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Anim M, Sogkas G, Camacho-Ordonez N, Schmidt G, Elsayed A, Proietti M, Witte T, Grimbacher B, Atschekzei F. Novel hypermorphic variants in IRF2BP2 identified in patients with common variable immunodeficiency and autoimmunity. Clin Immunol 2024:110326. [PMID: 39059757 DOI: 10.1016/j.clim.2024.110326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/12/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024]
Abstract
The interferon regulatory factor 2 binding protein 2 (IRF2BP2) is a transcriptional regulator, functioning a transcriptional corepressor by interacting with the interferon regulatory factor-2. The ubiquitous expression of IRF2BP2 by diverse cell types and tissues suggests its potential involvement in different cell signalling pathways. Variants inIRF2BP2have been recently identified to cause familial common variable immunodeficiency (CVID) characterized by immune dysregulation. This study investigated three rare novel variants inIRF2BP2, identified in patients with primary antibody deficiency and autoimmunity by whole exome-sequencing (WES). Following transient overexpression of EGFP-fused mutants in HEK293 cells and transfection in Jurkat cell lines, we used fluorescence microscopy, real-time PCR and Western blotting to analyze their effects on IRF2BP2 expression, subcellular localization, nuclear translocation of IRF2, and the transcriptional activation of NFκB1(p50). We found altered IRF2BP2 mRNA and protein expression levels in the mutants compared to the wild type after IRF2BP2 overexpression. In confocal fluorescence microscopy, variants in the C-terminal RING finger domain showed an irregular aggregate formation and distribution instead of the expected nuclear localization compared to the variants in the N-terminal zinc finger domain and their wildtype counterpart. Immunoblotting revealed an impaired IRF2 and NFκB1 (p50) nuclear localization in the mutants compared to the IRF2BP2 wildtype counterpart. LPS stimulation reduced IRF2BP2 mRNA expression in the variants compared to the wild type. Our findings significantly contribute to understanding the clinical significance of IRF2BP2 mutations in the pathogenesis of immunodeficiency and immune dysregulation. We observed impairment of the nuclear translocation of IRF2 and NFκB1 (p50) due to the upregulation of IRF2BP2, potentially affecting specific gene expressions involved in immune regulation.
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Affiliation(s)
- Manfred Anim
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; Hannover Biomedical Research School (HBRS), Hannover Medical School, Hanover, Germany
| | - Georgios Sogkas
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany
| | - Nadezhda Camacho-Ordonez
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Gunnar Schmidt
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Abdulwahab Elsayed
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Michele Proietti
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany.; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Torsten Witte
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany
| | - Bodo Grimbacher
- RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany.; Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Clinic of Rheumatology and Clinical Immunology, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany
| | - Faranaz Atschekzei
- Department of Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Hanover, Germany..
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Fischer S, Weber LM, Stielow B, Frech M, Simon C, Geller M, Könnecke J, Finkernagel F, Forné I, Nist A, Bauer UM, Stiewe T, Neubauer A, Liefke R. IRF2BP2 counteracts the ATF7/JDP2 AP-1 heterodimer to prevent inflammatory overactivation in acute myeloid leukemia (AML) cells. Nucleic Acids Res 2024; 52:7590-7609. [PMID: 38801077 PMCID: PMC11260449 DOI: 10.1093/nar/gkae437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 04/16/2024] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Acute myeloid leukemia (AML) is a hematological malignancy characterized by abnormal proliferation and accumulation of immature myeloid cells in the bone marrow. Inflammation plays a crucial role in AML progression, but excessive activation of cell-intrinsic inflammatory pathways can also trigger cell death. IRF2BP2 is a chromatin regulator implicated in AML pathogenesis, although its precise role in this disease is not fully understood. In this study, we demonstrate that IRF2BP2 interacts with the AP-1 heterodimer ATF7/JDP2, which is involved in activating inflammatory pathways in AML cells. We show that IRF2BP2 is recruited by the ATF7/JDP2 dimer to chromatin and counteracts its gene-activating function. Loss of IRF2BP2 leads to overactivation of inflammatory pathways, resulting in strongly reduced proliferation. Our research indicates that a precise equilibrium between activating and repressive transcriptional mechanisms creates a pro-oncogenic inflammatory environment in AML cells. The ATF7/JDP2-IRF2BP2 regulatory axis is likely a key regulator of this process and may, therefore, represent a promising therapeutic vulnerability for AML. Thus, our study provides new insights into the molecular mechanisms underlying AML pathogenesis and identifies a potential therapeutic target for AML treatment.
