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Chang H, Li M, Zhang L, Li M, Ong SH, Zhang Z, Zheng J, Xu X, Zhang Y, Wang J, Liu X, Li K, Luo Y, Wang H, Miao Z, Chen X, Zha J, Yu Y. Loss of histone deubiquitinase Bap1 triggers anti-tumor immunity. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00978-y. [PMID: 39141316 DOI: 10.1007/s13402-024-00978-y] [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] [Accepted: 07/26/2024] [Indexed: 08/15/2024] Open
Abstract
PURPOSE Immunotherapy using PD-L1 blockade is effective in only a small group of cancer patients, and resistance is common. This emphasizes the importance of understanding the mechanisms of cancer immune evasion and resistance. METHODS A genome-scale CRISPR-Cas9 screen identified Bap1 as a regulator of PD-L1 expression. To measure tumor size and survival, tumor cells were subcutaneously injected into both syngeneic WT mice and immunocompromised mice. The phenotypic and transcriptional characteristics of Bap1-deleted tumors were examined using flow cytometry, RNA-seq, and CUT&Tag-seq analysis. RESULTS We found that loss of histone deubiquitinase Bap1 in cancer cells activates a cDC1-CD8+ T cell-dependent anti-tumor immunity. The absence of Bap1 leads to an increase in genes associated with anti-tumor immune response and a decrease in genes related to immune evasion. As a result, the tumor microenvironment becomes inflamed, with more cDC1 cells and effector CD8+ T cells, but fewer neutrophils and regulatory T cells. We also found that the elimination of Bap1-deleted tumors depends on the tumor MHCI molecule and Fas-mediated CD8+ T cell cytotoxicity. Our analysis of TCGA data further supports these findings, showing a reverse correlation between BAP1 expression and mRNA signatures of activated DCs and T-cell cytotoxicity in various human cancers. CONCLUSION The histone deubiquitinase Bap1 could be used as a biomarker for tumor stratification and as a potential therapeutic target for cancer immunotherapies.
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Affiliation(s)
- Hong Chang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Mingxia Li
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Linlin Zhang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Meng Li
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1HH, UK
| | - Zhiwei Zhang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Jie Zheng
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xiang Xu
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yu Zhang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Jing Wang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Xingjie Liu
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Kairui Li
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Yao Luo
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Haiyun Wang
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence, Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200081, China
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Laboratory, Guangzhou Medical University, Guangzhou, China
| | - Xi Chen
- Department of Biology, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen, 518055, China
| | - Jie Zha
- Department of Hematology, The First Affiliated Hospital of Xiamen University and Institute of Hematology, School of Medicine, Xiamen University, Xiamen, China.
- Key Laboratory of Xiamen for Diagnosis and Treatment of Hematological Malignancy, Xiamen, China.
| | - Yong Yu
- Department of Hematology, Tongji Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, China.
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Wang Q, Du J, Ma R. White adipocyte-derived exosomal miR-23b inhibits thermogenesis by targeting Elf4 to regulate GLP-1R transcription. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:5847-5860. [PMID: 38334823 DOI: 10.1007/s00210-024-02984-1] [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: 05/18/2023] [Accepted: 01/28/2024] [Indexed: 02/10/2024]
Abstract
Promoting non-trembling thermogenesis of brown adipose tissue (BAT) and browning of white adipose tissue (WAT) helps prevent obesity. MiR-23b is highly expressed in adipose tissue-derived exosomes obtained from obese people, but the role of exosomal miR-23b in regulating thermogenesis and obesity progression remains to be further explored. Here, a mouse obesity model was established through high-fat diet (HFD), and inguinal WAT (iWAT)-derived exosomes and miR-23b antagomir were administered by intraperitoneal injection. The results showed that WAT-derived exosomal miR-23b upregulated body weight and adipocyte hypertrophy and enhanced insulin resistance. Moreover, exosomal miR-23b restrained mtDNA copy number and the expression of genes related to thermogenesis and mitochondrial biogenesis in BAT, and suppressed the expression of WAT browning-related genes under cold stimulation, indicating that exosomal miR-23b hindered non-trembling thermogenesis of BAT and WAT browning. Mechanism studies found that miR-23b targeted Elf4 to inhibit its expression. And Elf4 bound to the GLP-1R promoter region to promote GLP-1R transcription. In addition, silencing miR-23b effectively abolished the inhibitory effect of WAT-derived exosomes on thermogenic gene expression and mitochondrial respiration in adipocytes isolated from BAT and iWAT, which was reversed by GLP-1R knockdown. In conclusion, WAT-derived exosomal miR-23b suppressed thermogenesis by targeting Elf4 to regulate GLP-1R transcription, which contributed to the progression of obesity.
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Affiliation(s)
- Qian Wang
- Functional Experiment Center, Department of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China.
| | - Junkai Du
- Department of Emergency, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ruili Ma
- Functional Experiment Center, Department of Basic Medicine, Xi'an Medical University, Xi'an, 710021, China
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Sun L, Han Y, Li B, Yang Y, Fang Y, Ren X, An L, Hou X, Fan H, Wu Y. A Novel Frameshift Variant of the ELF4 Gene in a Patient with Autoinflammatory Disease: Clinical Features, Transcriptomic Profiling and Functional Studies. J Clin Immunol 2024; 44:127. [PMID: 38773005 DOI: 10.1007/s10875-024-01732-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 05/07/2024] [Indexed: 05/23/2024]
Abstract
We described the diagnosis and treatment of a patient with autoinflammatory disease, named "Deficiency in ELF4, X-linked (DEX)". A novel ELF4 variant was discovered and its pathogenic mechanism was elucidated. The data about clinical, laboratory and endoscopic features, treatment, and follow-up of a patient with DEX were analyzed. Whole exome sequencing and Sanger sequencing were performed to identify potential pathogenic variants. The mRNA and protein levels of ELF4 were analyzed by qPCR and Western blotting, respectively. The association of ELF4 frameshift variant with nonsense-mediated mRNA decay (NMD) in the pathogenesis DEX was examined. Moreover, RNA-seq was performed to identify the key molecular events triggered by ELF4 variant. The relationship between ELF4 and IFN-β activity was validated using a dual-luciferase reporter assay and a ChIP-qPCR assay. An 11-year-old boy presented with a Behçet's-like phenotype. The laboratory abnormality was the most obvious in elevated inflammatory indicators. Endoscopy revealed multiple ileocecal ulcers. Intestinal histopathology showed inflammatory cell infiltrations. The patient was treated with long-term immunosuppressant and TNF-α blocker (adalimumab), which reaped an excellent response over 16 months of follow-up. Genetic analysis identified a maternal hemizygote frameshift variant (c.1022del, p.Q341Rfs*30) in ELF4 gene in the proband. The novel variant decreased the mRNA level of ELF4 via the NMD pathway. Mechanistically, insufficient expression of ELF4 disturbed the immune system, leading to immunological disorders and pathogen susceptibility, and disrupted ELF4-activating IFN-β responses. This analysis detailed the clinical characteristics of a Chinese patient with DEX who harbored a novel ELF4 frameshift variant. For the first time, we used patient-derived cells and carried out transcriptomic analysis to delve into the mechanism of ELF4 variant in DEX.
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Affiliation(s)
- Lina Sun
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, No.28 Xianning West Road, Xi'an, Shaanxi, 710049, China
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Ya'nan Han
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Benchang Li
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Yang
- Shaanxi Institute of Pediatric Diseases, Xi'an Children's Hospital, Xi'an, China
| | - Ying Fang
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Xiaoxia Ren
- Department of Gastroenterology, Xi'an Children's Hospital, Xi'an, China
| | - Lu An
- Department of Pathology, Xi'an Children's Hospital, Xi'an, China
| | - Xin Hou
- Department of Imaging, Xi'an Children's Hospital, Xi'an, China
| | - Huafeng Fan
- Department of Education Science, Xi'an Children's Hospital, Xi'an, China
| | - Yi Wu
- MOE Key Laboratory of Environment and Genes Related to Diseases, School of Basic Medical Sciences, Xi'an Jiaotong University, No.28 Xianning West Road, Xi'an, Shaanxi, 710049, China.
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王 楠, 谢 咏, 汪 志. [Two Cases of Behcet's Disease-Like Syndrome with Gene Deficiency in ELF4]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2024; 55:756-761. [PMID: 38948265 PMCID: PMC11211776 DOI: 10.12182/20240560606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Indexed: 07/02/2024]
Abstract
The patient 1, a 13-year-old boy, was admitted due to "recurrent oral ulcers for 3 years, abdominal pain for 8 months, and perianal ulcers for 10 days"; The patient 2, a 3-year-old boy, was admitted due to "recurrent abdominal pain, diarrhea, and fever for over 3 months". Genetic testing of both patients revealed "deficiency in ELF4, X-linked" (DEX), and the patients were diagnosed with Behcet's disease-like syndrome due to deficiency in ELF4, accordingly. The patient 1 was successively given intravenous methylprednisolone pulses and oral prednisone and mesalazine for symptomatic treatment. The patient 2 was successively treated with corticosteroids combined with enteral nutrition, as well as oral mercaptopurine. Subsequently, both patients showed improvements in symptoms and were discharged.
