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Liu Y, Feng H, Zhao Q, Liang X, Wang Y, Xiao S, Shen S, Wu J. RNA binding motif protein 43 (RBM43) suppresses hepatocellular carcinoma metastasis by regulating Slug mRNA stability. Genes Dis 2024; 11:101192. [PMID: 39104422 PMCID: PMC11298866 DOI: 10.1016/j.gendis.2023.101192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/19/2023] [Indexed: 08/07/2024] Open
Affiliation(s)
- Yao Liu
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Huan Feng
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qi Zhao
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao Liang
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ying Wang
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuai Xiao
- The First Affiliated Hospital, Cancer Research Institute, Department of Gastrointestinal Surgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Suqin Shen
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiaxue Wu
- State Key Laboratory of Genetic Engineering and School of Life Sciences, Fudan University, Shanghai 200438, China
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Zhang P, Zhang W, Wang X, Li L, Lin Y, Wu N, Mao R, Lin J, Kang M, Ding C. BCLAF1 drives esophageal squamous cell carcinoma progression through regulation of YTHDF2-dependent SIX1 mRNA degradation. Cancer Lett 2024; 591:216874. [PMID: 38636894 DOI: 10.1016/j.canlet.2024.216874] [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: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/07/2024] [Indexed: 04/20/2024]
Abstract
Esophageal cancer ranks among the most prevalent malignant tumors, and esophageal squamous cell carcinoma (ESCC) constitutes its predominant histological form. Despite its impact, a thorough insight into the molecular intricacies of ESCC's development is still incomplete, which hampers the advancement of targeted molecular diagnostics and treatments. Recently, B-cell lymphoma-2-associated transcription factor 1 (BCLAF1) has come under investigation for its potential involvement in tumor biology, yet its specific role and mechanism in ESCC remain unclear. In this study, we observed a marked increase in BCLAF1 expression in ESCC tissues, correlating with advanced tumor stages and inferior patient outcomes. Our comprehensive in vitro and in vivo studies show that BCLAF1 augments glycolytic activity and the proliferation, invasion, and spread of ESCC cells. By employing mass spectrometry, we identified YTHDF2 as a key protein interacting with BCLAF1 in ESCC, with further validation provided by colocalization, co-immunoprecipitation, and GST pull-down assay. Further investigations involving MeRIP-seq and RIP-seq, alongside transcriptomic analysis, highlighted SIX1 mRNA as a molecule significantly upregulated and modified by N6-methyladenosine (m6A) in BCLAF1 overexpressing cells. BCLAF1 was found to reduce the tumor-suppressive activities of YTHDF2, and its effects on promoting glycolysis and cancer progression were shown to hinge on SIX1 expression. This research establishes that BCLAF1 fosters glycolysis and tumor progression in ESCC through the YTHDF2-SIX1 pathway in an m6A-specific manner, suggesting a potential target for future therapeutic intervention.
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Affiliation(s)
- Peipei Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Weiguang Zhang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Xiaoqing Wang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Lingling Li
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China
| | - Ye Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Ningzi Wu
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Renyan Mao
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Jihong Lin
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Mingqiang Kang
- Department of Thoracic Surgery, Fujian Medical University Union Hospital, Fuzhou, 350001, China; Department of Cardiothoracic Surgery, Affiliated Hospital of Putian University, Putian, 351100, China; Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, 350108, China.
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institutes of Biomedical Sciences, Human Phenome Institute, Fudan University, Shanghai, 200433, China.