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Affiliation(s)
- Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Miriam Frech
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Merle Geller
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Julie Könnecke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Florian Finkernagel
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, Marburg 35043, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried 82152, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Uta-Maria Bauer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
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Bishop JA, Nakaguro M, Urano M, Yamamoto Y, Utsumi Y, Li R, Weinreb I, Nagashima Y, Gangahar C, Yamashiro K, Hashimoto K, Rooper LM, Carlile B, Wang RC, Gagan J, Nagao T. Keratocystoma: A Distinctive Salivary Gland Neoplasm Characterized by RUNX2 Rearrangements. Am J Surg Pathol 2024; 48:317-328. [PMID: 38084005 DOI: 10.1097/pas.0000000000002169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Keratocystoma is a rare salivary gland lesion that has been reported primarily in children and young adults. Because of a scarcity of reported cases, very little is known about it, including its molecular underpinnings, biological potential, and histologic spectrum. Purported to be a benign neoplasm, keratocystoma bears a striking histologic resemblance to benign lesions like metaplastic Warthin tumor on one end of the spectrum and squamous cell carcinoma on the other end. This overlap can cause diagnostic confusion, and it raises questions about the boundaries and definition of keratocystoma as an entity. This study seeks to utilize molecular tools to evaluate the pathogenesis of keratocystoma as well as its relationship with its histologic mimics. On the basis of targeted RNA sequencing (RNA-seq) results on a sentinel case, RUNX2 break-apart fluorescence in situ hybridization (FISH) was successfully performed on 4 cases diagnosed as keratocystoma, as well as 13 cases originally diagnosed as tumors that morphologically resemble keratocystoma: 6 primary squamous cell carcinomas, 3 metaplastic/dysplastic Warthin tumors, 2 atypical squamous cysts, 1 proliferating trichilemmal tumor, and 1 cystadenoma. RNA-seq and/or reverse transcriptase-PCR were attempted on all FISH-positive cases. Seven cases were positive for RUNX2 rearrangement, including 3 of 4 tumors originally called keratocystoma, 2 of 2 called atypical squamous cyst, 1 of 1 called proliferating trichilemmal tumor, and 1 of 6 called squamous cell carcinoma. RNA-seq and/or reverse transcriptase-PCR identified IRF2BP2::RUNX2 in 6 of 7 cases; for the remaining case, the partner remains unknown. The cases positive for RUNX2 rearrangement arose in the parotid glands of 4 females and 3 males, ranging from 8 to 63 years old (mean, 25.4 years; median, 15 years). The RUNX2 -rearranged cases had a consistent histologic appearance: variably sized cysts lined by keratinizing squamous epithelium, plus scattered irregular squamous nests, with essentially no cellular atypia or mitotic activity. The background was fibrotic, often with patchy chronic inflammation and/or giant cell reaction. One case originally called squamous cell carcinoma was virtually identical to the other cases, except for a single focus of small nerve invasion. The FISH-negative case that was originally called keratocystoma had focal cuboidal and mucinous epithelium, which was not found in any FISH-positive cases. The tumors with RUNX2 rearrangement were all treated with surgery only, and for the 5 patients with follow-up, there were no recurrences or metastases (1 to 120 months), even for the case with perineural invasion. Our findings solidify that keratocystoma is a cystic neoplastic entity, one which appears to consistently harbor RUNX2 rearrangements, particularly IRF2BP2::RUNX2 . Having a diagnostic genetic marker now allows for a complete understanding of this rare tumor. They arise in the parotid gland and affect a wide age range. Keratocystoma has a consistent morphologic appearance, which includes large squamous-lined cysts that mimic benign processes like metaplastic Warthin tumor and also small, irregular nests that mimic squamous cell carcinoma. Indeed, RUNX2 analysis has considerable promise for resolving these differential diagnoses. Given that one RUNX2 -rearranged tumor had focal perineural invasion, it is unclear whether that finding is within the spectrum of keratocystoma or whether it could represent malignant transformation. Most important, all RUNX2 -rearranged cases behaved in a benign manner.
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Affiliation(s)
| | - Masato Nakaguro
- Departments of Pathology and Laboratory Medicine, Nagoya University Hospital
| | - Makoto Urano
- Department of Diagnostic Pathology, Bantane Hospital, Fujita Health University School of Medicine, Nagoya
| | | | | | - Rong Li
- Department of Pathology and Laboratory Medicine, Children's of Alabama, Birmingham, AL
| | - Ilan Weinreb
- Department of Pathology, University Health Network and the University of Toronto, Toronto, ON, Canada
| | - Yoji Nagashima
- Department of Surgical Pathology, Tokyo Women's Medical University Hospital, Tokyo
| | | | | | - Kimio Hashimoto
- Department of Pathology, Nishi-Kobe Medical Center, Kobe, Japan
| | - Lisa M Rooper
- Departments of Pathology and Oncology, The Johns Hopkins Medical Institutions, Baltimore, MD
| | - Brian Carlile
- Department of Pathology, Baylor Scott and White Health, All Saints Medical Center, Fort Worth, TX
| | - Richard C Wang
- Department of Dermatology, UT Southwestern Medical Center, Dallas
| | - Jeffrey Gagan
- Department of Pathology, UT Southwestern Medical Center
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Wang C, Zhou W, Zhang L, Fu L, Shi W, Qing Y, Lu F, Tang J, Gao X, Zhang A, Jia Z, Zhang Y, Zhao X, Zheng B. Diagnostic yield and novel candidate genes for neurodevelopmental disorders by exome sequencing in an unselected cohort with microcephaly. BMC Genomics 2023; 24:422. [PMID: 37501076 PMCID: PMC10373276 DOI: 10.1186/s12864-023-09505-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
OBJECTIVES Microcephaly is caused by reduced brain volume and most usually associated with a variety of neurodevelopmental disorders (NDDs). To provide an overview of the diagnostic yield of whole exome sequencing (WES) and promote novel candidates in genetically unsolved families, we studied the clinical and genetic landscape of an unselected Chinese cohort of patients with microcephaly. METHODS We performed WES in an unselected cohort of 103 NDDs patients with microcephaly as one of the features. Full evaluation of potential novel candidate genes was applied in genetically undiagnosed families. Functional validations of selected variants were conducted in cultured cells. To augment the discovery of novel candidates, we queried our genomic sequencing data repository for additional likely disease-causing variants in the identified candidate genes. RESULTS In 65 families (63.1%), causative sequence variants (SVs) and clinically relevant copy number variants (CNVs) with a pathogenic or likely pathogenic (P/LP) level were identified. By incorporating coverage analysis to WES, a pathogenic or likely pathogenic CNV was detected in 15 families (16/103, 15.5%). In another eight families (8/103, 7.8%), we identified variants in newly reported gene (CCND2) and potential novel neurodevelopmental disorders /microcephaly candidate genes, which involved in cell cycle and division (PWP2, CCND2), CDC42/RAC signaling related actin cytoskeletal organization (DOCK9, RHOF), neurogenesis (ELAVL3, PPP1R9B, KCNH3) and transcription regulation (IRF2BP1). By looking into our data repository of 5066 families with NDDs, we identified additional two cases with variants in DOCK9 and PPP1R9B, respectively. CONCLUSION Our results expand the morbid genome of monogenic neurodevelopmental disorders and support the adoption of WES as a first-tier test for individuals with microcephaly.
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Affiliation(s)
- Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Luyan Zhang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Luhan Fu
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Shi
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yan Qing
- Department of Neurosurgery, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Fen Lu
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Tang
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiucheng Gao
- Department of Radiology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Aihua Zhang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Zhanjun Jia
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Zhang
- Jiangsu Key Laboratory of Pediatrics, Nanjing Medical University, Nanjing, China.
| | - Xiaoke Zhao
- Department of Rehabilitation Medicine, Children's Hospital of Nanjing Medical University, Nanjing, China.
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China.
