight into its molecular mechanism of action. Moreover, accumulated results suggest that miR-20b exerts its effects through diverse signaling pathways, including PI3K/AKT/mTOR and ERK axes. Restoration of the altered expression levels of miR-20b induces cell apoptosis and reduces invasion and migration. Further, miR-20b can be used as a biomarker in cancer. The current comprehensive review could lead to a better understanding of the miR-20b in either tumorigenesis or tumor regression that may open new avenues for cancer treatment. Video Abstract.
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Affiliation(s)
- Ahmet İlhan
- grid.98622.370000 0001 2271 3229Department of Medical Biochemistry, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Shayan Golestani
- grid.411757.10000 0004 1755 5416Department of Oral and Maxillofacial Surgery, Dental School, Islamic Azad University, Isfahan (Khorasgan) Branch, Isfahan, Iran
| | - Seyyed Ghavam Shafagh
- grid.411746.10000 0004 4911 7066Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Asadi
- grid.488474.30000 0004 0494 1414Department of Genetics, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Danyal Daneshdoust
- grid.411495.c0000 0004 0421 4102School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | | | - Mohammed Mahdi Nemati
- grid.412763.50000 0004 0442 8645Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Fateme Khalatbari
- grid.411768.d0000 0004 1756 1744Department of Pathology, Mashhad Medical Sciences Branch, Islamic Azad University, Mashhad, Iran
| | - Amirhossein Fakhre Yaseri
- grid.412606.70000 0004 0405 433XDepartment of Genetic, Faculty of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran
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Vadrot N, Ader F, Moulin M, Merlant M, Chapon F, Gandjbakhch E, Labombarda F, Maragnes P, Réant P, Rooryck C, Probst V, Donal E, Richard P, Ferreiro A, Buendia B. Abnormal Cellular Phenotypes Induced by Three TMPO/LAP2 Variants Identified in Men with Cardiomyopathies. Cells 2023; 12:337. [PMID: 36672271 PMCID: PMC9857342 DOI: 10.3390/cells12020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
A single missense variant of the TMPO/LAP2α gene, encoding LAP2 proteins, has been associated with cardiomyopathy in two brothers. To further evaluate its role in cardiac muscle, we included TMPO in our cardiomyopathy diagnostic gene panel. A screening of ~5000 patients revealed three novel rare TMPO heterozygous variants in six males diagnosed with hypertrophic or dilated cardiomypathy. We identified in different cellular models that (1) the frameshift variant LAP2α p.(Gly395Glufs*11) induced haploinsufficiency, impeding cell proliferation and/or producing a truncated protein mislocalized in the cytoplasm; (2) the C-ter missense variant LAP2α p.(Ala240Thr) led to a reduced proximity events between LAP2α and the nucleosome binding protein HMGN5; and (3) the LEM-domain missense variant p.(Leu124Phe) decreased both associations of LAP2α/β with the chromatin-associated protein BAF and inhibition of the E2F1 transcription factor activity which is known to be dependent on Rb, partner of LAP2α. Additionally, the LAP2α expression was lower in the left ventricles of male mice compared to females. In conclusion, our study reveals distinct altered properties of LAP2 induced by these TMPO/LAP2 variants, leading to altered cell proliferation, chromatin structure or gene expression-regulation pathways, and suggests a potential sex-dependent role of LAP2 in myocardial function and disease.