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Affiliation(s)
- 楠 王
- 四川大学华西第二医院 儿科 (成都 610041)Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, Sichuan University, Chengdu 610041, China
- 四川大学华西临床医学院 (成都 610041)West China College of Clinical Medicine, Sichuan University, Chengdu 610041, China
| | - 咏梅 谢
- 四川大学华西第二医院 儿科 (成都 610041)Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, Sichuan University, Chengdu 610041, China
| | - 志凌 汪
- 四川大学华西第二医院 儿科 (成都 610041)Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children of the Ministry of Education, Sichuan University, Chengdu 610041, China
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Du HQ, Zhao XD. Current understanding of ELF4 deficiency: a novel inborn error of immunity. World J Pediatr 2024; 20:444-450. [PMID: 38733460 DOI: 10.1007/s12519-024-00807-0] [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: 10/18/2023] [Accepted: 03/12/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND ELF4 deficiency has been recently recognized as a novel disorder within the spectrum of inborn errors of immunity (IEIs), specifically categorized as a "disease of immune dysregulation." Cases of this condition, reported by our team and others, are very limited worldwide. As such, our current knowledge of this new disease remains preliminary. This review aims to provide a brief overview of the clinical manifestations, pathogenesis, and treatment strategies for this novel IEI. DATA SOURCES A comprehensive review was conducted after an extensive literature search in the PubMed/Medline database and websites concerning transcriptional factor ELF4 and reports concerning patients with ELF4 deficiency. Our search strategy was "ELF4 OR ETS-related transcription factor Elf-4 OR EL4-like factor 4 OR myeloid Elf-1-like factor" as of the time of manuscript submission. RESULTS The current signature manifestations of ELF4 deficiency disorder are recurrent and prolonged oral ulcer, abdominal pain, and diarrhea in pediatric males. In some cases, immunodeficiency and autoimmunity can also be prominent. Targeted Sanger sequencing or whole exome sequencing can be used to detect variation in ELF4 gene. Western blotting for ELF4 expression of the patient's cells can confirm the pathogenic effect of the variant. To fully confirm the pathogenicity of the variant, further functional test is strongly advised. Glucocorticoid and biologics are the mainstream management of ELF4 deficiency disorder. CONCLUSIONS Pediatric males presenting with recurring ulcerations in digestive tract epithelium with or without recurrent fever should be suspected of DEX. When atypical presentations are prominent, variations in ELF4 gene should be carefully evaluated functionally due to the complex nature of ELF4 function. Experience of treating DEX includes use of glucocorticoid and biologics and more precise treatment needs more patients to identify and further mechanistic study.
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Affiliation(s)
- Hong-Qiang Du
- Department of Rheumatology & Immunology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Zhongshan Er Road 136Yuzhong District, Chongqing, China
| | - Xiao-Dong Zhao
- Department of Rheumatology & Immunology, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Rare Diseases in Infection and Immunity, Children's Hospital of Chongqing Medical University, Zhongshan Er Road 136Yuzhong District, Chongqing, China.
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Xu A, Sun M, Li Z, Chu Y, Fang K, Zhang Y, Lian J, Zhang L, Chen T, Xu M. ELF4 contributes to esophageal squamous cell carcinoma growth and metastasis by augmenting cancer stemness via FUT9. Acta Biochim Biophys Sin (Shanghai) 2024; 56:129-139. [PMID: 37674363 PMCID: PMC10875363 DOI: 10.3724/abbs.2023225] [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: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 09/08/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) commonly has aggressive properties and a poor prognosis. Investigating the molecular mechanisms underlying the progression of ESCC is crucial for developing effective therapeutic strategies. Here, by performing transcriptome sequencing in ESCC and adjacent normal tissues, we find that E74-like transcription factor 4 (ELF4) is the main upregulated transcription factor in ESCC. The results of the immunohistochemistry show that ELF4 is overexpressed in ESCC tissues and is significantly correlated with cancer staging and prognosis. Furthermore, we demonstrate that ELF4 could promote cancer cell proliferation, migration, invasion, and stemness by in vivo assays. Through RNA-seq and ChIP assays, we find that the stemness-related gene fucosyltransferase 9 ( FUT9) is transcriptionally activated by ELF4. Meanwhile, ELF4 is verified to affect ESCC cancer stemness by regulating FUT9 expression. Overall, we first discover that the transcription factor ELF4 is overexpressed in ESCC and can promote ESCC progression by transcriptionally upregulating the stemness-related gene FUT9.
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Affiliation(s)
- Aiping Xu
- Endoscopy CenterZhongshan HospitalSchool of MedicineFudan UniversityShanghai200032China
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
- Department of Gastroenterology and HepatologyJing’an District Centre HospitalFudan UniversityShanghai20032China
| | - Mingchuang Sun
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Zhaoxing Li
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Yuan Chu
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Kang Fang
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Yunwei Zhang
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Jingjing Lian
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Li Zhang
- Department of PathologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Tao Chen
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
| | - Meidong Xu
- Endoscopy CenterDepartment of GastroenterologyShanghai East HospitalSchool of MedicineTongji UniversityShanghai200120China
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Cao M, Chen P, Peng B, Cheng Y, Xie J, Hou Z, Chen H, Ye L, Li H, Wang H, Ren L, Xiong L, Geng L, Gong S. The transcription factor ELF4 alleviates inflammatory bowel disease by activating IL1RN transcription, suppressing inflammatory TH17 cell activity, and inducing macrophage M2 polarization. Front Immunol 2023; 14:1270411. [PMID: 38022496 PMCID: PMC10657822 DOI: 10.3389/fimmu.2023.1270411] [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: 07/31/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Background Inflammatory bowel disease (IBD) is a chronic immune-mediated disorder affecting millions worldwide. Due to the complexity of its pathogenesis, the treatment options for IBD are limited. This study focuses on ELF4, a member of the ETS transcription factor family, as a target to elucidate its role in IBD and investigate its mechanism of action in alleviating IBD symptoms by activating IL1RN transcription to suppress the activity of inflammatory TH17 cells. Methods Using the GEO database, this study examined LPS-induced intestinal inflammatory genes and their regulation mechanisms. We examined the colon length of LPS-treated mice and derived the Disease Activity Index (DAI). H&E staining, ELISA, and flow cytometry were used to detect mice colon tissue damage, inflammatory factor levels in mouse serum, mouse macrophage types and inflammatory TH17 cell activity. RT-qPCR and Western blot detected ELF4, IL1RN, M1, and M2 polarization markers. In Vitro, using dual-luciferase and ChIP assays, we tested mouse bone marrow-derived macrophages (BMDMs) and mouse intestinal epithelial cells for IL1RN promoter activity and ELF4 enrichment. Results Bioinformatics showed that LPS-induced colitis animals have reduced ELF4 expression in their colon tissue. In vivo tests confirmed reduced ELF4 expression in mice with LPS-induced colitis. ELF4 overexpression reduced mouse intestinal inflammation. ELF4 activated IL1RN transcription in bioinformatics and in vitro tests. ELF4 promoted IL1RN transcription and macrophage M2 polarization to limit intestinal epithelial cell death and inflammation and reduce mouse intestinal inflammation in vitro. ELF4 also reduced the Th17/Treg ratio by increasing IL1RN transcription. Conclusion ELF4 activates IL1RN transcription, suppresses inflammatory TH17 cells, and induces macrophage M2 polarization to treat IBD.
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Affiliation(s)
- Meiwan Cao
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Peiyu Chen
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Baoling Peng
- Center for Child Health and Mental Health, Shenzhen Childen’s Hospital, Shenzhen, China
| | - Yang Cheng
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jing Xie
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ziang Hou
- Department of Internal, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huan Chen
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liping Ye
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huiwen Li
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hongli Wang
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lu Ren
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liya Xiong
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lanlan Geng
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Sitang Gong
- Department of Gastroenterology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
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Wang M, Yu F, Li P. Noncoding RNAs as an emerging resistance mechanism to immunotherapies in cancer: basic evidence and therapeutic implications. Front Immunol 2023; 14:1268745. [PMID: 37767098 PMCID: PMC10520974 DOI: 10.3389/fimmu.2023.1268745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The increasing knowledge in the field of oncoimmunology has led to extensive research into tumor immune landscape and a plethora of clinical immunotherapy trials in cancer patients. Immunotherapy has become a clinically beneficial alternative to traditional treatments by enhancing the power of the host immune system against cancer. However, it only works for a minority of cancers. Drug resistance continues to be a major obstacle to the success of immunotherapy in cancer. A fundamental understanding of the detailed mechanisms underlying immunotherapy resistance in cancer patients will provide new potential directions for further investigations of cancer treatment. Noncoding RNAs (ncRNAs) are tightly linked with cancer initiation and development due to their critical roles in gene expression and epigenetic modulation. The clear appreciation of the role of ncRNAs in tumor immunity has opened new frontiers in cancer research and therapy. Furthermore, ncRNAs are increasingly acknowledged as a key factor influencing immunotherapeutic treatment outcomes. Here, we review the available evidence on the roles of ncRNAs in immunotherapy resistance, with an emphasis on the associated mechanisms behind ncRNA-mediated immune resistance. The clinical implications of immune-related ncRNAs are also discussed, shedding light on the potential ncRNA-based therapies to overcome the resistance to immunotherapy.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | | | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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Lu J, Zhang Q, Mo L, Chen W, Mao L. Comprehensive analysis of E47‑like factors and verification of ELF4 in clear cell renal cell carcinoma. Oncol Lett 2023; 26:395. [PMID: 37600328 PMCID: PMC10433703 DOI: 10.3892/ol.2023.13981] [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: 02/05/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prominent subtype of renal cancer and E47-like factors (ELFs) are important in tumorigenesis; however, the specific role of key ELFs in ccRCC remains unclear. The present study comprehensively analyzed RNA sequencing and clinical data from multiple databases, and identified differentially expressed ELFs (ELF3-5) in ccRCC. The DNA promoter methylation, genetic variation and clinical significance of ELF3-5 in ccRCC were analyzed using the cBioPortal and UALCAN databases. The association between ELF3-5 and multiple immune cell infiltration was analyzed using Tumor Immune Estimation Resource. Subsequently, ELF4 was selected and its association with biological functions was assessed. Cell counting kit-8 (CCK-8), colony formation, Transwell, macrophage chemotaxis and polarization assays were conducted to validate the functions of ELF4. Notably, the mRNA expression levels of ELF4 were significantly upregulated in ccRCC, whereas ELF3 and ELF5 mRNA expression levels were significantly downregulated. Clinical significance analysis revealed that ELF4 showed a high clinical significance with tumor grade, clear cell type A and B subtypes, and incidence rates of amplification in genetic variation. Further analyses indicated that ELF4 may be involved in multiple immune cell differentiation. Additionally, cell experiments revealed that ELF4 inhibition downregulated 769-P and 786-O proliferation, migration and invasion. Knockdown of ELF4 in cancer cells also inhibited M2 macrophage polarization and chemotaxis towards 769-P and 786-O cells. Conclusively, the present findings indicated the clinical significance of ELF4 in ccRCC, and verified its key role in driving cell proliferation, migration and invasion, and promoting M2 macrophage polarization and chemotaxis in ccRCC.