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Kim J, Sim AY, Barua S, Kim JY, Lee JE. Agmatine-IRF2BP2 interaction induces M2 phenotype of microglia by increasing IRF2-KLF4 signaling. Inflamm Res 2023:10.1007/s00011-023-01741-z. [PMID: 37314519 DOI: 10.1007/s00011-023-01741-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Following central nervous system (CNS) injury, the investigation for neuroinflammation is vital because of its pleiotropic role in both acute injury and long-term recovery. Agmatine (Agm) is well known for its neuroprotective effects and anti-neuroinflammatory properties. However, Agm's mechanism for neuroprotection is still unclear. We screened target proteins that bind to Agm using a protein microarray; the results showed that Agm strongly binds to interferon regulatory factor 2 binding protein (IRF2BP2), which partakes in the inflammatory response. Based on these prior data, we attempted to elucidate the mechanism by which the combination of Agm and IRF2BP2 induces a neuroprotective phenotype of microglia. METHODS To confirm the relationship between Agm and IRF2BP2 in neuroinflammation, we used microglia cell-line (BV2) and treated with lipopolysaccharide from Escherichia coli 0111:B4 (LPS; 20 ng/mL, 24 h) and interleukin (IL)-4 (20 ng/mL, 24 h). Although Agm bound to IRF2BP2, it failed to enhance IRF2BP2 expression in BV2. Therefore, we shifted our focus onto interferon regulatory factor 2 (IRF2), which is a transcription factor and interacts with IRF2BP2. RESULTS IRF2 was highly expressed in BV2 after LPS treatment but not after IL-4 treatment. When Agm bound to IRF2BP2 following Agm treatment, the free IRF2 translocated to the nucleus of BV2. The translocated IRF2 activated the transcription of Kruppel-like factor 4 (KLF4), causing KLF4 to be induced in BV2. The expression of KLF4 increased the CD206-positive cells in BV2. CONCLUSIONS Taken together, unbound IRF2, resulting from the competitive binding of Agm to IRF2BP2, may provide neuroprotection against neuroinflammation via an anti-inflammatory mechanism of microglia involving the expression of KLF4.
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Affiliation(s)
- Jiwon Kim
- Department of Anatomy, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - A Young Sim
- Department of Anatomy, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Sumit Barua
- Department of Anatomy, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea
| | - Jong Youl Kim
- Department of Anatomy, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
| | - Jong Eun Lee
- Department of Anatomy, Yonsei University College of Medicine, 50-1, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea.
- Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Brain Research Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.
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Pan Y, Shang G, Li J, Zhang Y, Liu J, Ji Y, Ding J, Wang X. Case Report: A novel IRF2BP2 mutation in an IEI patient with recurrent infections and autoimmune disorders. Front Immunol 2023; 14:967345. [PMID: 37350971 PMCID: PMC10282741 DOI: 10.3389/fimmu.2023.967345] [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: 06/26/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Introduction Inborn errors of immunity (IEI) are a heterogeneous group of disorders characterized by increased risk of infections, autoimmunity, autoinflammatory diseases, malignancy and allergy. Next-generation sequencing has revolutionized the identification of genetic background of these patients and assists in diagnosis and treatment. In this study, we identified a probable unique monogenic cause of IEI, and evaluated the immunological methods and pathogenic detections. Methods A family with a member with a clinical diagnosis of IEI was screened by whole genomic sequencing (WGS). Demographic data, clinical manifestations, medical history, physical examination, laboratory findings and imaging features of the patient were extracted from medical records. Comprehensive immune monitoring methods include a complete blood count with differential, serum levels of cytokines and autoantibodies, T-cell and B-cell subsets analysis and measurement of serum immunoglobulins. In addition, metagenomic sequencing (mNGS) of blood, cerebrospinal fluid and biopsy from small intestine were used to detect potential pathogens. Results The patient manifested with recurrent infections and autoimmune disorders, who was eventually diagnosed with IEI. Repetitive mNGS tests of blood, cerebrospinal fluid and biopsy from small intestine didn't detect pathogenic microorganism. Immunological tests showed a slightly decreased level of IgG than normal, elevated levels of tumor necrosis factor and interleukin-6. Lymphocyte flow cytometry showed elevated total B cells and natural killer cells, decreased total T cells and B-cell plasmablasts. WGS of the patient identified a novel heterozygous mutation in IRF2BP2 (c.439_450dup p. Thr147_Pro150dup), which was also confirmed in his father. The mutation was classified as variant of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics guidelines. Conclusion We identified a novel IRF2BP2 mutation in a family with a member diagnosed with IEI. Immune monitoring and WGS as auxiliary tests are helpful in identifying genetic defects and assisting diagnosis in patients with clinically highly suspected immune abnormalities and deficiencies in inflammation regulation. In addition, mNGS techniques allow a more comprehensive assessment of the pathogenic characteristics of these patients. This report further validates the association of IRF2BP2 deficiency and IEI, and expands IEI phenotypes.
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Affiliation(s)
- Yiwen Pan
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guoguo Shang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Li
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuwen Zhang
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianying Liu
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Ding
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xin Wang
- Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai, China
- The State Key Laboratory of Medical Neurobiology and Ministry of Education Frontiers Center for Brain Science, The Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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Qiao X, Wang S, Zong Y, Gu X, Jin Y, Li Y, Wei Z, Wang L, Song L. An IRF2BP member (CgIRF2BP) involved in negative regulation of CgIFNLP expression in oyster Crassostrea gigas. FISH & SHELLFISH IMMUNOLOGY 2023; 134:108576. [PMID: 36775182 DOI: 10.1016/j.fsi.2023.108576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The IRF2BP family of transcription regulators act as corepressor molecules by inhibiting both enhancer-activated and basal transcription involving in many biological contexts. In the present study, an IRF2BP homologue (CgIRF2BP) was identified from oyster C. gigas. Its open reading frame is of 1809 bp encoding a polypeptide of 602 amino acids, which contains an IRF-2BP1_2 domain and a RING domain. The mRNA transcripts of CgIRF2BP were detected in all tested tissues with highest level in haemocytes (28.99-fold of that in mantle, p < 0.05). After poly (I:C) stimulation, the expression level of CgIRF2BP was significantly down-regulated at 3 h (0.50-fold of that in control group, p < 0.001) and gradually increased from 6 h to 48 h (2.69-fold of that in control group, p < 0.01). The recombinant protein of CgIRF2BP (rCgIRF2BP) showed high affinity to both rCgIRF1 and rCgIRF8 with Kd value of 1.02 × 10-7 and 2.09 × 10-7, respectively. In CgIRF2BP-RNAi oysters, the mRNA expression of CgIFNLP, CgMx1, CgViperin and CgIFI44L were significantly increased after poly (I:C) stimulation, which were 2.88 (p < 0.01), 1.83 (p < 0.05), 2.47 (p < 0.05), and 1.99-fold (p < 0.01) of that in EGFP group, respectively. These findings suggested that CgIRF2BP negatively regulated CgIFNLP expression by binding with CgIRF1 and CgIRF8.