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Wang D, Wang S, Jin M, Zuo Y, Wang J, Niu Y, Zhou Q, Chen J, Tang X, Tang W, Liu X, Yu H, Yan W, Wei H, Huang G, Song S, Tang S. Hypoxic Exosomal circPLEKHM1-Mediated Crosstalk between Tumor Cells and Macrophages Drives Lung Cancer Metastasis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309857. [PMID: 38509870 PMCID: PMC11165461 DOI: 10.1002/advs.202309857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Intercellular communication often relies on exosomes as messengers and is critical for cancer metastasis in hypoxic tumor microenvironment. Some circular RNAs (circRNAs) are enriched in cancer cell-derived exosomes, but little is known about their ability to regulate intercellular communication and cancer metastasis. Here, by systematically analyzing exosomes secreted by non-small cell lung cancer (NSCLC) cells, a hypoxia-induced exosomal circPLEKHM1 is identified that drives NSCLC metastasis through polarizing macrophages toward to M2 type. Mechanistically, exosomal circPLEKHM1 promoted PABPC1-eIF4G interaction to facilitate the translation of the oncostatin M receptor (OSMR), thereby promoting macrophage polarization for cancer metastasis. Importantly, circPLEKHM1-targeted therapy significantly reduces NSCLC metastasis in vivo. circPLEKHM1 serves as a prognostic biomarker for metastasis and poor survival in NSCLC patients. This study unveils a new circRNA-mediated mechanism underlying how cancer cells crosstalk with macrophages within the hypoxic tumor microenvironment to promote metastasis, highlighting the importance of exosomal circPLEKHM1 as a prognostic biomarker and therapeutic target for lung cancer metastasis.
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Lyu J, Bai L, Li Y, Wang X, Xu Z, Ji T, Yang H, Song Z, Wang Z, Shang Y, Ren L, Li Y, Zang A, Jia Y, Ding C. Plasma proteome profiling reveals dynamic of cholesterol marker after dual blocker therapy. Nat Commun 2024; 15:3860. [PMID: 38719824 PMCID: PMC11078984 DOI: 10.1038/s41467-024-47835-y] [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: 06/28/2023] [Accepted: 04/10/2024] [Indexed: 05/12/2024] Open
Abstract
Dual blocker therapy (DBT) has the enhanced antitumor benefits than the monotherapy. Yet, few effective biomarkers are developed to monitor the therapy response. Herein, we investigate the DBT longitudinal plasma proteome profiling including 113 longitudinal samples from 22 patients who received anti-PD1 and anti-CTLA4 DBT therapy. The results show the immune response and cholesterol metabolism are upregulated after the first DBT cycle. Notably, the cholesterol metabolism is activated in the disease non-progressive group (DNP) during the therapy. Correspondingly, the clinical indicator prealbumin (PA), free triiodothyronine (FT3) and triiodothyronine (T3) show significantly positive association with the cholesterol metabolism. Furthermore, by integrating proteome and radiology approach, we observe the high-density lipoprotein partial remodeling are activated in DNP group and identify a candidate biomarker APOC3 that can reflect DBT response. Above, we establish a machine learning model to predict the DBT response and the model performance is validated by an independent cohort with balanced accuracy is 0.96. Thus, the plasma proteome profiling strategy evaluates the alteration of cholesterol metabolism and identifies a panel of biomarkers in DBT.
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Affiliation(s)
- Jiacheng Lyu
- Center for Cell and Gene Therapy, Fudan University Clinical Research Center for Cell-based Immunotherapy, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Shanghai Pudong Hospital, Fudan University, Shanghai, 200433, China
| | - Lin Bai
- Center for Cell and Gene Therapy, Fudan University Clinical Research Center for Cell-based Immunotherapy, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Shanghai Pudong Hospital, Fudan University, Shanghai, 200433, China
| | - Yumiao Li
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Xiaofang Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Zeya Xu
- Center for Cell and Gene Therapy, Fudan University Clinical Research Center for Cell-based Immunotherapy, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Shanghai Pudong Hospital, Fudan University, Shanghai, 200433, China
| | - Tao Ji
- Center for Cell and Gene Therapy, Fudan University Clinical Research Center for Cell-based Immunotherapy, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Shanghai Pudong Hospital, Fudan University, Shanghai, 200433, China
| | - Hua Yang
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Zizheng Song
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Zhiyu Wang
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Yanhong Shang
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Lili Ren
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Yan Li
- Department of Haematology, Hebei General Hospital, No. 348, Heping West Road, Shijiazhuang, Hebei, 050051, China
| | - Aimin Zang
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China
| | - Youchao Jia
- Department of Medical Oncology, Affiliated Hospital of Hebei University; Hebei Key Laboratory of Cancer Radiotherapy and Chemotherapy, 212 Yuhua East Road, Baoding, Hebei, 071000, China.
| | - Chen Ding
- Center for Cell and Gene Therapy, Fudan University Clinical Research Center for Cell-based Immunotherapy, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Shanghai Pudong Hospital, Fudan University, Shanghai, 200433, China.