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Affiliation(s)
- Jun Lu
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
| | - Qianqian Zhang
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
| | - Licai Mo
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
| | - Weiying Chen
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
| | - Linghong Mao
- Department of Urology, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Taizhou, Zhejiang 310000, P.R. China
- Department of Urology, Enze Hospital, Taizhou Enze Medical Center, Taizhou, Zhejiang 310000, P.R. China
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10
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Li L, Wang S, Wang W. Knockdown of ELF4 aggravates renal injury in ischemia/reperfusion mice through promotion of pyroptosis, inflammation, oxidative stress, and endoplasmic reticulum stress. BMC Mol Cell Biol 2023; 24:22. [PMID: 37474923 PMCID: PMC10360327 DOI: 10.1186/s12860-023-00485-2] [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: 01/17/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Renal ischemia/reperfusion (I/R) injury is a major cause of acute kidney injury (AKI). Dysfunction of E74-like ETS transcription factor 4 (ELF4) leads to inflammation. This research intended to look into the function and mechanisms of ELF4 in I/R and oxygen-glucose deprivation/reperfusion (OGD/R) model. RESULTS In I/R and OGD/R model, ELF4 expression was downregulated. ELF4 knockout aggravated I/R-induced kidney injury, oxidative stress (OS), endoplasmic reticulum stress (ERS), apoptosis, inflammation, and pyroptosis in mice. In HK-2 cells treated with OGD/R, suppression of ELF4 expression inhibited cell proliferation and promoted cell apoptosis, OS, ERS, inflammation, and pyroptosis. Moreover, ELF4 overexpression led to the opposite results. CONCLUSION ELF4 deficiency aggravated I/R induced AKI, which was involved in apoptosis, OS, ERS, inflammation, and pyroptosis. Targeting ELF4 may be a promising new therapeutic strategy for preventing inflammation after IR-AKI.
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Affiliation(s)
- Li Li
- Department of Nephrology, Jinan City People's Hospital, No. 001, Changshao North Road, Laiwu District, Jinan, Shandong, 271199, People's Republic of China.
| | - Shunying Wang
- Department of Cadre Health Section, Jinan City People's Hospital, Jinan, Shandong, 271199, People's Republic of China
| | - Wenming Wang
- Department of Cadre Health Section, Jinan City People's Hospital, Jinan, Shandong, 271199, People's Republic of China
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11
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Sun G, Wu M, Lv Q, Yang X, Wu J, Tang W, Dai R, Zhou L, Ding Y, Zhang Z, An Y, Tang X, Zheng X, Wang Z, Sun L, Xie Y, Zhao X, Du H. A Multicenter Cohort Study of Immune Dysregulation Disorders Caused by ELF4 Variants in China. J Clin Immunol 2023; 43:933-939. [PMID: 36823308 DOI: 10.1007/s10875-023-01453-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
Patients with DEX (deficiency in ELF4, X-linked) were recently reported by our team and others, and cases are very limited worldwide. Our knowledge of this new disease is currently preliminary. In this study, we described 5 more cases presenting mainly with oral ulcer, inflammatory bowel disease-like symptoms, fever of unknown origin, anemia, or systemic lupus erythematosus. Whole exome sequencing identified potential pathogenic ELF4 variants in all cases. The pathogenicity of these variants was confirmed by the detection of ELF4 expression in peripheral blood mononuclear cells from patients and utilizing a simple IFN-b luciferase reporter assay, as previously reported. Our findings significantly contribute to the current understanding of DEX.
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Affiliation(s)
- Gan Sun
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Maolan Wu
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Qianying Lv
- Department of Rheumatology, Children's Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China
| | - Xi Yang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Junfeng Wu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Wenjing Tang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Rongxin Dai
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lina Zhou
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Ding
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xiangrong Zheng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China.
| | - Li Sun
- Department of Rheumatology, Children's Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China.
| | - Yongmei Xie
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Sichuan province, Chengdu, China.
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
| | - Hongqiang Du
- National Clinical Research Center for Child Health and Disorders (Chongqing), Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.
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12
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McAllan L, Baranasic D, Villicaña S, Brown S, Zhang W, Lehne B, Adamo M, Jenkinson A, Elkalaawy M, Mohammadi B, Hashemi M, Fernandes N, Lambie N, Williams R, Christiansen C, Yang Y, Zudina L, Lagou V, Tan S, Castillo-Fernandez J, King JWD, Soong R, Elliott P, Scott J, Prokopenko I, Cebola I, Loh M, Lenhard B, Batterham RL, Bell JT, Chambers JC, Kooner JS, Scott WR. Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes. Nat Commun 2023; 14:2784. [PMID: 37188674 PMCID: PMC10185556 DOI: 10.1038/s41467-023-38439-z] [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: 10/13/2021] [Accepted: 05/03/2023] [Indexed: 05/17/2023] Open
Abstract
DNA methylation variations are prevalent in human obesity but evidence of a causative role in disease pathogenesis is limited. Here, we combine epigenome-wide association and integrative genomics to investigate the impact of adipocyte DNA methylation variations in human obesity. We discover extensive DNA methylation changes that are robustly associated with obesity (N = 190 samples, 691 loci in subcutaneous and 173 loci in visceral adipocytes, P < 1 × 10-7). We connect obesity-associated methylation variations to transcriptomic changes at >500 target genes, and identify putative methylation-transcription factor interactions. Through Mendelian Randomisation, we infer causal effects of methylation on obesity and obesity-induced metabolic disturbances at 59 independent loci. Targeted methylation sequencing, CRISPR-activation and gene silencing in adipocytes, further identifies regional methylation variations, underlying regulatory elements and novel cellular metabolic effects. Our results indicate DNA methylation is an important determinant of human obesity and its metabolic complications, and reveal mechanisms through which altered methylation may impact adipocyte functions.
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Affiliation(s)
- Liam McAllan
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Damir Baranasic
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Sergio Villicaña
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Scarlett Brown
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Marco Adamo
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Andrew Jenkinson
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Mohamed Elkalaawy
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Borzoueh Mohammadi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Majid Hashemi
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Nathalie Lambie
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Richard Williams
- Imperial BRC Genomics Facility, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Colette Christiansen
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Youwen Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- School of Cardiovascular and Metabolic Medicine and Sciences, James Black Centre, King's College London British Heart Foundation Centre of Excellence, 125 Coldharbour Lane, London, SE5 9NU, UK
| | - Liudmila Zudina
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
| | - Vasiliki Lagou
- Department of Microbiology and Immunology, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Sili Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | | | - James W D King
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Richie Soong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Institute for Health Research Biomedical Research Centre, Imperial College London, London, UK
| | - James Scott
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - Inga Prokopenko
- Department of Clinical & Experimental Medicine, University of Surrey, Guildford, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre Russian Academy of Sciences, Ufa, Russian Federation
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Marie Loh
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Translational Laboratory in Genetic Medicine (TLGM), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Level 5, Singapore, 138648, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
| | - Rachel L Batterham
- UCLH Bariatric Centre for Weight Loss, Weight Management and Metabolic and Endocrine Surgery, University College London Hospitals, Ground Floor West Wing, 250 Euston Road, London, NW1 2PG, UK
- Centre for Obesity Research, Rayne Institute, Department of Medicine, University College, London, WC1E 6JJ, UK
- National Institute of Health Research University College London Hospitals Biomedical Research Centre, London, W1T 7DN, UK
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - John C Chambers
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, London North West University Healthcare NHS Trust, Middlesex, UB1 3HW, UK
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, W12 0NN, UK
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK
| | - William R Scott
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, W12 0NN, UK.
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK.
- Imperial College Healthcare NHS Trust, London, W12 0HS, UK.
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13
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Chen X, Chen J, Feng W, Huang W, Wang G, Sun M, Luo X, Wang Y, Nie Y, Fan D, Wu K, Xia L. FGF19-mediated ELF4 overexpression promotes colorectal cancer metastasis through transactivating FGFR4 and SRC. Theranostics 2023; 13:1401-1418. [PMID: 36923538 PMCID: PMC10008733 DOI: 10.7150/thno.82269] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/07/2023] [Indexed: 03/14/2023] Open
Abstract
Background: Metastasis accounts for the high lethality of colorectal cancer (CRC) patients. Unfortunately, the molecular mechanism manipulating metastasis in CRC is still elusive. Here, we investigated the function of E74-like factor 4 (ELF4), an ETS family member, in facilitating CRC progression. Methods: The expression of ELF4 in human CRC samples and CRC cell lines was determined by quantitative real-time PCR, immunohistochemistry and immunoblotting. The migratory and invasive phenotypes of CRC cells were evaluated by in vitro transwell assays and in vivo metastatic models. The RNA sequencing was used to explore the downstream targets of ELF4. The luciferase reporter assays and chromatin immunoprecipitation assays were used to ascertain the transcriptional regulation related to ELF4. Results: We found elevated ELF4 was positively correlated with distant metastasis, advanced AJCC stages, and dismal outcomes in CRC patients. ELF4 expression was also an independent predictor of poor prognosis. Overexpression of ELF4 boosted CRC metastasis via transactivating its downstream target genes, fibroblast growth factor receptor 4 (FGFR4) and SRC proto-oncogene, non-receptor tyrosine kinase, SRC. Fibroblast growth factor 19 (FGF19) upregulated ELF4 expression through the ERK1/2/SP1 axis. Clinically, ELF4 expression had a positive correlation with FGF19, FGFR4 and SRC, and CRC patients who positively coexpressed FGF19/ELF4, ELF4/FGFR4, or ELF4/SRC exhibited the worst clinical outcomes. Furthermore, the combination of the FGFR4 inhibitor BLU-554 and the SRC inhibitor KX2-391 dramatically suppressed ELF4-mediated CRC metastasis. Conclusions: We demonstrated the essentiality of ELF4 in the metastatic process of CRC, and targeting the ELF4-relevant positive feedback circuit might represent a novel therapeutic strategy.