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Affiliation(s)
- Xue Qiao
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Sicong Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yanan Zong
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Xiaoyu Gu
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Yuhao Jin
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Youjing Li
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Zhuorui Wei
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
| | - Lingling Wang
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China.
| | - Linsheng Song
- Liaoning Key Laboratory of Marine Animal Immunology, Dalian Ocean University, Dalian, 116023, China; Southern Laboratory of Ocean Science and Engineering (Guangdong, Zhuhai), Zhuhai, 519000, China; Liaoning Key Laboratory of Marine Animal Immunology and Disease Control, Dalian Ocean University, Dalian, 116023, China; Dalian Key Laboratory of Aquatic Animal Disease Prevention and Control, Dalian Ocean University, Dalian, 116023, China
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Comparative Transcriptional Signature Analysis of Peripheral Blood Mononuclear Cells in Early Stage of Hepatitis B-related Hepatocellular Carcinoma. HEPATITIS MONTHLY 2023. [DOI: 10.5812/hepatmon-130862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Background: Hepatocellular carcinoma (HCC) is a prevalent and life-threatening tumor with high morbidity and mortality. Proper prediction and prognosis are incredibly stressed to diagnose HCC and increase patient survival. Objectives: This research aims to evaluate gene expression levels of pre-differentiated transcripts for those suffering from chronic hepatitis B (CHB) and HCC. Methods: To examine the previously analyzed peripheral blood mononuclear cells (PBMCs) transcriptomic array data, we selected seven differentially expressed genes (DEGs) in normal versus CHB and CHB versus HCC (CD44, SP3, USP8, E2F2, UFM1, IFN regulative factor binding protein 2 (IRF2BP2), and T-cell intracellular antigen 1 (TIA1)). The study included individuals with treatment-naïve CHB (n = 30) and primary HCC (n = 25) and healthy controls (n = 15). Subsequently, the expression of genes was assayed using qRT-PCR. A phylogenetic evaluation was performed using direct sequencing of HBsAg. Results: In HCC patients, 60% (n = 15) were HBeAg-positive. HBeAg was negative in all CHB patients, but all were anti-HBe-positive. The hepatitis B virus (HBV) load of HCC patients was more than that of CHB subjects. All patients were of the Iranian race and HBV D genotype. The expression of five transcriptional markers (CD44, SP3, USP8, E2F2, and UFM1) was higher in HCC patients than in CHB and healthy subjects, which was similar to the initial microarray data analysis. Conclusions: Transcriptional signatures may be related to the pathogenesis of HCC and used as diagnostic biological markers for the initial monitoring and prediction of HCC.
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LncRNA ATP1A1-AS1 inhibits cell proliferation and promotes cell apoptosis in thyroid carcinoma by regulating the miR-620/IRF2BP2 axis. Am J Med Sci 2023; 365:73-83. [PMID: 36002076 DOI: 10.1016/j.amjms.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/28/2022] [Accepted: 08/15/2022] [Indexed: 01/04/2023]
Abstract
BACKGROUND Thyroid carcinoma (THCA) is a common malignancy of the endocrine system. Further understanding of the molecular mechanism underlying THCA is crucial to develop effective diagnostic therapy and improve its treatments. In this study, we intended to provide novel direction for THCA targeted therapy from the aspect of lncRNA-miRNA-mRNA interaction. We aimed to investigate the function and molecular mechanism of lncRNA ATP1A1-AS1 in THCA. METHODS Gene expression was assessed by reverse transcription quantitative polymerase chain reaction (RT-qPCR). Cell growth was detected by CCK-8 and EdU assays. Flow cytometry was applied for analyzing cell apoptosis. The binding of ATP1A1-AS1 or IRF2BP2 to miR-620 was validated by RNA pulldown and luciferase reporter assays. The protein levels were examined by western blotting. RESULTS ATP1A1-AS1 was decreased in THCA cells and tissues. ATP1A1-AS1 overexpression attenuated cell growth and promoted apoptosis. MiR-620, which was upregulated in THCA, was identified as a direct target of ATP1A1-AS1. Furthermore, IRF2BP2 was discovered to be a target of miR-620, which displayed low expression in THCA cells and tissues. Importantly, IRF2BP2 knockdown reversed the influence of ATP1A1-AS1 overexpression on THCA cell proliferation and apoptosis. CONCLUSIONS LncRNA ATP1A1-AS1 inhibited cell growth and promotes apoptosis in THCA via the miR-620/IRF2BP2 axis.
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Liu Y, Yang Y, Lin Y, Wei B, Hu X, Xu L, Zhang W, Lu J. N 6 -methyladenosine-modified circRNA RERE modulates osteoarthritis by regulating β-catenin ubiquitination and degradation. Cell Prolif 2023; 56:e13297. [PMID: 35733354 DOI: 10.1111/cpr.13297] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVES N6 -methyladenosine (m6A) is one of the most abundant internal RNA modifications. We investigated the role of m6A-modified circRERE in osteoarthritis (OA) and its mechanism. MATERIALS AND METHODS CircRERE and IRF2BPL were screened by microarrays. The role of m6A-modification in circRERE was examined by methylated RNA precipitation and morpholino oligo (MOs) treatment. The axis of circRERE/miR-195-5p/IRF2BPL/β-catenin was determined using flow cytometry, western blotting and immunofluorescence in human chondrocytes (HCs) and corroborated using a mouse model of destabilization of medial meniscus (DMM) with intra-articular (IA) injection of adeno-associated viruses (AAV). RESULTS CircRERE was decreased in OA cartilage and chondrocytes compared with control. CircRERE downregulation was likely attributed to its increased m6A modification prone to endoribonucleolytic cleavage by YTHDF2-HRSP12-RNase P/MRP in OA chondrocytes. MOs transfection targeting HRSP12 binding motifs in circRERE partially reversed decreased circRERE expression and increased apoptosis in HCs treated with IL-1β for 6 h. CircRERE exerted chondroprotective effects by targeting miR-195-5p/IRF2BPL, thus regulating the ubiquitination and degradation of β-catenin. CircRere (mouse homologue) overexpression by IA-injection of AAV-circRere into mice attenuated the severity of DMM-induced OA, whereas AAV-miR-195a-5p or AAV-sh-Irf2bpl reduced the protective effects. The detrimental effects of AAV-sh-Irf2bpl on DMM-induced OA were substantially counteracted by ICG-001, an inhibitor of β-catenin. CONCLUSIONS Our study is a proof-of-concept demonstration for targeting m6A-modified circRERE and its target miR-195-5p/IRF2BPL/β-catenin as potential therapeutic strategies for OA treatment.