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Wang J, Tan S, Zhang Y, Xu J, Li Y, Cheng Q, Ding C, Liu X, Chang J. Set7/9 aggravates ischemic brain injury via enhancing glutamine metabolism in a blocking Sirt5 manner. Cell Death Differ 2024; 31:511-523. [PMID: 38365969 PMCID: PMC11043079 DOI: 10.1038/s41418-024-01264-y] [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: 07/09/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
The aberrant expression of methyltransferase Set7/9 plays a role in various diseases. However, the contribution of Set7/9 in ischemic stroke remains unclear. Here, we show ischemic injury results in a rapid elevation of Set7/9, which is accompanied by the downregulation of Sirt5, a deacetylase reported to protect against injury. Proteomic analysis identifies the decrease of chromobox homolog 1 (Cbx1) in knockdown Set7/9 neurons. Mechanistically, Set7/9 promotes the binding of Cbx1 to H3K9me2/3 and forms a transcription repressor complex at the Sirt5 promoter, ultimately repressing Sirt5 transcription. Thus, the deacetylation of Sirt5 substrate, glutaminase, which catalyzes the hydrolysis of glutamine to glutamate and ammonia, is decreased, promoting glutaminase expression and triggering excitotoxicity. Blocking Set7/9 eliminates H3K9me2/3 from the Sirt5 promoter and normalizes Sirt5 expression and Set7/9 knockout efficiently ameliorates brain ischemic injury by reducing the accumulation of ammonia and glutamate in a Sirt5-dependent manner. Collectively, the Set7/9-Sirt5 axis may be a promising epigenetic therapeutic target.
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Affiliation(s)
- Jinghuan Wang
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Subei Tan
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 201203, China
| | - Yuyu Zhang
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Jie Xu
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Yuhui Li
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Qianwen Cheng
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, 201203, China.
| | - Xinhua Liu
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China.
| | - Jun Chang
- Shanghai Key Labortary of Vascular Lesions Regulation and Remodeling, Shanghai Pudong Hospital, Pharmacophenomics Laboratory, Human Phenome Institute, Fudan University, Shanghai, 201203, China.
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Berggren KA, Schwartz RE, Kleiner RE, Ploss A. The impact of epitranscriptomic modifications on liver disease. Trends Endocrinol Metab 2024; 35:331-346. [PMID: 38212234 DOI: 10.1016/j.tem.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024]
Abstract
RNA modifications have emerged as important mechanisms of gene regulation. Developmental, metabolic, and cell cycle regulatory processes are all affected by epitranscriptomic modifications, which control gene expression in a dynamic manner. The hepatic tissue is highly metabolically active and has an impressive ability to regenerate after injury. Cell proliferation, differentiation, and metabolism, which are all essential to the liver response to injury and regeneration, are regulated via RNA modification. Two such modifications, N6-methyladenosine (m6A)and 5-methylcytosine (m5C), have been identified as prognostic disease markers and potential therapeutic targets for liver diseases. Here, we describe progress in understanding the role of RNA modifications in liver biology and disease and discuss specific areas where unexpected results could lead to improved future understanding.