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Affiliation(s)
- Xilang Chen
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Jie Chen
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Weibo Feng
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Wenjie Huang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology; Clinical Medicine Research Center for Hepatic Surgery of Hubei Province; Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, Hubei, 430030, China
| | - Guodong Wang
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Mengyu Sun
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Xiangyuan Luo
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Yijun Wang
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
- ✉ Corresponding authors: Dr. Limin Xia, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China; Phone: 86 27 6937 8507; Fax: 86 27 8366 2832; Dr. Kaichun Wu, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China; Dr. Daiming Fan, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China;
| | - Kaichun Wu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
- ✉ Corresponding authors: Dr. Limin Xia, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China; Phone: 86 27 6937 8507; Fax: 86 27 8366 2832; Dr. Kaichun Wu, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China; Dr. Daiming Fan, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China;
| | - Limin Xia
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China
- ✉ Corresponding authors: Dr. Limin Xia, Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei Province, China; Phone: 86 27 6937 8507; Fax: 86 27 8366 2832; Dr. Kaichun Wu, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China; Dr. Daiming Fan, State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an 710032, Shaanxi Province, China;
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14
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Zhu T, Zheng JY, Huang LL, Wang YH, Yao DF, Dai HB. Human PARP1 substrates and regulators of its catalytic activity: An updated overview. Front Pharmacol 2023; 14:1137151. [PMID: 36909172 PMCID: PMC9995695 DOI: 10.3389/fphar.2023.1137151] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a key DNA damage sensor that is recruited to damaged sites after DNA strand breaks to initiate DNA repair. This is achieved by catalyzing attachment of ADP-ribose moieties, which are donated from NAD+, on the amino acid residues of itself or other acceptor proteins. PARP inhibitors (PARPi) that inhibit PARP catalytic activity and induce PARP trapping are commonly used for treating BRCA1/2-deficient breast and ovarian cancers through synergistic lethality. Unfortunately, resistance to PARPi frequently occurs. In this review, we present the novel substrates and regulators of the PARP1-catalyzed poly (ADP-ribosyl)ation (PARylatison) that have been identified in the last 3 years. The overall aim is the presentation of protein interactions of potential therapeutic intervention for overcoming the resistance to PARPi.
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Affiliation(s)
- Tao Zhu
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ju-Yan Zheng
- Institute of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Ling-Ling Huang
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan-Hong Wang
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Di-Fei Yao
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hai-Bin Dai
- Department of Pharmacy, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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15
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Ramezankhani R, Ghavidel AA, Rashidi S, Rojhannezhad M, Abolkheir HR, Mirhosseini M, Taleahmad S, Vosough M. Gender-related differentially expressed genes in pancreatic cancer: possible culprits or accomplices? Front Genet 2022; 13:966941. [DOI: 10.3389/fgene.2022.966941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic cancer (PC) is one of the leading causes of cancer mortality worldwide, and its incidence and mortality rate in several regions is higher in male patients. Although numerous efforts have been made to enhance the clinical outcomes of existing therapeutic regimens, their efficiency is still low, and drug resistance usually occurs in many patients. In addition, the exact underlying molecular basis that makes PC slightly more prevalent among males remains unknown. Providing information regarding the possible association between gender and PC tumorigenesis may offer important clues for how certain molecular cross-talks can affect PC initiation and/or progression. In this study, we used several microarray expression data to identify the common up- and downregulated genes within one specific gender, which were also specified to have binding sites for androgen and/or estrogen receptors. Using functional enrichment analysis among the others, for all the gene sets found in this study, we have shed light on the plausible importance of the androgenic effectors in tumorigenesis, such as the androgen-regulated expression of the GLI transcription factor and the potential role of testosterone in the extracellular matrix (ECM)–cell interaction, which are known for their importance in tumorigenesis. Moreover, we demonstrated that the biological process axon guidance was highlighted regarding the upregulated genes in male patients. Overall, identification of gene candidates as the possible link between gender and PC progression or survival rates may help in developing strategies to reduce the incidence of this cancer.
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16
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Gao J, Ao YQ, Zhang LX, Deng J, Wang S, Wang HK, Jiang JH, Ding JY. Exosomal circZNF451 restrains anti-PD1 treatment in lung adenocarcinoma via polarizing macrophages by complexing with TRIM56 and FXR1. J Exp Clin Cancer Res 2022; 41:295. [PMID: 36209117 PMCID: PMC9547453 DOI: 10.1186/s13046-022-02505-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although success was achieved in the therapy for a minority of advanced lung adenocarcinoma (LUAD) patients, anti-programmed death 1 (PD1) resistance was found in most LUAD patients. Here, we aimed to uncover a potential role of exosomal circular RNAs (circRNAs) in LUAD refractory to PD1 blockade. METHODS: circRNA sequencing and qRT-PCR were performed to determine the level of exosomal circRNAs in LUAD patients subsequently treated with anti-PD1. Then, the RNA pulldown, RNA immunoprecipitation, mass spectrometry, chromatin immunoprecipitation, luciferase reporter assays, flow cytometry, RNA sequencing, and in vitro and in vivo models were used to uncover the biological functions and underlying mechanism of circZNF451 in LUAD anti-PD1 treatment resistance. RESULTS circRNA sequencing and qRT-PCR identified the up-regulation of exosomal circZNF451 from LUAD patients with progressive disease (PD) compared to those with partial remission (PR) after PD1 blockade therapy. Furthermore, elevated circZNF451 was revealed to be associated with poor prognosis of LUAD patients. Additionally, exosomal circZNF451 was demonstrated to induce an anti-inflammatory phenotype in macrophages and exhaustion of cytotoxic CD8+ T cells, and enhanced TRIM56-mediated degradation of FXR1 to activate the ELF4-IRF4 pathway in macrophages. By transgenic mice, knockout of ELF4 in macrophages was found to rescue immunotherapy efficacy in tumors with high level of exosomal circZNF451. CONCLUSION Exosomal circZNF451 reshapes the tumor immune microenvironment by inducing macrophages polarization via the FXR1- ELF4-IRF4 axis and is a novel biomarker for predicting the sensitivity of PD1 blockade in LUAD.
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Affiliation(s)
- Jian Gao
- grid.413087.90000 0004 1755 3939Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 People’s Republic of China ,grid.413087.90000 0004 1755 3939Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong-Qiang Ao
- grid.413087.90000 0004 1755 3939Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 People’s Republic of China ,grid.413087.90000 0004 1755 3939Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ling-Xian Zhang
- grid.412455.30000 0004 1756 5980Department of Cardiothoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi China
| | - Jie Deng
- grid.412540.60000 0001 2372 7462Institute of Vascular Disease, Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shuai Wang
- grid.413087.90000 0004 1755 3939Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 People’s Republic of China ,grid.413087.90000 0004 1755 3939Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hai-Kun Wang
- grid.429007.80000 0004 0627 2381CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Jia-Hao Jiang
- grid.413087.90000 0004 1755 3939Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 People’s Republic of China ,grid.413087.90000 0004 1755 3939Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian-Yong Ding
- grid.413087.90000 0004 1755 3939Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032 People’s Republic of China ,grid.413087.90000 0004 1755 3939Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, China
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Li J, Du H, Ji X, Chen Y, Li Y, Heng BC, Xu J. ETV2 promotes osteogenic differentiation of human dental pulp stem cells through the ERK/MAPK and PI3K-Akt signaling pathways. Stem Cell Res Ther 2022; 13:495. [PMID: 36195958 PMCID: PMC9533526 DOI: 10.1186/s13287-022-03052-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 07/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background The repair of cranio-maxillofacial bone defects remains a formidable clinical challenge. The Ets variant 2 (ETV2) transcription factor, which belongs to the E26 transformation-specific (ETS) family, has been reported to play a key role in neovascularization. However, the role of ETV2 in the osteogenesis of human dental pulp stem cells (hDPSCs) remains unexplored. Methods Transgenic overexpression of ETV2 was achieved using a lentiviral vector, based on a Dox-inducible system. The effects of Dox-induced overexpression of ETV2 on the osteogenesis of hDPSCs were evaluated by quantitative real-time polymerase chain reaction (qRT-PCR), western blot, immunofluorescence staining, alkaline phosphatase (ALP) staining, and Alizarin Red S (ARS) staining. Additionally, RNA-sequencing (RNA-Seq) analysis was performed to analyze the underlying mechanisms of ETV2-induced osteogenesis. Additionally, the role of ETV2 overexpression in bone formation in vivo was validated by animal studies with a rat calvarial defect model and a nude mice model. Results Our results demonstrated that ETV2 overexpression significantly upregulated the mRNA and protein expression levels of osteogenic markers, markedly enhanced ALP activity, and promoted matrix mineralization of hDPSCs. Moreover, the results of RNA-Seq analysis and western blot showed that the ERK/MAPK and PI3K-Akt signaling pathways were activated upon transgenic overexpression of ETV2. The enhanced osteogenic differentiation of hDPSCs due to ETV2 overexpression was partially reversed by treatment with inhibitors of ERK/MAPK or PI3K-AKT signaling. Furthermore, the results of in vivo studies demonstrated that ETV2 overexpression improved bone healing in a rat calvarial defect model and increased ectopic bone formation in nude mice. Conclusions Collectively, our results indicated that ETV2 overexpression exerted positive effects on the osteogenesis of hDPSCs, at least partially via the ERK/MAPK and PI3K/AKT signaling pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-03052-2.