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Affiliation(s)
- Nathalie Vadrot
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Flavie Ader
- APHP—Sorbonne Université, Unité Fonctionnelle de Cardiogénétique et Myogénétique Moléculaire, Service de Biochimie Métabolique, HU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
- Faculté de Pharmacie Paris Descartes, Département 3, Université Paris Cité, F-75006 Paris, France
| | - Maryline Moulin
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Marie Merlant
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | | | - Estelle Gandjbakhch
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
- Département de cardiologie, APHP—Sorbonne Université, HU Pitié Salpêtrière- Charles Foix, F-75610 Paris, France
| | - Fabien Labombarda
- Service de Cardiologie, CHU de Caen, Université de Caen Normandie, F-14000 Caen, France
| | - Pascale Maragnes
- Cardiologie pédiatrique, Service de pédiatrie, CHU de Caen, F-14000 Caen, France
| | - Patricia Réant
- Service de Cardiologie, Hôpital Haut Lévêque, CHU de Bordeaux, INSERM 1045, Université de Bordeaux, F-33000 Bordeaux, France
| | - Caroline Rooryck
- Service de Génétique Médicale, CHU Bordeaux, F-33000 Bordeaux, France
| | - Vincent Probst
- Centre de référence des maladies rythmiques cardiaques, CHU de Nantes, F-44000 Nantes, France
| | - Erwan Donal
- Centre Cardio-Pneumologique, CHU de Rennes Hôpital de Pontchaillou, F-35000 Rennes, France
| | - Pascale Richard
- APHP—Sorbonne Université, Unité Fonctionnelle de Cardiogénétique et Myogénétique Moléculaire, Service de Biochimie Métabolique, HU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
- INSERM, UMR_S 1166, Sorbonne Université, F-75005 Paris, France
| | - Ana Ferreiro
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
- APHP, Centre de référence des Maladies Neuromusculaires, Institut de Myologie, Neuromyology Department, CHU Pitié Salpêtrière—Charles Foix, F-75013 Paris, France
| | - Brigitte Buendia
- Basic and Translational Myology Laboratory, Université Paris Cité, BFA, UMR 8251, CNRS, F-75013 Paris, France
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Zangouei AS, Zangoue M, Taghehchian N, Zangooie A, Rahimi HR, Saburi E, Alavi MS, Moghbeli M. Cell cycle related long non-coding RNAs as the critical regulators of breast cancer progression and metastasis. Biol Res 2023; 56:1. [PMID: 36597150 PMCID: PMC9808980 DOI: 10.1186/s40659-022-00411-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Cell cycle is one of the main cellular mechanisms involved in tumor progression. Almost all of the active molecular pathways in tumor cells directly or indirectly target the cell cycle progression. Therefore, it is necessary to assess the molecular mechanisms involved in cell cycle regulation in tumor cells. Since, early diagnosis has pivotal role in better cancer management and treatment, it is required to introduce the non-invasive diagnostic markers. Long non-coding RNAs (LncRNAs) have higher stability in body fluids in comparison with mRNAs. Therefore, they can be used as efficient non-invasive markers for the early detection of breast cancer (BCa). In the present review we have summarized all of the reported lncRNAs involved in cell cycle regulation in BCa. It has been reported that lncRNAs mainly affect the cell cycle in G1/S transition through the CCND1/CDK4-6 complex. Present review paves the way of introducing the cell cycle related lncRNAs as efficient markers for the early detection of BCa.
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Affiliation(s)
- Amir Sadra Zangouei
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Zangoue
- grid.411701.20000 0004 0417 4622Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran ,grid.411701.20000 0004 0417 4622Department of Anesthesiology, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Negin Taghehchian
- grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Zangooie
- grid.411701.20000 0004 0417 4622Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran ,grid.411701.20000 0004 0417 4622Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamid Reza Rahimi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahya Sadat Alavi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Abballe L, Alfano V, Antonacci C, Cefalo MG, Cacchione A, Del Baldo G, Pezzullo M, Po A, Moretti M, Mastronuzzi A, De Smaele E, Ferretti E, Locatelli F, Miele E. β-arrestin1-E2F1-ac axis regulates physiological apoptosis and cell cycle exit in cellular models of early postnatal cerebellum. Front Cell Dev Biol 2023; 11:990711. [PMID: 36923256 PMCID: PMC10010392 DOI: 10.3389/fcell.2023.990711] [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: 07/10/2022] [Accepted: 02/17/2023] [Indexed: 03/01/2023] Open
Abstract
Development of the cerebellum is characterized by rapid proliferation of cerebellar granule cell precursors (GCPs) induced by paracrine stimulation of Sonic hedgehog (Shh) signaling from Purkinje cells, in the external granular layer (EGL). Then, granule cell precursors differentiate and migrate into the inner granular layer (IGL) of the cerebellum to form a terminally differentiated cell compartment. Aberrant activation of Sonic hedgehog signaling leads to granule cell precursors hyperproliferation and the onset of Sonic hedgehog medulloblastoma (MB), the most common embryonal brain tumor. β-arrestin1 (ARRB1) protein plays an important role downstream of Smoothened, a component of the Sonic hedgehog pathway. In the medulloblastoma context, β-arrestin1 is involved in a regulatory axis in association with the acetyltransferase P300, leading to the acetylated form of the transcription factor E2F1 (E2F1-ac) and redirecting its activity toward pro-apoptotic gene targets. This axis in the granule cell precursors physiological context has not been investigated yet. In this study, we demonstrate that β-arrestin1 has antiproliferative and pro-apoptotic functions in cerebellar development. β-arrestin1 silencing increases proliferation of Sonic hedgehog treated-cerebellar precursor cells while decreases the transcription of E2F1-ac pro-apoptotic targets genes, thus impairing apoptosis. Indeed, chromatin immunoprecipitation experiments show a direct interaction between β-arrestin1 and the promoter regions of the pro-apoptotic E2F1 target gene and P27, indicating the double role of β-arrestin1 in controlling apoptosis and cell cycle exit in a physiological context. Our data elucidate the role of β-arrestin1 in the early postnatal stages of cerebellar development, in those cell compartments that give rise to medulloblastoma. This series of experiments suggests that the physiological function of β-arrestin1 in neuronal progenitors is to directly control, cooperating with E2F1 acetylated form, transcription of pro-apoptotic genes.