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Affiliation(s)
- Keith A Berggren
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Ralph E Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Alexander Ploss
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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Kim Y, Jung KY, Kim YH, Xu P, Kang BE, Jo Y, Pandit N, Kwon J, Gariani K, Gariani J, Lee J, Verbeek J, Nam S, Bae SJ, Ha KT, Yi HS, Shong M, Kim KH, Kim D, Jung HJ, Lee CW, Kim KR, Schoonjans K, Auwerx J, Ryu D. Inhibition of SIRT7 overcomes sorafenib acquired resistance by suppressing ERK1/2 phosphorylation via the DDX3X-mediated NLRP3 inflammasome in hepatocellular carcinoma. Drug Resist Updat 2024; 73:101054. [PMID: 38277756 PMCID: PMC10935544 DOI: 10.1016/j.drup.2024.101054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 01/28/2024]
Abstract
AIMS Sirtuin 7 (SIRT7) plays an important role in tumor development, and has been characterized as a potent regulator of cellular stress. However, the effect of SIRT7 on sorafenib acquired resistance remains unclear and a possible anti-tumor mechanism beyond this process in HCC has not been clarified. We examined the therapeutic potential of SIRT7 and determined whether it functions synergistically with sorafenib to overcome chemoresistance. METHODS Cancer Genome Atlas-liver HCC data and unbiased gene set enrichment analyses were used to identify SIRT7 as a potential effector molecule in sorafenib acquired resistance. Two types of SIRT7 chemical inhibitors were developed to evaluate its therapeutic properties when synergized with sorafenib. Mass spectrometry was performed to discover a direct target of SIRT7, DDX3X, and DDX3X deacetylation levels and protein stability were explored. Moreover, an in vivo xenograft model was used to confirm anti-tumor effect of SIRT7 and DDX3X chemical inhibitors combined with sorafenib. RESULTS SIRT7 inhibition mediated DDX3X depletion can re-sensitize acquired sorafenib resistance by disrupting NLRP3 inflammasome assembly, finally suppressing hyperactive ERK1/2 signaling in response to NLRP3 inflammasome-mediated IL-1β inhibition. CONCLUSIONS SIRT7 is responsible for sorafenib acquired resistance, and its inhibition would be beneficial when combined with sorafenib by suppressing hyperactive pro-cell survival ERK1/2 signaling.
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Affiliation(s)
- Yuna Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea.
| | - Kwan-Young Jung
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Yun Hak Kim
- Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea; Department of Biomedical Informatics, School of Medicine, Pusan National University, Yangsan, Republic of Korea
| | - Pan Xu
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Baeki E Kang
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Yunju Jo
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Navin Pandit
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Jeongho Kwon
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Karim Gariani
- Service of Endocrinology, Diabetes, Nutrition and Therapeutic Patient Education, Geneva University Hospitals, Geneva, Switzerland
| | - Joanna Gariani
- Department of radiology, Hirslanden Grangettes Clinic, Geneva, Switzerland
| | - Junguee Lee
- Department of Pathology, Daejeon St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Daejeon, Republic of Korea
| | - Jef Verbeek
- Laboratory of Hepatology, Department of Chronic Diseases and Metabolism (CHROMETA), KU Leuven, Belgium; Department of Gastroenterology and Hepatology, University Hospitals KU Leuven, Leuven, Belgium
| | - Seungyoon Nam
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea; Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Republic of Korea
| | - Sung-Jin Bae
- Department of Molecular Biology and Immunology, Kosin University College of Medicine, Busan, Republic of Korea
| | - Ki-Tae Ha
- Department of Korean Medical Science, Pusan National University School of Korean Medicine, Yangsan, Republic of Korea
| | - Hyon-Seung Yi
- Laboratory of Endocrinology and Immune System, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Minho Shong
- Research Center for Endocrine and Metabolic Diseases, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Kyun-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Doyoun Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Hee Jung Jung
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kwang Rok Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, Daejeon, Republic of Korea.
| | - Kristina Schoonjans
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea; Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea.