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Affiliation(s)
- Jing Li
- School of Stomatology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250000, People's Republic of China
| | - Haoran Du
- Key Lab of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, 69 Meishan Road, Hefei, 230032, People's Republic of China
| | - Xin Ji
- Key Lab of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, 69 Meishan Road, Hefei, 230032, People's Republic of China
| | - Yihan Chen
- Key Lab of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, 69 Meishan Road, Hefei, 230032, People's Republic of China
| | - Yishuai Li
- Key Lab of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, 69 Meishan Road, Hefei, 230032, People's Republic of China
| | - Boon Chin Heng
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, People's Republic of China
| | - Jianguang Xu
- Key Lab of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, 69 Meishan Road, Hefei, 230032, People's Republic of China.
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18
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Identification of Prognostic Factors in Cholangiocarcinoma Based on Integrated ceRNA Network Analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:7102736. [PMID: 36158120 PMCID: PMC9499749 DOI: 10.1155/2022/7102736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/08/2022] [Accepted: 08/13/2022] [Indexed: 12/03/2022]
Abstract
This study is aimed at screening prognostic biomarkers in cholangiocarcinoma (CHOL) based on competitive endogenous RNA (ceRNA) regulatory network analysis. Microarray data for lncRNAs, mRNA, and miRNAs were downloaded from the GEO and TCGA databases. Differentially expressed RNAs (DERs) were identified in CHOL and normal liver tissue samples. WGCNA was used to identify disease-related gene modules. By integrating the information from the starBase and DIANA-LncBasev2 databases, we constructed a ceRNA network. Survival analysis was performed, and a prognostic gene-based prognostic score (PS) model was generated. The correlation between gene expression and immune cell infiltration or immune-related feature genes was analyzed using TIMER. Finally, real-time quantitative PCR (RT-qPCR) was used to verify the expression of the 10 DERs with independent prognosis. A large cohort of DERs was identified in the CHOL and control samples. The ceRNA network consisted of 6 lncRNAs, 2 miRNAs, 90 mRNAs, and 98 nodes. Ten genes were identified as prognosis-related genes, and a ten-gene signature PS model was constructed, which exhibited a good prognosis predictive ability for risk assessment of CHOL patients (AUC value = 0.975). Four genes, ELF4, AGXT, ABCG2, and LDHD, were associated with immune cell infiltration and closely correlated with immune-related feature genes (CD14, CD163, CD33, etc.) in CHOL. Additionally, the consistency rate of the RT-qPCR results and bioinformatics analysis was 80%, implying a relatively high reliability of the bioinformatic analysis results. Our findings suggest that the ten-signature gene PS model has significant prognostic predictive value for patients with CHOL. These four immune-related DERs are involved in the progression of CHOL and may be useful prognostic biomarkers for CHOLs.
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19
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Shi L, Zhai Y, Zhao Y, Kong X, Zhang D, Yu H, Li Z. ELF4 is critical to zygotic gene activation and epigenetic reprogramming during early embryonic development in pigs. Front Vet Sci 2022; 9:954601. [PMID: 35928113 PMCID: PMC9343831 DOI: 10.3389/fvets.2022.954601] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 06/27/2022] [Indexed: 11/28/2022] Open
Abstract
Zygotic gene activation (ZGA) and epigenetic reprogramming are critical in early embryonic development in mammals, and transcription factors are involved in regulating these events. However, the effects of ELF4 on porcine embryonic development remain unclear. In this study, the expression of ELF4 was detected in early porcine embryos and different tissues. By knocking down ELF4, the changes of H3K9me3 modification, DNA methylation and ZGA-related genes were analyzed. Our results showed that ELF4 was expressed at all stages of early porcine embryos fertilized in vitro (IVF), with the highest expression level at the 8-cell stage. The embryonic developmental competency and blastocyst quality decreased after ELF4 knockdown (20.70% control vs. 17.49% si-scramble vs. 2.40% si-ELF4; p < 0.001). Knockdown of ELF4 induced DNA damage at the 4-cell stage. Interfering with ELF4 resulted in abnormal increases in H3K9me3 and DNA methylation levels at the 4-cell stage and inhibited the expression of genes related to ZGA. These results suggest that ELF4 affects ZGA and embryonic development competency in porcine embryos by maintaining genome integrity and regulating dynamic changes of H3K9me3 and DNA methylation, and correctly activating ZGA-related genes to promote epigenetic reprogramming. These results provide a theoretical basis for further studies on the regulatory mechanisms of ELF4 in porcine embryos.
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Affiliation(s)
- Lijing Shi
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
- College of Animal Science, Jilin University, Changchun, China
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Yuanshen Zhao
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Xiangjie Kong
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
| | - Hao Yu
- College of Animal Science, Jilin University, Changchun, China
- Hao Yu
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education, First Hospital, Jilin University, Changchun, China
- *Correspondence: Ziyi Li
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20
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Wang Q, Zhang C, Cao S, Zhao H, Jiang R, Li Y. Tumor-derived exosomes orchestrate the microRNA-128-3p/ELF4/CDX2 axis to facilitate the growth and metastasis of gastric cancer via delivery of LINC01091. Cell Biol Toxicol 2022:10.1007/s10565-022-09728-y. [PMID: 35674868 DOI: 10.1007/s10565-022-09728-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/10/2022] [Indexed: 01/13/2023]
Abstract
It has been manifested that tumor-derived exosomes (Exos) can deliver long noncoding RNAs to participate in gastric cancer (GC) progression. In this research, we intended to dissect out whether tumor-derived Exos carried LINC01091 to afflict the growth and metastasis of GC. GC tissues and human GC cells were attained for RNA and protein quantification. Accordingly, LINC01091, ELF4, and CDX2 were abundant but microRNA (miR)-128-3p was underexpressed in GC tissues and cells. Exos were isolated from LINC01091-silenced GC cells (Exo-sh-LINC01091). GC cells were co-cultured with Exo-sh-LINC01091 or manipulated with miR mimic, inhibitor, or overexpressing or silencing plasmids. Exo-sh-LINC01091, LINC01091, ELF4 or CDX2 silencing, or miR-128-3p upregulation augmented GC cell proliferative, migrating, and invasive properties. In addition, luciferase, RNA pull-down, and ChIP assays offered evidence supporting the mechanism that LINC01091 bound to miR-128-3p that inversely targeted ELF4, and ELF4 transcriptionally activated CDX2 by binding to its promoter in GC cells. Moreover, Exo-sh-LINC01091 modulated the miR-128-3p/ELF4/CDX2 axis and restrained the tumorigenesis and metastasis in vivo. Conclusively, LINC01091 shuttled by tumor-derived Exos might expedite GC development by activating the ELF4/CDX2 axis via miR-128-3p downregulation.
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Affiliation(s)
- Qiang Wang
- Department of Radiotherapy, Xuzhou Cancer Hospital, Xuzhou Third People's Hospital, Xuzhou, 221005, People's Republic of China
| | - Chunmei Zhang
- Department of Medical Oncology, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Shengya Cao
- Clinical Laboratory, Xuzhou Cancer Hospital, Xuzhou Third People's Hospital, Xuzhou, 221005, People's Republic of China
| | - Hongying Zhao
- Department of Medical Oncology, Xuzhou Cancer Hospital, Xuzhou Third People's Hospital, No. 131, Huancheng Road, Xuzhou, 221005, People's Republic of China.
| | - Rongke Jiang
- Department of Hematology and Oncology, Xuzhou Cancer Hospital, Xuzhou Third People's Hospital, Xuzhou, 221005, People's Republic of China
| | - Yanfang Li
- Department of Medical Oncology, Xuzhou Cancer Hospital, Xuzhou Third People's Hospital, No. 131, Huancheng Road, Xuzhou, 221005, People's Republic of China
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21
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Franklin R, Guo Y, He S, Chen M, Ji F, Zhou X, Frankhouser D, Do BT, Chiem C, Jang M, Blanco MA, Vander Heiden MG, Rockne RC, Ninova M, Sykes DB, Hochedlinger K, Lu R, Sadreyev RI, Murn J, Volk A, Cheloufi S. Regulation of chromatin accessibility by the histone chaperone CAF-1 sustains lineage fidelity. Nat Commun 2022; 13:2350. [PMID: 35487911 PMCID: PMC9054786 DOI: 10.1038/s41467-022-29730-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/25/2022] [Indexed: 12/13/2022] Open
Abstract
Cell fate commitment is driven by dynamic changes in chromatin architecture and activity of lineage-specific transcription factors (TFs). The chromatin assembly factor-1 (CAF-1) is a histone chaperone that regulates chromatin architecture by facilitating nucleosome assembly during DNA replication. Accumulating evidence supports a substantial role of CAF-1 in cell fate maintenance, but the mechanisms by which CAF-1 restricts lineage choice remain poorly understood. Here, we investigate how CAF-1 influences chromatin dynamics and TF activity during lineage differentiation. We show that CAF-1 suppression triggers rapid differentiation of myeloid stem and progenitor cells into a mixed lineage state. We find that CAF-1 sustains lineage fidelity by controlling chromatin accessibility at specific loci, and limiting the binding of ELF1 TF at newly-accessible diverging regulatory elements. Together, our findings decipher key traits of chromatin accessibility that sustain lineage integrity and point to a powerful strategy for dissecting transcriptional circuits central to cell fate commitment.
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Affiliation(s)
- Reuben Franklin
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, United States
| | - Yiming Guo
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, United States
| | - Shiyang He
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
| | - Meijuan Chen
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, United States
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States
| | - Xinyue Zhou
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - David Frankhouser
- Department of Population Sciences City of Hope National Medical Center, Duarte, CA, United States
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, United States
| | - Carmen Chiem
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, United States
| | - Mihyun Jang
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - M Andres Blanco
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, United States
- Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, United States
| | - Russell C Rockne
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, City of Hope National Medical Center, Duarte, CA, United States
| | - Maria Ninova
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States
- Department of Genetics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, United States
- Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA, 02138, United States
- Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States
| | - Rui Lu
- Division of Hematology/Oncology, O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA, 02114, United States
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States
| | - Jernej Murn
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States.
| | - Andrew Volk
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.
| | - Sihem Cheloufi
- Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, United States.