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Affiliation(s)
- Yuxi Liu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yunhan Yang
- School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, China
| | - Yucheng Lin
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Bing Wei
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Xinyue Hu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Li Xu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Weituo Zhang
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Jun Lu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
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Zhang JK, Li Y, Yu ZT, Jiang JW, Tang H, Tu GL, Xia Y. OIP5-AS1 Inhibits Oxidative Stress and Inflammation in Ischemic Stroke Through miR-155-5p/IRF2BP2 Axis. Neurochem Res 2022; 48:1382-1394. [PMID: 36460840 DOI: 10.1007/s11064-022-03830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/14/2022] [Accepted: 11/14/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND Ischemic stroke is a very dangerous disease with high incidence, fatality and disability rate in human beings. Massive evidence has indicated that oxidative stress and inflammation are intimately correlated with progression of ischemic stroke. Additionally, LncRNAs were reported to be involved in ischemic stroke. Here, we aim to explore the effects and molecular mechanism of lncRNA OIP5-AS1 on oxidative stress and inflammation in ischemic stroke. METHODS HMC3 and SH-SY5Y cells were under the condition of oxygen-glucose deprivation/reoxygenation (OGD/R) treatment to establish cell models of ischemic stroke. Commercial kits were employed to detect the indicators of oxidative stress including ROS, MDA and SOD. The expression of OIP5-AS1, miR-155-5p and IRF2BP2 mRNA was determined using RT-qPCR. The protein levels of inflammatory factors including TNF-α, IL-1β and IL-6 and IRF2BP2 were assessed by western blot and/or ELISA. Luciferase activity assay was employed to validate their correlations among OIP5-AS1, miR-155-5p and IRF2BP2. RESULTS In OGD/R-induced HMC3 and SH-SY5Y cells, the expression of OIP5-AS1 and IRF2BP2 was reduced while miR-155-5p was elevated. OGD/R induction promoted oxidative stress and inflammatory response in HMC3 and SH-SY5Y cells, while OIP5-AS1 or IRF2BP2 sufficiency as well as miR-155-5p inhibitor attenuated OGD/R-induced these influences. In addition, IRF2BP2 knockdown abolished the suppressive impacts of OIP5-AS1 overexpression on oxidative stress and inflammatory response in OGD/R-induced HMC3 and SH-SY5Y cells. Mechanistically, OIP5-AS1 enhanced IRF2BP2 expression via sponging miR-155-5p. CONCLUSION OIP5-AS1 suppressed oxidative stress and inflammatory response to alleviate cell injury caused by OGD/R induction in HMC3 and SH-SY5Y cells through regulating miR-155-5p/IRF2BP2 axis, which might offer novel targeted molecules for ischemic stroke therapy.
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Davies CJ, Fan Z, Morgado KP, Liu Y, Regouski M, Meng Q, Thomas AJ, Yun SI, Song BH, Frank JC, Perisse IV, Van Wettere A, Lee YM, Polejaeva IA. Development and characterization of type I interferon receptor knockout sheep: A model for viral immunology and reproductive signaling. Front Genet 2022; 13:986316. [PMID: 36246651 PMCID: PMC9556006 DOI: 10.3389/fgene.2022.986316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Type I interferons (IFNs) initiate immune responses to viral infections. Their effects are mediated by the type I IFN receptor, IFNAR, comprised of two subunits: IFNAR1 and IFNAR2. One or both chains of the sheep IFNAR were disrupted in fetal fibroblast lines using CRISPR/Cas9 and 12 lambs were produced by somatic cell nuclear transfer (SCNT). Quantitative reverse transcription-polymerase chain reaction for IFN-stimulated gene expression showed that IFNAR deficient sheep fail to respond to IFN-alpha. Furthermore, fibroblast cells from an IFNAR2−/− fetus supported significantly higher levels of Zika virus (ZIKV) replication than wild-type fetal fibroblast cells. Although many lambs have died from SCNT related problems or infections, one fertile IFNAR2−/− ram lived to over 4 years of age, remained healthy, and produced more than 80 offspring. Interestingly, ZIKV infection studies failed to demonstrate a high level of susceptibility. Presumably, these sheep compensated for a lack of type I IFN signaling using the type II, IFN-gamma and type III, IFN-lambda pathways. These sheep constitute a unique model for studying the pathogenesis of viral infection. Historical data supports the concept that ruminants utilize a novel type I IFN, IFN-tau, for pregnancy recognition. Consequently, IFNAR deficient ewes are likely to be infertile, making IFNAR knockout sheep a valuable model for studying pregnancy recognition. A breeding herd of 32 IFNAR2+/− ewes, which are fertile, has been developed for production of IFNAR2−/− sheep for both infection and reproduction studies.