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Affiliation(s)
- Luana Abballe
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Vincenzo Alfano
- Cancer Research Center of Lyon (CRCL), UMR Inserm U1052/CNRS 5286, Lyon, France
| | - Celeste Antonacci
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Maria Giuseppina Cefalo
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Antonella Cacchione
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Giada Del Baldo
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Marco Pezzullo
- Pathology Unit, Core Research Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Agnese Po
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Marta Moretti
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Angela Mastronuzzi
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
| | - Enrico De Smaele
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy.,Department of Gynecology/Obstetrics and Paediatrics, Sapienza University, Rome, Italy
| | - Evelina Miele
- Department of Pediatric Hematology/Oncology and Cellular and Gene Therapy, Bambino Gesù Children's Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, Rome, Italy
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Shah ZA, Nouroz F, Ejaz S, Tayyeb A. An Insight into the Role of E2F1 in Breast Cancer Progression, Drug Resistance, and Metastasis. Curr Mol Med 2023; 23:365-376. [PMID: 35260053 DOI: 10.2174/1566524022666220308095834] [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: 05/15/2021] [Revised: 11/25/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022]
Abstract
AIMS This study aimed to investigate the role of E2F1 in breast cancer biology. BACKGROUND Expression of E2F1, a transcription factor of many oncogenes and tumor suppressor genes, is lowered in several malignancies, including breast carcinoma. OBJECTIVES In the present study, we analyzed the status of E2F1 expression in association with diverse attributes of breast malignancy and its impact on cancer progression. METHODS For this purpose, we used various freely available online applications for gene enrichment, expression, and methylation analysis to extract mutation-based E2F1 map, to measure E2F1 drug sensitivity, and to determine E2F1 association with DNA damage response proteins. RESULTS Results revealed tissue-specific regulatory behavior of E2F1. Moreover, the key role of E2F1 in the promotion of metastasis, stem cell-mediated carcinogenesis, estrogen-mediated cell proliferation, and cellular defense system, has therefore highlighted it as a metaplastic marker and hot member of key resistome pathways. CONCLUSION The information thus generated can be employed for future implications in devising rational therapeutic strategies. Moreover, this study has provided a more detailed insight into the diagnostic and prognostic potential of E2F1.