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Piranfar A, Souri M, Rahmim A, Soltani M. Localized radiotherapy of solid tumors using radiopharmaceutical loaded implantable system: insights from a mathematical model. Front Oncol 2024; 14:1320371. [PMID: 38559559 PMCID: PMC10979490 DOI: 10.3389/fonc.2024.1320371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/06/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Computational models yield valuable insights into biological interactions not fully elucidated by experimental approaches. This study investigates an innovative spatiotemporal model for simulating the controlled release and dispersion of radiopharmaceutical therapy (RPT) using 177Lu-PSMA, a prostate-specific membrane antigen (PSMA) targeted radiopharmaceutical, within solid tumors via a dual-release implantable delivery system. Local delivery of anticancer agents presents a strategic approach to mitigate adverse effects while optimizing therapeutic outcomes. Methods This study evaluates various factors impacting RPT efficacy, including hypoxia region extension, binding affinity, and initial drug dosage, employing a novel 3-dimensional computational model. Analysis gauges the influence of these factors on radiopharmaceutical agent concentration within the tumor microenvironment. Furthermore, spatial and temporal radiopharmaceutical distribution within both the tumor and surrounding tissue is explored. Results Analysis indicates a significantly higher total concentration area under the curve within the tumor region compared to surrounding normal tissue. Moreover, drug distribution exhibits notably superior efficacy compared to the radiation source. Additionally, low microvascular density in extended hypoxia regions enhances drug availability, facilitating improved binding to PSMA receptors and enhancing therapeutic effectiveness. Reductions in the dissociation constant (KD) lead to heightened binding affinity and increased internalized drug concentration. Evaluation of initial radioactivities (7.1×107, 7.1×108, and 7.1×109 [Bq]) indicates that an activity of 7.1×108 [Bq] offers a favorable balance between tumor cell elimination and minimal impact on normal tissues. Discussion These findings underscore the potential of localized radiopharmaceutical delivery strategies and emphasize the crucial role of released drugs relative to the radiation source (implant) in effective tumor treatment. Decreasing the proximity of the drug to the microvascular network and enhancing its distribution within the tumor promote a more effective therapeutic outcome. The study furnishes valuable insights for future experimental investigations and clinical trials, aiming to refine medication protocols and minimize reliance on in vivo testing.
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Affiliation(s)
- Anahita Piranfar
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
| | - Mohammad Souri
- Department of NanoBiotechnology, Pasteur Institute of Iran, Tehran, Iran
| | - Arman Rahmim
- Departments of Radiology and Physics, University of British Columbia, Vancouver, BC, Canada
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Madjid Soltani
- Department of Mechanical Engineering, K. N. Toosi University of Technology, Tehran, Iran
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, Canada
- Centre for Biotechnology and Bioengineering (CBB), University of Waterloo, Waterloo, ON, Canada
- Centre for Sustainable Business, International Business University, Toronto, ON, Canada
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9
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Ma E, Li J, Shen C, Gu Y, Zhang X, Li L, Zhao J, Wang Z. The m 6A-related gene signature stratifies poor prognosis patients and characterizes immunosuppressive microenvironment in hepatocellular carcinoma. Front Immunol 2023; 14:1227593. [PMID: 37691948 PMCID: PMC10485364 DOI: 10.3389/fimmu.2023.1227593] [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: 05/23/2023] [Accepted: 08/04/2023] [Indexed: 09/12/2023] Open
Abstract
Background N6-methyladenosine (m6A) is the most abundant epitranscriptomic modification of RNA, which can affect RNA metabolism and protein translation. The m6A modification plays a critical role in cancer development, including hepatocellular carcinoma (HCC). Despite several m6A-related signatures in HCC, most of them lack the necessary validation and the reliability is still elusive. Methods Differentially expressed genes (DEGs) in the Cancer Genome Atlas were comprehensively analyzed to identify m6A signature associated with HCC prognosis. Gene set enrichment analysis, tumor mutation burden (TMB), immune infiltration, and therapeutic response were evaluated. Importantly, mass spectrometry proteomics and multiplex immunofluorescence assays were performed for validation. Results The m6A-related protein-coding gene signature was established, which can divide HCC into high-/low-risk subgroups with markedly different overall survival (OS) and clinical stages. Furthermore, we validated its reliability and robustness in our 101 independent HCC specimens using proteomic detection and confirmed that our signature readily identified high-risk HCC patients with 3-year survival rates of 44.1% vs. 71.8% in the low-risk group. Functional analysis indicated that the high-risk group might stimulate the cell cycle and activate oncogenic pathways such as MAPK, mTOR, and VEGF, whereas the low-risk group mainly regulated amino acid, fatty acid, and drug metabolism. Additionally, the high-risk group had more TMB, upregulated immune checkpoint molecule expression, including PD-1, CTLA4, TIM3, and LAG3, and preferentially formed an immunosuppressive microenvironment. Accordingly, potential therapeutic responses showed that high-risk patients were potentially sensitive to inhibitors targeting the cell cycle and MAPK signaling, with patients possibly benefiting from immunotherapy. Moreover, multiplex immunofluorescence assays indicated that high-risk HCC samples displayed distinct immunosuppressive features, with abundant M2-polarized macrophages and T-regulatory cell infiltration. Conclusion The m6A signature had a prominent capacity to evaluate OS and characterize the tumor immune microenvironment of HCC, which may serve as a useful approach for risk stratification management and provide a valuable clue to choosing rational therapeutic strategies.