- Stem Cell Center, University of California, Riverside, 900 University Ave, Riverside, CA, 92521, United States.
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22
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Intestinal ELF4 Deletion Exacerbates Alcoholic Liver Disease by Disrupting Gut Homeostasis. Int J Mol Sci 2022; 23:ijms23094825. [PMID: 35563234 PMCID: PMC9102452 DOI: 10.3390/ijms23094825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/24/2022] [Accepted: 04/24/2022] [Indexed: 02/04/2023] Open
Abstract
Alcohol liver disease (ALD) is characterized by intestinal barrier disruption and gut dysbiosis. Dysfunction of E74-like ETS transcription factor 4 (ELF4) leads to colitis. We aimed to test the hypothesis that intestinal ELF4 plays a critical role in maintaining the normal function of intestinal barrier and gut homeostasis in a mouse model of ALD. Intestinal ELF4 deficiency resulted in dysfunction of the intestinal barrier. Elf4−/− mice exhibited gut microbiota (GM) dysbiosis with the characteristic of a larger proportion of Proteobacteria. The LPS increased in Elf4−/− mice and was the most important differential metabolite between Elf4−/− mice and WT mice. Alcohol exposure increased liver-to-body weight ratio, and hepatic inflammation response and steatosis in WT mice. These deleterious effects were exaggerated in Elf4−/− mice. Alcohol exposure significantly increased serum levels of TG, ALT, and AST in Elf4−/− mice but not in WT mice. In addition, alcohol exposure resulted in enriched expression of genes associated with cholesterol metabolism and lipid metabolism in livers from Elf4−/− mice. 16S rRNA sequencing showed a decrease abundance of Akkermansia and Bilophila in Elf4−/− mice. In conclusion, intestinal ELF4 is an important host protective factor in maintaining gut homeostasis and alleviating alcohol exposure-induced hepatic steatosis and injury.
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23
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Mann Z, Sengar M, Verma YK, Rajalingam R, Raghav PK. Hematopoietic Stem Cell Factors: Their Functional Role in Self-Renewal and Clinical Aspects. Front Cell Dev Biol 2022; 10:664261. [PMID: 35399522 PMCID: PMC8987924 DOI: 10.3389/fcell.2022.664261] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/14/2022] [Indexed: 01/29/2023] Open
Abstract
Hematopoietic stem cells (HSCs) possess two important properties such as self-renewal and differentiation. These properties of HSCs are maintained through hematopoiesis. This process gives rise to two subpopulations, long-term and short-term HSCs, which have become a popular convention for treating various hematological disorders. The clinical application of HSCs is bone marrow transplant in patients with aplastic anemia, congenital neutropenia, sickle cell anemia, thalassemia, or replacement of damaged bone marrow in case of chemotherapy. The self-renewal attribute of HSCs ensures long-term hematopoiesis post-transplantation. However, HSCs need to be infused in large numbers to reach their target site and meet the demands since they lose their self-renewal capacity after a few passages. Therefore, a more in-depth understanding of ex vivo HSCs expansion needs to be developed to delineate ways to enhance the self-renewability of isolated HSCs. The multifaceted self-renewal process is regulated by factors, including transcription factors, miRNAs, and the bone marrow niche. A developed classical hierarchical model that outlines the hematopoiesis in a lineage-specific manner through in vivo fate mapping, barcoding, and determination of self-renewal regulatory factors are still to be explored in more detail. Thus, an in-depth study of the self-renewal property of HSCs is essentially required to be utilized for ex vivo expansion. This review primarily focuses on the Hematopoietic stem cell self-renewal pathway and evaluates the regulatory molecular factors involved in considering a targeted clinical approach in numerous malignancies and outlining gaps in the current knowledge.
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Affiliation(s)
- Zoya Mann
- Independent Researcher, New Delhi, India
| | - Manisha Sengar
- Department of Zoology, Deshbandhu College, University of Delhi, Delhi, India
| | - Yogesh Kumar Verma
- Stem Cell and Gene Therapy Research Group, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, India
| | - Raja Rajalingam
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, United States
| | - Pawan Kumar Raghav
- Immunogenetics and Transplantation Laboratory, Department of Surgery, University of California San Francisco, San Francisco, CA, United States
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24
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Sun G, Qiu L, Yu L, An Y, Ding Y, Zhou L, Wu J, Yang X, Zhang Z, Tang X, Xia H, Cao L, You F, Zhao X, Du H. Loss of Function Mutation in ELF4 Causes Autoinflammatory and Immunodeficiency Disease in Human. J Clin Immunol 2022; 42:798-810. [PMID: 35266071 DOI: 10.1007/s10875-022-01243-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/28/2022] [Indexed: 02/04/2023]
Abstract
Monogenic autoinflammatory diseases (mAIDs) are a heterogeneous group of diseases affecting primarily innate immunity, with various genetic causes. Genetic diagnosis of mAIDs can assist in the patient's management and therapy. However, a large number of sporadic and familial cases remain genetically uncharacterized. Deficiency in ELF4, X-linked (DEX) is recently identified as a novel mAID. Here, we described a pediatric patient suffering from recurrent viral and bacterial respiratory infection, refractory oral ulcer, constipation, and arthritis. Whole-exome sequencing found a hemizygous variant in ELF4 (chrX:129205133 A > G, c.691 T > C, p.W231R). Using cells from patient and point mutation mice, we showed mutant cells failed to restrict viral replication effectively and produced more pro-inflammatory cytokines. RNA-seq identified several potential critical antiviral and anti-inflammation genes with decreased expression, and ChIP-qPCR assay suggested mutant ELF4 failed to bind to the promoters of these genes. Thus, we presented the second report of DEX.
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Affiliation(s)
- Gan Sun
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Luyao Qiu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lang Yu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yunfei An
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Ding
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Lina Zhou
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Junfeng Wu
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Yang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Zhiyong Zhang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Xuemei Tang
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Huawei Xia
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Lili Cao
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Fuping You
- Beijing Key Laboratory of Tumor Systems Biology, Department of Immunology, School of Basic Medical Sciences, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, 100000, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400014, China.
| | - Hongqiang Du
- National Clinical Research Center for Child Health and Disorders (Chongqing), Children's Hospital of Chongqing Medical University, Chongqing, China.
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China.
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China.
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Ben-David Y, Gajendran B, Sample KM, Zacksenhaus E. Current insights into the role of Fli-1 in hematopoiesis and malignant transformation. Cell Mol Life Sci 2022; 79:163. [PMID: 35412146 PMCID: PMC11072361 DOI: 10.1007/s00018-022-04160-1] [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: 11/01/2021] [Revised: 01/05/2022] [Accepted: 01/19/2022] [Indexed: 11/27/2022]
Abstract
Fli-1, a member of the ETS family of transcription factors, was discovered in 1991 through retroviral insertional mutagenesis as a driver of mouse erythroleukemias. In the past 30 years, nearly 2000 papers have defined its biology and impact on normal development and cancer. In the hematopoietic system, Fli-1 controls self-renewal of stem cells and their differentiation into diverse mature blood cells. Fli-1 also controls endothelial survival and vasculogenesis, and high and low levels of Fli-1 are implicated in the auto-immune diseases systemic lupus erythematosus and systemic sclerosis, respectively. In addition, aberrant Fli-1 expression is observed in, and is essential for, the growth of multiple hematological malignancies and solid cancers. Here, we review the historical context and latest research on Fli-1, focusing on its role in hematopoiesis, immune response, and malignant transformation. The importance of identifying Fli-1 modulators (both agonists and antagonists) and their potential clinical applications is discussed.
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Affiliation(s)
- Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China.
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
- School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Klarke M Sample
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Province Science City, High Tech Zone, Baiyun District, Guiyang, 550014, Guizhou Province, People's Republic of China
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province, Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Eldad Zacksenhaus
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Research Institute, Max Bell Research Centre, University Health Network, 101 College Street, Toronto, ON, Canada
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26
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Einarsson H, Salvatore M, Vaagensø C, Alcaraz N, Bornholdt J, Rennie S, Andersson R. Promoter sequence and architecture determine expression variability and confer robustness to genetic variants. eLife 2022; 11:80943. [PMID: 36377861 PMCID: PMC9844987 DOI: 10.7554/elife.80943] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability can be largely explained by a promoter's DNA sequence and its binding sites for specific transcription factors. We show that promoter expression variability reflects the biological process of a gene, demonstrating a selective trade-off between stability for metabolic genes and plasticity for responsive genes and those involved in signaling. Promoters with a rigid transcription start site architecture are more prone to have variable expression and to be associated with genetic variants with large effect sizes, while a flexible usage of transcription start sites within a promoter attenuates expression variability and limits genotypic effects. Our work provides insights into the variable nature of responsive genes and reveals a novel mechanism for supplying transcriptional and mutational robustness to essential genes through multiple transcription start site regions within a promoter.
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Affiliation(s)
| | - Marco Salvatore
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | | | - Nicolas Alcaraz
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Jette Bornholdt
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Sarah Rennie
- Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Robin Andersson
- Department of Biology, University of CopenhagenCopenhagenDenmark
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27
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ELK1 Promotes Epithelial-Mesenchymal Transition and the Progression of Lung Adenocarcinoma by Upregulating B7-H3. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2021:2805576. [PMID: 34970415 PMCID: PMC8714344 DOI: 10.1155/2021/2805576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/05/2021] [Accepted: 11/16/2021] [Indexed: 01/06/2023]
Abstract
In previous studies, we found that B7 homolog 3 (B7-H3) was highly expressed in lung adenocarcinoma (LUAD) and promoted epithelial-to-mesenchymal transition (EMT) of LUAD cells. However, the underlying molecular mechanism is unclear. This study is aimed at evaluating the role of Ets-like protein 1 (ELK1) as a transcriptional regulator of B7-H3 for mediating the development and progression of LUAD in vitro and in vivo. We confirmed that ELK1 is highly expressed in LUAD and is associated with poor patient prognosis. ELK1 was found to promote proliferation, invasion, migration, and EMT of LUAD cells through in vivo and in vitro experiments. In terms of mechanism, ELK1 binds to the B7-H3 promoter region and induces the upregulation of B7-H3 in LUAD. Our data suggest that ELK1 plays an important role in the development of LUAD and could be used as a prognostic marker and therapeutic target for LUAD.