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Affiliation(s)
- Zafar Abbas Shah
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Faisal Nouroz
- Department of Bioinformatics, Hazara University Mansehra, Mansehra, Pakistan
| | - Samina Ejaz
- Department of Biochemistry, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Asima Tayyeb
- School of Biological Sciences, University of the Punjab, Lahore, Pakistan
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48
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Du J, Rui F, Hao Z, Hang Y, Shu J. Transcription Factor E2F1 Regulates the Expression of ADRB2. Int J Anal Chem 2023; 2023:8210685. [PMID: 37128280 PMCID: PMC10148742 DOI: 10.1155/2023/8210685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/09/2023] [Accepted: 02/24/2023] [Indexed: 05/03/2023] Open
Abstract
Adrenergic beta-2-receptor (ADRB2) is highly expressed in various tissue cells, affecting the susceptibility, development, and drug efficacy of diseases such as bronchial asthma and malignant tumor. However, the transcriptional regulatory mechanism of the human ADRB2 gene remains unclear. This study aimed to clarify whether E2F transcription factor 1 (E2F1) was involved in the transcriptional regulation of the human ADRB2 gene. First, the 5' flanking region of the human ADRB2 gene was cloned, and its activity was detected using A549 and BEAS-2B cells. Second, it was found that the overexpression of E2F1 could increase promoter activity by a dual-luciferase reporter gene assay. In contrast, treatment of knockdown of E2F1 significantly resulted in a decrease in its promoter activity. Moreover, mutation of the binding site of E2F1 greatly reduced the potential of human ADRB2 promoter transcriptional activity to be regulated by E2F1 overexpression and knockdown. Additionally, by real-time quantitative PCR and Western blot analysis, we demonstrated that overexpression of E2F1 elevated the ADRB2 mRNA expression and protein levels while si-E2F1 reduced its expression. Finally, the consequence of the chromatin immunoprecipitation assay showed that E2F1 was able to bind to the promoter region of ADRB2 in vivo. These results confirmed that E2F1 upregulated the expression of the human ADRB2 gene.
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Affiliation(s)
- Juan Du
- Department of Pediatrics, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Feifei Rui
- Department of Neonatology, Changzhou Maternal and Child Health Hospital, Changzhou, Jiangsu, China
| | - Zhongfen Hao
- Department of Pediatrics, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yun Hang
- Department of Pediatrics, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jin Shu
- Department of Pediatrics, The Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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49
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Chen Y, Yu Y, Lv M, Shi Q, Li X. E2F1-mediated up-regulation of TOP2A promotes viability, migration, and invasion, and inhibits apoptosis of gastric cancer cells. J Biosci 2022. [DOI: 10.1007/s12038-022-00322-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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50
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Liu Z, Shi H, Xu J, Yang Q, Ma Q, Mao X, Xu Z, Zhou Y, Da Q, Cai Y, Fulton DJ, Dong Z, Sodhi A, Caldwell RB, Huo Y. Single-cell transcriptome analyses reveal microglia types associated with proliferative retinopathy. JCI Insight 2022; 7:160940. [PMID: 36264636 PMCID: PMC9746914 DOI: 10.1172/jci.insight.160940] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 10/18/2022] [Indexed: 01/14/2023] Open
Abstract
Pathological angiogenesis is a major cause of irreversible blindness in individuals of all age groups with proliferative retinopathy (PR). Mononuclear phagocytes (MPs) within neovascular areas contribute to aberrant retinal angiogenesis. Due to their cellular heterogeneity, defining the roles of MP subsets in PR onset and progression has been challenging. Here, we aimed to investigate the heterogeneity of microglia associated with neovascularization and to characterize the transcriptional profiles and metabolic pathways of proangiogenic microglia in a mouse model of oxygen-induced PR (OIR). Using transcriptional single-cell sorting, we comprehensively mapped all microglia populations in retinas of room air (RA) and OIR mice. We have unveiled several unique types of PR-associated microglia (PRAM) and identified markers, signaling pathways, and regulons associated with these cells. Among these microglia subpopulations, we found a highly proliferative microglia subset with high self-renewal capacity and a hypermetabolic microglia subset that expresses high levels of activating microglia markers, glycolytic enzymes, and proangiogenic Igf1. IHC staining shows that these PRAM were spatially located within or around neovascular tufts. These unique types of microglia have the potential to promote retinal angiogenesis, which may have important implications for future treatment of PR and other pathological ocular angiogenesis-related diseases.
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Affiliation(s)
- Zhiping Liu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Huidong Shi
- Georgia Cancer Center and,Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Jiean Xu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qiuhua Yang
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qian Ma
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Xiaoxiao Mao
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Zhimin Xu
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Yaqi Zhou
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Qingen Da
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yongfeng Cai
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - David J.R. Fulton
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Zheng Dong
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Charlie Norwood Veterans Affairs Medical Center, Augusta, Georgia, USA
| | - Akrit Sodhi
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Ruth B. Caldwell
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Yuqing Huo
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA.,James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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