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Affiliation(s)
- Christopher J. Davies
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- *Correspondence: Christopher J. Davies, ; Irina A. Polejaeva,
| | - Zhiqiang Fan
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Kira P. Morgado
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Ying Liu
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Misha Regouski
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Qinggang Meng
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Aaron J. Thomas
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Center for Integrated BioSystems, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Sang-Im Yun
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Byung-Hak Song
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Jordan C. Frank
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Iuri V. Perisse
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Arnaud Van Wettere
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Young-Min Lee
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Irina A. Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- *Correspondence: Christopher J. Davies, ; Irina A. Polejaeva,
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Abstract
An effective innate immune response to virus infection requires the induction of type I interferons and up-regulation of hundreds of interferon-stimulated genes (ISGs) that instruct antiviral functions and immune regulation. Deciphering the regulatory mechanisms that direct expression of the ISG network is critical for understanding the fundamental organization of the innate immune response and the development of antiviral therapies. We define a regulatory role for the primate-specific long noncoding RNA CHROMR in coordinating ISG transcription. CHROMR sequesters the interferon regulatory factor (IRF)-2/IRF2BP2 complex that restrains ISG transcription and thus is required to restrict influenza virus replication. These data identify a novel regulator of the antiviral gene program in humans and provide insights into the multilayered regulatory network that controls the innate immune response. Long noncoding RNAs (lncRNAs) have emerged as critical regulators of gene expression, yet their contribution to immune regulation in humans remains poorly understood. Here, we report that the primate-specific lncRNA CHROMR is induced by influenza A virus and SARS-CoV-2 infection and coordinates the expression of interferon-stimulated genes (ISGs) that execute antiviral responses. CHROMR depletion in human macrophages reduces histone acetylation at regulatory regions of ISG loci and attenuates ISG expression in response to microbial stimuli. Mechanistically, we show that CHROMR sequesters the interferon regulatory factor (IRF)-2-dependent transcriptional corepressor IRF2BP2, thereby licensing IRF-dependent signaling and transcription of the ISG network. Consequently, CHROMR expression is essential to restrict viral infection of macrophages. Our findings identify CHROMR as a key arbitrator of antiviral innate immune signaling in humans.
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Genomic landscape of Epstein-Barr virus-positive extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue. Mod Pathol 2022; 35:938-945. [PMID: 34952945 DOI: 10.1038/s41379-021-01002-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022]
Abstract
Epstein-Barr virus (EBV)-positive extranodal marginal zone lymphomas of mucosa-associated lymphoid tissue (MALT lymphomas) were initially described in solid organ transplant recipients, and, more recently, in other immunodeficiency settings. The overall prevalence of EBV-positive MALT lymphomas has not been established, and little is known with respect to their genomic characteristics. Eight EBV-positive MALT lymphomas were identified, including 1 case found after screening a series of 88 consecutive MALT lymphomas with EBER in situ hybridization (1%). The genomic landscape was assessed in 7 of the 8 cases with a targeted high throughput sequencing panel and array comparative genomic hybridization. Results were compared to published data for MALT lymphomas. Of the 8 cases, 6 occurred post-transplant, 1 in the setting of primary immunodeficiency, and 1 case was age-related. Single pathogenic/likely pathogenic mutations were identified in 4 of 7 cases, including mutations in IRF8, BRAF, TNFAIP3, and SMARCA4. Other than TNFAIP3, these genes are mutated in <3% of EBV-negative MALT lymphomas. Copy number abnormalities were identified in 6 of 7 cases with a median of 6 gains and 2 losses per case, including 4 cases with gains in regions encompassing several IRF family or interacting genes (IRF2BP2, IRF2, and IRF4). There was no evidence of trisomies of chromosomes 3 or 18. In summary, EBV-positive MALT lymphomas are rare and, like other MALT lymphomas, are usually genetically non-complex. Conversely, while EBV-negative MALT lymphomas typically show mutational abnormalities in the NF-κB pathway, other than the 1 TNFAIP3-mutated case, no other NF-κB pathway mutations were identified in the EBV-positive cases. EBV-positive MALT lymphomas often have either mutations or copy number abnormalities in IRF family or interacting genes, suggesting that this pathway may play a role in these lymphomas.
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15
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Lin X, Zhang H, Liu J, Wu CL, McDavid A, Boyce BF, Xing L. Aged Callus Skeletal Stem/Progenitor Cells Contain an Inflammatory Osteogenic Population With Increased IRF and NF-κB Pathways and Reduced Osteogenic Potential. Front Mol Biosci 2022; 9:806528. [PMID: 35755815 PMCID: PMC9218815 DOI: 10.3389/fmolb.2022.806528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/29/2022] [Indexed: 11/15/2022] Open
Abstract
Skeletal stem/progenitor cells (SSPCs) are critical for fracture repair by providing osteo-chondro precursors in the callus, which is impaired in aging. However, the molecular signatures of callus SSPCs during aging are not known. Herein, we performed single-cell RNA sequencing on 11,957 CD45-CD31-Ter119- SSPCs isolated from young and aged mouse calluses. Combining unsupervised clustering, putative makers, and DEGs/pathway analyses, major SSPC clusters were annotated as osteogenic, proliferating, and adipogenic populations. The proliferating cluster had a differentiating potential into osteogenic and adipogenic lineages by trajectory analysis. The osteoblastic/adipogenic/proliferating potential of individual clusters was further evidenced by elevated expression of genes related to osteoblasts, adipocytes, or proliferation. The osteogenic cluster was sub-clustered into house-keeping and inflammatory osteogenic populations that were decreased and increased in aged callus, respectively. The majority of master regulators for the inflammatory osteogenic population belong to IRF and NF-κB families, which was confirmed by immunostaining, RT-qPCR, and Western blot analysis. Furthermore, cells in the inflammatory osteogenic sub-cluster had reduced osteoblast differentiation capacity. In conclusion, we identified 3 major clusters in callus SSPCs, confirming their heterogeneity and, importantly, increased IRF/NF-κB-mediated inflammatory osteogenic population with decreased osteogenic potential in aged cells.
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Affiliation(s)
- X. Lin
- Department of Pathology and Laboratory Medicine, Rochester, NY, United States
| | - H. Zhang
- Department of Pathology and Laboratory Medicine, Rochester, NY, United States
| | - J. Liu
- Department of Pathology and Laboratory Medicine, Rochester, NY, United States
| | - C L. Wu
- Center for Musculoskeletal Research, Rochester, NY, United States
| | - A. McDavid
- Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - B. F. Boyce
- Department of Pathology and Laboratory Medicine, Rochester, NY, United States
- Center for Musculoskeletal Research, Rochester, NY, United States
| | - L. Xing
- Department of Pathology and Laboratory Medicine, Rochester, NY, United States
- Center for Musculoskeletal Research, Rochester, NY, United States
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Guarnera L, Ottone T, Fabiani E, Divona M, Savi A, Travaglini S, Falconi G, Panetta P, Rapanotti MC, Voso MT. Atypical Rearrangements in APL-Like Acute Myeloid Leukemias: Molecular Characterization and Prognosis. Front Oncol 2022; 12:871590. [PMID: 35494081 PMCID: PMC9039303 DOI: 10.3389/fonc.2022.871590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 02/25/2022] [Indexed: 02/02/2023] Open
Abstract
Acute promyelocytic leukemia (APL) accounts for 10–15% of newly diagnosed acute myeloid leukemias (AML) and is typically caused by the fusion of promyelocytic leukemia with retinoic acid receptor α (RARA) gene. The prognosis is excellent, thanks to the all-trans retinoic acid (ATRA) and arsenic trioxide (ATO) combination therapy. A small percentage of APLs (around 2%) is caused by atypical transcripts, most of which involve RARA or other members of retinoic acid receptors (RARB or RARG). The diagnosis of these forms is difficult, and clinical management is still a challenge for the physician due to variable response rates to ATRA and ATO. Herein we review variant APL cases reported in literature, including genetic landscape, incidence of coagulopathy and differentiation syndrome, frequent causes of morbidity and mortality in these patients, sensitivity to ATRA, ATO, and chemotherapy, and outcome. We also focus on non-RAR rearrangements, complex rearrangements (involving more than two chromosomes), and NPM1-mutated AML, an entity that can, in some cases, morphologically mimic APL.