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28
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Gong R, Li ZQ, Fu K, Ma C, Wang W, Chen JC. Long Noncoding RNA PVT1 Promotes Stemness and Temozolomide Resistance through miR-365/ELF4/SOX2 Axis in Glioma. Exp Neurobiol 2021; 30:244-255. [PMID: 34230224 PMCID: PMC8278140 DOI: 10.5607/en20060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 12/23/2022] Open
Abstract
Long non-coding RNA (lncRNA) are a class of non-coding RNAs demonstrated to play pivotal roles in regulating tumor progression. Therefore, deciphering the regulatory role of lncRNA in the development of glioma may offer a promising therapeutic target for treatment of glioma. We performed RT-qPCR analysis on the expression of lncRNA plasmacytoma variant translocation 1 (PVT1) and miR-365 in glioma tissues and cell lines. Cell proliferation and viability was assessed with CCK8 assay. Cell migration was assessed by wound healing assay. Transwell assay was used to assess cell invasion capacity. Expression of CD133+ cells was detected by flow cytometry. Western blot assay was used to detection the expression of ELF4 and stemness-related protein SOX2, Oct4 and Nanog. Bioinformatics and dual-luciferase assay were used to predict and validate the interaction between PVT1 and miR-365. Elevated PVT1 expression was observed in glioma tissues and cells. Knockdown of PVT1 and overexpression of miR-365 inhibited proliferation, migration, invasion and promoted stemness and Temozolomide (TMZ) resistance of glioma cells. PVT1 regulated ELF4 expression by competitively binds to miR-365. PVT1 regulated the stemness and sensitivity of TMZ of glioma cells through miR-365/ELF4/SOX2 axis. This study identified that PVT1 promoted glioma stemness through miR-365/ELF4/SOX2 axis.
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Affiliation(s)
- Rui Gong
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
| | - Zhi-Qiang Li
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
| | - Kai Fu
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
| | - Chao Ma
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
| | - Wei Wang
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
| | - Jin-Cao Chen
- Departments of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuchang 430071, Hubei, P.R. China
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29
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Kafita D, Daka V, Nkhoma P, Zulu M, Zulu E, Tembo R, Ngwira Z, Mwaba F, Sinkala M, Munsaka S. High ELF4 expression in human cancers is associated with worse disease outcomes and increased resistance to anticancer drugs. PLoS One 2021; 16:e0248984. [PMID: 33836003 PMCID: PMC8034723 DOI: 10.1371/journal.pone.0248984] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/09/2021] [Indexed: 12/12/2022] Open
Abstract
The malignant phenotype of tumour cells is fuelled by changes in the expression of various transcription factors, including some of the well-studied proteins such as p53 and Myc. Despite significant progress made, little is known about several other transcription factors, including ELF4, and how they help shape the oncogenic processes in cancer cells. To this end, we performed a bioinformatics analysis to facilitate a detailed understanding of how the expression variations of ELF4 in human cancers are related to disease outcomes and the cancer cell drug responses. Here, using ELF4 mRNA expression data of 9,350 samples from the Cancer Genome Atlas pan-cancer project, we identify two groups of patient's tumours: those that expressed high ELF4 transcripts and those that expressed low ELF4 transcripts across 32 different human cancers. We uncover that patients segregated into these two groups are associated with different clinical outcomes. Further, we find that tumours that express high ELF4 mRNA levels tend to be of a higher-grade, afflict a significantly older patient population and have a significantly higher mutation burden. By analysing dose-response profiles to 397 anti-cancer drugs of 612 well-characterised human cancer cell lines, we discover that cell lines that expressed high ELF4 mRNA transcript are significantly less responsive to 129 anti-cancer drugs, and only significantly more response to three drugs: dasatinib, WH-4-023, and Ponatinib, all of which remarkably target the proto-oncogene tyrosine-protein kinase SRC and tyrosine-protein kinase ABL1. Collectively our analyses have shown that, across the 32 different human cancers, the patients afflicted with tumours that overexpress ELF4 tended to have a more aggressive disease that is also is more likely more refractory to most anti-cancer drugs, a finding upon which we could devise novel categorisation of patient tumours, treatment, and prognostic strategies.
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Affiliation(s)
- Doris Kafita
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Victor Daka
- Department of Pathology and Microbiology, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Mildred Zulu
- Department of Clinical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | - Ephraim Zulu
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Rabecca Tembo
- Department of Clinical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | - Zifa Ngwira
- Department of Clinical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | - Florence Mwaba
- Department of Clinical Sciences, School of Medicine, Copperbelt University, Ndola, Zambia
| | - Musalula Sinkala
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
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30
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Du H, Xia H, Liu T, Li Y, Liu J, Xie B, Chen J, Liu T, Cao L, Liu S, Li S, Wang P, Wang D, Zhang Z, Li Y, Guo X, Wu A, Li M, You F. Suppression of ELF4 in ulcerative colitis predisposes host to colorectal cancer. iScience 2021; 24:102169. [PMID: 33665583 PMCID: PMC7907480 DOI: 10.1016/j.isci.2021.102169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 01/12/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease, characterized by relapsing and remitting colon mucosal inflammation. For patients suffering from UC, a higher risk of colon cancer has been widely recognized. Here, we found that Elf4−/− mice developed colon tumors with 3 cycles of dextran sulfate sodium salt (DSS) treatment alone. We further showed that ELF4 suppression was prevalent in both patients with UC and DSS-induced mice models, and this suppression was caused by promoter region methylation. ELF4, upon PARylation by PARP1, transcriptionally regulated multiple DNA damage repair machinery components. Consistently, ELF4 deficiency leads to more severe DNA damage both in vitro and in vivo. Oral administration of montmorillonite powder can prevent the reduction of ELF4 in DSS-induced colitis models and lower the risk of colon tumor development during azoxymethane (AOM) and DSS induced colitis-associated cancer (CAC). These data provided additional mechanism of CAC initiation and supported the “epigenetic priming model of tumor initiation”. Elf4 expression is suppressed in both colitis and colitis-associated cancer (CAC). Elf4 deficiency leads to increased hyper-susceptibility to colitis and CAC in mice Elf4 promotes DNA damage repair upon PARylation by PARP1 Oral administration of montmorillonite lowers risk of CAC development
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Affiliation(s)
- Hongqiang Du
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Huawei Xia
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Tongtong Liu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Yingjie Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing 100000, China
| | - Jilong Liu
- Department of surgical oncology, ChuiYangLiu Hospital affiliated to Tsinghua University, Beijing 100000, China
| | - Bingteng Xie
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100000, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100000, China
| | - Jingxuan Chen
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Tong Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163000, China
| | - Lili Cao
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Shengde Liu
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Siji Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Peiyan Wang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Dandan Wang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Zeming Zhang
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Yunfei Li
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
| | - Xiaohuan Guo
- Institute of Immunology, Tsinghua University School of Medicine, Beijing 100000, China
| | - Aiwen Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing 100000, China
| | - Mo Li
- Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100000, China.,Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100000, China
| | - Fuping You
- Institute of Systems Biomedicine, Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing 100000, China
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31
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Qu H, Zhao H, Zhang X, Liu Y, Li F, Sun L, Song Z. Integrated Analysis of the ETS Family in Melanoma Reveals a Regulatory Role of ETV7 in the Immune Microenvironment. Front Immunol 2020; 11:612784. [PMID: 33424867 PMCID: PMC7786291 DOI: 10.3389/fimmu.2020.612784] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
The ETS family modulates immune response and drug efficiency to targeted therapies, but their role in melanoma is largely unclear. In this study, the ETS family was systematically analyzed in multiple public data sets. Bioinformatics tools were used to characterize the function of ETV7 in melanoma. A prognostic model was constructed using the LASSO Cox regression method. We found that ETV7 was the only differentially expressed gene with significant prognostic relevance in melanoma. Enrichment analysis of seven independent data sets indicated ETV7 participation in various immune-related pathways. ETV7 particularly showed a strong positive correlation with CD8+ T cell infiltration. The prognostic model based on ETV7 and its hub genes showed a relatively good predictive value in training and testing data sets. Thus, ETV7 can potentially regulate the immune microenvironment in melanoma.
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Affiliation(s)
- Hui Qu
- Department of Plastic Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Hui Zhao
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xi Zhang
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yang Liu
- Department of Pathology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Feng Li
- Department of Plastic Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Liyan Sun
- Department of Plastic Surgery, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Taiyuan, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
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32
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Laaref AM, Manchon L, Bareche Y, Lapasset L, Tazi J. The core spliceosomal factor U2AF1 controls cell-fate determination via the modulation of transcriptional networks. RNA Biol 2020; 17:857-871. [PMID: 32150510 PMCID: PMC7549707 DOI: 10.1080/15476286.2020.1733800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/16/2022] Open
Abstract
Alternative splicing (AS) plays a central role during cell-fate determination. However, how the core spliceosomal factors (CSFs) are involved in this process is poorly understood. Here, we report the down-regulation of the U2AF1 CSF during stem cell differentiation. To investigate its function in stemness and differentiation, we downregulated U2AF1 in human induced pluripotent stem cells (hiPSCs), using an inducible-shRNA system, to the level found in differentiated ectodermal, mesodermal and endodermal cells. RNA sequencing and computational analysis reveal that U2AF1 down-regulation modulates the expression of development-regulating genes and regulates transcriptional networks involved in cell-fate determination. Furthermore, U2AF1 down-regulation induces a switch in the AS of transcription factors (TFs) required to establish specific cell lineages, and favours the splicing of a differentiated cell-specific isoform of DNMT3B. Our results showed that the differential expression of the core spliceosomal factor U2AF1, between stem cells and the precursors of the three germ layers regulates a cell-type-specific alternative splicing programme and a transcriptional network involved in cell-fate determination via the modulation of gene expression and alternative splicing of transcription regulators.