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Affiliation(s)
- Ensi Ma
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Jianhua Li
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Conghuan Shen
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Yange Gu
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Li Li
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
| | - Jing Zhao
- Hepatobiliary Surgery, Department of General Surgery, Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai, China
| | - Zhengxin Wang
- Liver Transplantation Center, General Surgery, Huashan Hospital, Fudan University, Shanghai, China
- Institute of Organ Transplantation, Fudan University, Shanghai, China
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10
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Luo J, Cao J, Chen C, Xie H. Emerging role of RNA acetylation modification ac4C in diseases: Current advances and future challenges. Biochem Pharmacol 2023; 213:115628. [PMID: 37247745 DOI: 10.1016/j.bcp.2023.115628] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/20/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
The oldest known highly conserved modification of RNA, N4-acetylcytidine, is widely distributed from archaea to eukaryotes and acts as a posttranscriptional chemical modification of RNA, contributing to the correct reading of specific nucleotide sequences during translation, stabilising mRNA and improving transcription efficiency. Yeast Kre33 and human NAT10, the only known authors of ac4C, modify tRNA with the help of the Tan1/THUMPD1 adapter to stabilise its structure. Currently, the mRNA for N4-acetylcytidine (ac4C), catalysed by NAT10 (N-acetyltransferase 10), has been implicated in a variety of human diseases, particularly cancer. This article reviews advances in the study of ac4C modification of RNA and the ac4C-related gene NAT10 in normal physiological cell development, cancer, premature disease and viral infection and discusses its therapeutic promise and future research challenges.
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Affiliation(s)
- Jie Luo
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Jingsong Cao
- Department of Endocrinology and Metabolism, The First Affiliated Hospital, Institute of Clinical Medicine, University of South China, Hengyang 421001, China
| | - Cong Chen
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Haitao Xie
- Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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11
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Chang K, Su J, Li C, Anwaier A, Liu W, Xu W, Qu Y, Zhang H, Ye D. Multi-omics profiles refine L-dopa decarboxylase (DDC) as a reliable biomarker for prognosis and immune microenvironment of clear cell renal cell carcinoma. Front Oncol 2022; 12:1079446. [PMID: 36544704 PMCID: PMC9760914 DOI: 10.3389/fonc.2022.1079446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/11/2022] [Indexed: 12/07/2022] Open
Abstract
Background Increasing evidence indicates that L-dopa decarboxylase (DDC), which mediates aberrant amino acid metabolism, is significantly associated with tumor progression. However, the impacts of DDC are not elucidated clearly in clear cell renal cell carcinoma (ccRCC). This study aimed to evaluate DDC prognostic value and potential mechanisms for ccRCC patients. Methods Transcriptomic and proteomic expressions of and clinical data including 532 patients with ccRCC (The Cancer Genome Atlas RNA-seq data), 226 ccRCC samples (Gene Expression Omnibus), 101 ccRCC patients from the E-MTAB-1980 cohort, and 232 patients with ccRCC with proteogenomic data (Fudan University Shanghai Cancer Center) were downloaded and analyzed to investigate the prognostic implications of DDC expression. Cox regression analyses were implemented to explore the effect of DDC expression on the prognosis of pan-cancer. The "limma" package identified the differentially expressed genes (DEGs) between high DDC subgroups and low DDC groups. Functional enrichments were performed based DEGs between DDC subgroups. The differences of immune cell infiltrations and immune checkpoint genes between DDC subgroups were analyzed to identify potential influence on immune microenvironment. Results We found significantly decreased DDC expression in ccRCC tissues compared with normal tissues from multiple independent cohorts based on multi-omics data. We also found that DDC expression was correlated with tumor grades and stages.The following findings revealed that lower DDC expression levels significantly correlated with shorter overall survival (P <0.001) of patients with ccRCC. Moreover, we found that DDC expression significantly correlated with an immunosuppressive tumor microenvironment, higher intra-tumoral heterogeneity, elevated expression of immune checkpoint CD274, and possibly mediated malignant behaviors of ccRCC cells via the PI3k/Akt signaling pathway. Conclusion The present study is the first to our knowledge to indicate that decreased DDC expression is significantly associated with poor survival and an immune-suppressive tumor microenvironment in ccRCC. These findings suggest that DDC could serve as a biomarker for guiding molecular diagnosis and facilitating the development of novel individual therapeutic strategies for patients with advanced ccRCC.