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Affiliation(s)
- Luca Guarnera
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Tiziana Ottone
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuro-Oncohematology, Rome, Italy
| | - Emiliano Fabiani
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Department of Biomedicine and Prevention, UniCamillus-Saint Camillus International University of Health Sciences, Rome, Italy
| | - Mariadomenica Divona
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Arianna Savi
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Serena Travaglini
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Giulia Falconi
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Paola Panetta
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy
| | - Maria Cristina Rapanotti
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Department of Experimental Medicine, Tor Vergata University of Rome, Rome, Italy
| | - Maria Teresa Voso
- Department of Biomedicine and Prevention, University of Tor Vergata, Rome, Italy.,Santa Lucia Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (I.R.C.C.S.) Neuro-Oncohematology, Rome, Italy
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Molecular diagnosis of childhood immune dysregulation, polyendocrinopathy, and enteropathy, and implications for clinical management. J Allergy Clin Immunol 2022; 149:327-339. [PMID: 33864888 PMCID: PMC8526646 DOI: 10.1016/j.jaci.2021.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/13/2021] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Most patients with childhood-onset immune dysregulation, polyendocrinopathy, and enteropathy have no genetic diagnosis for their illness. These patients may undergo empirical immunosuppressive treatment with highly variable outcomes. OBJECTIVE We sought to determine the genetic basis of disease in patients referred with Immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like (IPEX-like) disease, but with no mutation in FOXP3; then to assess consequences of genetic diagnoses for clinical management. METHODS Genomic DNA was sequenced using a panel of 462 genes implicated in inborn errors of immunity. Candidate mutations were characterized by genomic, transcriptional, and (for some) protein analysis. RESULTS Of 123 patients with FOXP3-negative IPEX-like disease, 48 (39%) carried damaging germline mutations in 1 of the following 27 genes: AIRE, BACH2, BCL11B, CARD11, CARD14, CTLA4, IRF2BP2, ITCH, JAK1, KMT2D, LRBA, MYO5B, NFKB1, NLRC4, POLA1, POMP, RAG1, SH2D1A, SKIV2L, STAT1, STAT3, TNFAIP3, TNFRSF6/FAS, TNRSF13B/TACI, TOM1, TTC37, and XIAP. Many of these genes had not been previously associated with an IPEX-like diagnosis. For 42 of the 48 patients with genetic diagnoses, knowing the critical gene could have altered therapeutic management, including recommendations for targeted treatments and for or against hematopoietic cell transplantation. CONCLUSIONS Many childhood disorders now bundled as "IPEX-like" disease are caused by individually rare, severe mutations in immune regulation genes. Most genetic diagnoses of these conditions yield clinically actionable findings. Barriers are lack of testing or lack of repeat testing if older technologies failed to provide a diagnosis.
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Baesjou JP, Wellenreuther M. Genomic Signatures of Domestication Selection in the Australasian Snapper ( Chrysophrys auratus). Genes (Basel) 2021; 12:1737. [PMID: 34828341 PMCID: PMC8623400 DOI: 10.3390/genes12111737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 01/10/2023] Open
Abstract
Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.
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Affiliation(s)
- Jean-Paul Baesjou
- The New Zealand Institute for Plant and Food Research Ltd., 1025 Auckland, New Zealand;
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd., 7010 Nelson, New Zealand
- School of Biological Sciences, University of Auckland, 1010 Auckland, New Zealand
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19
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Ebstein F, Küry S, Papendorf JJ, Krüger E. Neurodevelopmental Disorders (NDD) Caused by Genomic Alterations of the Ubiquitin-Proteasome System (UPS): the Possible Contribution of Immune Dysregulation to Disease Pathogenesis. Front Mol Neurosci 2021; 14:733012. [PMID: 34566579 PMCID: PMC8455891 DOI: 10.3389/fnmol.2021.733012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/10/2021] [Indexed: 12/15/2022] Open
Abstract
Over thirty years have passed since the first description of ubiquitin-positive structures in the brain of patients suffering from Alzheimer’s disease. Meanwhile, the intracellular accumulation of ubiquitin-modified insoluble protein aggregates has become an indisputable hallmark of neurodegeneration. However, the role of ubiquitin and a fortiori the ubiquitin-proteasome system (UPS) in the pathogenesis of neurodevelopmental disorders (NDD) is much less described. In this article, we review all reported monogenic forms of NDD caused by lesions in genes coding for any component of the UPS including ubiquitin-activating (E1), -conjugating (E2) enzymes, ubiquitin ligases (E3), ubiquitin hydrolases, and ubiquitin-like modifiers as well as proteasome subunits. Strikingly, our analysis revealed that a vast majority of these proteins have a described function in the negative regulation of the innate immune response. In this work, we hypothesize a possible involvement of autoinflammation in NDD pathogenesis. Herein, we discuss the parallels between immune dysregulation and neurodevelopment with the aim at improving our understanding the biology of NDD and providing knowledge required for the design of novel therapeutic strategies.