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Affiliation(s)
| | | | - Yacine Bareche
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Breast Cancer Translational Research Laboratory, J. C. Heuson, Institut Jules Bordet, Université Libre De Bruxelles, Brussels, Belgium
| | - Laure Lapasset
- IGMM, CNRS, University of Montpellier, Montpellier, France
- VP research, CNRS, University of Montpellier, Montpellier, France
| | - Jamal Tazi
- IGMM, CNRS, University of Montpellier, Montpellier, France
- Lead Contact
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33
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Progress in the Knowledge, Application and Influence of Extremely Low Frequency Signals. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10103494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This paper describes the characteristics of contributions made by researchers worldwide in the field of ELF (extremely low frequency) waves from 1957 to 2019. The data were collected through the Scopus database and processed with analytical and bibliometric techniques. The selection of the keywords is an essential step, because ELF has a very different meaning in some areas of medicine, where it is associated with a gene. A total of 12,436 documents were worked on in 12 thematic communities according to their collaborative relationships between authors and documents. Studies included authors publishing in the different thematic areas and the country where the USA stands first with more researchers in this theme than China and Japan. Documents were analyzed from the temporal perspective, their overall contribution, means of publication, and the language of the publication. Research requires extra effort and multidisciplinary collaboration to improve the knowledge, the application, and influence of these fields.
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34
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Cai WL, Greer CB, Chen JF, Arnal-Estapé A, Cao J, Yan Q, Nguyen DX. Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain. BMC Med Genomics 2020; 13:33. [PMID: 32143622 PMCID: PMC7060551 DOI: 10.1186/s12920-020-0695-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/11/2020] [Indexed: 12/17/2022] Open
Abstract
Background Few somatic mutations have been linked to breast cancer metastasis, whereas transcriptomic differences among primary tumors correlate with incidence of metastasis, especially to the lungs and brain. However, the epigenomic alterations and transcription factors (TFs) which underlie these alterations remain unclear. Methods To identify these, we performed RNA-seq, Chromatin Immunoprecipitation and sequencing (ChIP-seq) and Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) of the MDA-MB-231 cell line and its brain (BrM2) and lung (LM2) metastatic sub-populations. We incorporated ATAC-seq data from TCGA to assess metastatic open chromatin signatures, and gene expression data from human metastatic datasets to nominate transcription factor biomarkers. Results Our integrated epigenomic analyses found that lung and brain metastatic cells exhibit both shared and distinctive signatures of active chromatin. Notably, metastatic sub-populations exhibit increased activation of both promoters and enhancers. We also integrated these data with chromosome conformation capture coupled with ChIP-seq (HiChIP) derived enhancer-promoter interactions to predict enhancer-controlled pathway alterations. We found that enhancer changes are associated with endothelial cell migration in LM2, and negative regulation of epithelial cell proliferation in BrM2. Promoter changes are associated with vasculature development in LM2 and homophilic cell adhesion in BrM2. Using ATAC-seq, we identified a metastasis open-chromatin signature that is elevated in basal-like and HER2-enriched breast cancer subtypes and associates with worse prognosis in human samples. We further uncovered TFs associated with the open chromatin landscapes of metastatic cells and whose expression correlates with risk for metastasis. While some of these TFs are associated with primary breast tumor subtypes, others more specifically correlate with lung or brain metastasis. Conclusions We identify distinctive epigenomic properties of breast cancer cells that metastasize to the lung and brain. We also demonstrate that signatures of active chromatin sites are partially linked to human breast cancer subtypes with poor prognosis, and that specific TFs can independently distinguish lung and brain relapse.
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Affiliation(s)
- Wesley L Cai
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Celeste B Greer
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Department of Pharmacology, Vanderbilt University School of Medicine, 2209 Garland Ave, Nashville, TN, 37240-0002, USA
| | - Jocelyn F Chen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Anna Arnal-Estapé
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Present address: Rutgers Cancer Institute of New Jersey, Rutgers, 195 Little Albany St, New Brunswick, NJ, 08903-2681, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA.
| | - Don X Nguyen
- Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Cancer Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Yale Stem Cell Center, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA. .,Department of Pathology, Yale School of Medicine, P.O. Box 208023, New Haven, CT, 06520-8023, USA. .,Department of Medicine (Medical Oncology), Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.
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The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. Sci Rep 2020; 10:1522. [PMID: 32001787 PMCID: PMC6992634 DOI: 10.1038/s41598-020-58470-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. Moreover, E. fraudatrix can quickly restore parts of its body and entire organ systems, yet at the moment, there is no data on the participation of stem cells in the process. To the contrary, it has been repeatedly confirmed that this process is only due to the transformation of terminally differentiated cells. In this study, we examine changes in gene expression during gut regeneration of the holothurian E. fraudatrix. Transcriptomes of intestinal anlage of the three stages of regeneration, as well as the normal gut, were sequenced with an Illumina sequencer (San Diego, CA, USA). We identified 14,617 sea urchin protein homologs, of which 308 were transcription factors. After analysing the dynamics of gene expression during regeneration and the map of biological processes in which they participate, we identified 11 factors: Ef-EGR1, Ef-ELF, Ef-GATA3, Ef-ID2, Ef-KLF1/2/4, Ef-MSC, Ef-PCGF2, Ef-PRDM9, Ef-SNAI2, Ef-TBX20, and Ef-TCF24. With the exception of TCF24, they are all involved in the regeneration, development, epithelial-mesenchymal transition, and immune response in other animals. We suggest that these transcription factors may also be involved in the transdifferentiation of coelomic epithelial cells into enterocytes in holothurians.
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36
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Wang D, Zhang Z, Cui S, Zhao Y, Craft S, Fikrig E, You F. ELF4 facilitates innate host defenses against Plasmodium by activating transcription of Pf4 and Ppbp. J Biol Chem 2019; 294:7787-7796. [PMID: 30898878 DOI: 10.1074/jbc.ra118.006321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/08/2019] [Indexed: 12/12/2022] Open
Abstract
Platelet factor 4 (PF4) is an anti-Plasmodium component of platelets. It is expressed in megakaryocytes and released from platelets following infection with Plasmodium Innate immunity is crucial for the host anti-Plasmodium response, in which type I interferon plays an important role. Whether there is cross-talk between innate immune signaling and the production of anti-Plasmodium defense peptides is unknown. Here we demonstrate that E74, like ETS transcription factor 4 (ELF4), a type I interferon activator, can help protect the host from Plasmodium yoelii infection. Mechanically, ELF4 binds to the promoter of genes of two C-X-C chemokines, Pf4 and pro-platelet basic protein (Ppbp), initiating the transcription of these two genes, thereby enhancing PF4-mediated killing of parasites from infected erythrocytes. Elf4 -/- mice are much more susceptible to Plasmodium infection than WT littermates. The expression level of Pf4 and Ppbp in megakaryocytes from Elf4 -/- mice is much lower than in those from control animals, resulting in increased parasitemia. In conclusion, our study uncovered a distinct role of ELF4, an innate immune molecule, in host defense against malaria.
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Affiliation(s)
- Dandan Wang
- From the Institute of Systems Biomedicine, Department of Immunology, and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China 100191
| | - Zeming Zhang
- From the Institute of Systems Biomedicine, Department of Immunology, and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China 100191
| | - Shuang Cui
- the Key Laboratory for Neuroscience, Neuroscience Research Institute, Peking University, Beijing, China 100191.,the National Health and Family Planning Commission of the People's Republic of China, Ministry of Education, Beijing, China 100083, and
| | - Yingchi Zhao
- From the Institute of Systems Biomedicine, Department of Immunology, and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China 100191
| | - Samuel Craft
- the Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Erol Fikrig
- the Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520
| | - Fuping You
- From the Institute of Systems Biomedicine, Department of Immunology, and Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China 100191,
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Rovira-Rigau M, Raimondi G, Marín MÁ, Gironella M, Alemany R, Fillat C. Bioselection Reveals miR-99b and miR-485 as Enhancers of Adenoviral Oncolysis in Pancreatic Cancer. Mol Ther 2018; 27:230-243. [PMID: 30341009 DOI: 10.1016/j.ymthe.2018.09.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/14/2022] Open
Abstract
Oncolytic viruses are designed for cancer treatment. Cell-virus interactions are key determinants for successful viral replication. Therefore, the extensive reprogramming of gene expression that occurs in tumor cells might create a hurdle for viral propagation. We used a replication-based approach of a microRNA (miRNA) adenoviral library encoding up to 243 human miRNAs as a bioselection strategy to identify miRNAs that facilitate adenoviral oncolytic activity in pancreatic ductal adenocarcinoma. We identify two miRNAs, miR-99b and miR-485, that function as enhancers of adenoviral oncolysis by improving the intra- and extracellular yield of mature virions. An increased adenoviral activity is the consequence of enhanced E1A and late viral protein expression, which is probably mediated by the downregulation of the transcriptional repressors ELF4, MDM2, and KLF8, which we identify as miR-99b or miR-485 target genes. Arming the oncolytic adenovirus ICOVIR15 with miR-99b or miR-485 enhances its fitness and its antitumoral activity. Our results demonstrate the potential of this strategy to improve oncolytic adenovirus potency, and they highlight miR-99b and miR-485 as sensitizers of adenoviral replication.
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Affiliation(s)
- Maria Rovira-Rigau
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Giulia Raimondi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Miguel Ángel Marín
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Meritxell Gironella
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Gastrointestinal & Pancreatic Oncology Group, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), 08036 Barcelona, Spain
| | - Ramon Alemany
- Institut Català d'Oncologia-IDIBELL, 08907 L'Hospitalet de Llobregat, Spain
| | - Cristina Fillat
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain; Facultat de Medicina i Ciències de la Salut. Universitat de Barcelona (UB), 08036 Barcelona, Spain.
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