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Affiliation(s)
- Kun Chang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Jiaqi Su
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Aihetaimujiang Anwaier
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Wangrui Liu
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Yuanyuan Qu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Genitourinary Cancer Institute, Shanghai, China
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12
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Yang J, Xu J, Gao Q, Wu F, Han W, Yu C, Shi Y, Qiu Y, Chen Y, Zhou X. Identification of adenylate cyclase 2 methylation in bladder cancer with implications for prognosis and immunosuppressive microenvironment. Front Oncol 2022; 12:1025195. [PMID: 36313639 PMCID: PMC9614257 DOI: 10.3389/fonc.2022.1025195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
Background The incidence and mortality of bladder cancer (BCa) are increasing, while the existing diagnostic methods have limitations. Therefore, for early detection and response prediction, it is crucial to improve the prognosis and treatment strategies. However, with existing diagnostic methods, detecting BCa in the early stage is challenging. Hence, novel biomarkers are urgently needed to improve early diagnosis and treatment efficiency. Methods The gene expression profile and gene methylation profile dataset were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs), differentially methylated genes (DMGs), and methylation-regulated differentially expressed genes (MeDEGs) were gradually identified. A cancer genome map was obtained using online gene expression profile interaction analysis, and survival implications were produced using Kaplan-Meier survival analysis. GSEA was employed to predict the marker pathways where DEGs were significantly involved. The study used bisulfite PCR amplification combined with bisulfite amplicon sequencing (BSAS) to screen for methylation analysis of multiple candidate regions of the adenylate cyclase 2 (ADCY2) based on the sequence design of specific gene regions and CpG islands. Results In this study, DEGs and DMGs with significantly up- or down-regulated expression were selected. The intersection method was used to screen the MeDEGs. The interaction network group in STRING was then visualized using Cytoscape, and the PPI network was constructed to identify the key genes. The key genes were then analyzed using functional enrichment. To compare the relationship between key genes and the prognosis of BCa patients, we further investigated ADCY2 and found that ADCY2 can be a potential clinical biomarker in BCa prognosis and immunotherapy response prediction. In human BCa 5637 and MGH1 cells, we developed and verified the effectiveness of ADCY2 primers using BSAS technology. The findings revealed that the expression of ADCY2 is highly regulated by the methylation of the promoter regions. Conclusion This study revealed that increased expression of ADCY2 was significantly correlated with increased tumor heterogeneity, predicting worse survival and immunotherapy response in BCa patients.
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Affiliation(s)
- Jianfeng Yang
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jin Xu
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Qian Gao
- Wound Treatment Center Affiliated Xinhua Hospital of Medicine College of Shanghai Jiaotong University, Shanghai, China
| | - Fan Wu
- Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Han
- Institute of Regenerative Biology and Medicine, Helmholtz Zentrum München, Munich, Germany
| | - Chao Yu
- Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youyang Shi
- Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yunhua Qiu
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanbiao Chen
- Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Xiqiu Zhou
- Department of Surgery, Shangnan Branch of Longhua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
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