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Affiliation(s)
- Frédéric Ebstein
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France.,l'Institut du Thorax, CNRS, INSERM, CHU Nantes, Université de Nantes, Nantes, France
| | - Jonas Johannes Papendorf
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, Greifswald, Germany
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20
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Palmroth M, Viskari H, Seppänen MRJ, Keskitalo S, Virtanen A, Varjosalo M, Silvennoinen O, Isomäki P. IRF2BP2 Mutation Is Associated with Increased STAT1 and STAT5 Activation in Two Family Members with Inflammatory Conditions and Lymphopenia. Pharmaceuticals (Basel) 2021; 14:ph14080797. [PMID: 34451894 PMCID: PMC8402006 DOI: 10.3390/ph14080797] [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: 07/02/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Interferon regulatory factor 2 binding protein 2 (IRF2BP2) is a transcriptional coregulator that has an important role in the regulation of the immune response. IRF2BP2 has been associated with the Janus kinase (JAK)-signal transducers and activators of transcription (STAT) pathway, but its exact role remains elusive. Here, we identified a novel clinical variant, IRF2BP2 c.625_665del, from two members of a family with inflammatory conditions and investigated the function of IRF2BP2 and c.625_665del mutation in JAK-STAT pathway activation and inflammatory signaling. The levels of constitutive and cytokine-induced phosphorylation of STATs and total STAT1 in peripheral blood monocytes, T cells, and B cells from the patients and four healthy controls were measured by flow cytometry. Inflammation-related gene expression was studied in peripheral blood mononuclear cells using direct digital detection of mRNA (NanoString). Finally, we studied the relationship between IRF2BP2 and STAT1 activation using a luciferase reporter system in a cell model. Our results show that patients having the IRF2BP2 c.625_665del mutation presented overexpression of STAT1 protein and increased constitutive activation of STAT1. In addition, interferon-induced JAK-STAT signaling was upregulated, and several interferon-inducible genes were overexpressed. Constitutive phosphorylation of STAT5 was also found to be upregulated in CD4+ T cells from the patients. Using a cell model, we show that IRF2BP2 was needed to attenuate STAT1 transcriptional activity and that IRF2BP2 c.625_665del mutation failed in this. We conclude that IRF2BP2 has an important role in suppressing immune responses elicited by STAT1 and STAT5 and suggest that aberrations in IRF2BP2 can lead to abnormal function of intrinsic immunity.
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Affiliation(s)
- Maaria Palmroth
- Molecular Immunology Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (M.P.); (A.V.); (O.S.)
| | - Hanna Viskari
- Department of Internal Medicines, Tampere University Hospital, 33520 Tampere, Finland;
- Faculty of Medicine and Life Sciences, Tampere University, 33520 Tampere, Finland
| | - Mikko R. J. Seppänen
- Rare Disease and Pediatric Research Centers, Children’s Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland;
| | - Salla Keskitalo
- Molecular Systems Biology Group, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland; (S.K.); (M.V.)
| | - Anniina Virtanen
- Molecular Immunology Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (M.P.); (A.V.); (O.S.)
| | - Markku Varjosalo
- Molecular Systems Biology Group, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland; (S.K.); (M.V.)
| | - Olli Silvennoinen
- Molecular Immunology Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (M.P.); (A.V.); (O.S.)
- Fimlab Laboratories, Pirkanmaa Hospital District, 33520 Tampere, Finland
- HiLIFE Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Pia Isomäki
- Molecular Immunology Group, Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland; (M.P.); (A.V.); (O.S.)
- Centre for Rheumatic Diseases, Tampere University Hospital, 33520 Tampere, Finland
- Correspondence:
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21
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Magidey-Klein K, Cooper TJ, Kveler K, Normand R, Zhang T, Timaner M, Raviv Z, James BP, Gazit R, Ronai ZA, Shen-Orr S, Shaked Y. IL-6 contributes to metastatic switch via the differentiation of monocytic-dendritic progenitors into prometastatic immune cells. J Immunother Cancer 2021; 9:jitc-2021-002856. [PMID: 34140316 PMCID: PMC8212411 DOI: 10.1136/jitc-2021-002856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Metastasis is the major cause of death in patients with cancer. Myeloid skewing of hematopoietic cells is a prominent promoter of metastasis. However, the reservoir of these cells in the bone marrow (BM) compartment and their differentiation pattern from hematopoietic stem and progenitor cells (HSPCs) have not been explored. METHODS We used a unique model system consisting of tumor cell clones with low metastatic potential or high metastatic potential (met-low and met-high, respectively) to investigate the fate of HSPC differentiation using murine melanoma and breast carcinoma. Single-cell RNA sequencing (scRNA-seq) analysis was performed on HSPC obtained from the BM of met-low and met-high tumors. A proteomic screen of tumor-conditioned medium integrated with the scRNA-seq data analysis was performed to analyze the potential cross talk between cancer cells and HSPCs. Adoptive transfer of tumor-educated HSPC subsets obtained from green fluorescent protein (GFP)+ tagged mice was then carried out to identify the contribution of committed HSPCs to tumor spread. Peripheral mononuclear cells obtained from patients with breast and lung cancer were analyzed for HSPC subsets. RESULTS Mice bearing met-high tumors exhibited a significant increase in the percentage of HSPCs in the BM in comparison with tumor-free mice or mice bearing met-low tumors. ScRNA-seq analysis of these HSPCs revealed that met-high tumors enriched the monocyte-dendritic progenitors (MDPs) but not granulocyte-monocyte progenitors (GMPs). A proteomic screen of tumor- conditioned medium integrated with the scRNA-seq data analysis revealed that the interleukin 6 (IL-6)-IL-6 receptor axis is highly active in HSPC-derived MDP cells. Consequently, loss of function and gain of function of IL-6 in tumor cells resulted in decreased and increased metastasis and corresponding MDP levels, respectively. Importantly, IL-6-educated MDPs induce metastasis within mice bearing met-low tumors-through further differentiation into immunosuppressive macrophages and not dendritic cells. Consistently, MDP but not GMP levels in peripheral blood of breast and lung cancer patients are correlated with tumor aggressiveness. CONCLUSIONS Our study reveals a new role for tumor-derived IL-6 in hijacking the HSPC differentiation program toward prometastatic MDPs that functionally differentiate into immunosuppressive monocytes to support the metastatic switch.
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Affiliation(s)
| | - Tim J Cooper
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Ksenya Kveler
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Rachelly Normand
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Tongwu Zhang
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institute of Health, Bethesda, Maryland, USA
| | - Michael Timaner
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Ziv Raviv
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Brian P James
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Roi Gazit
- Department for Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Southern, Israel
| | - Ze'ev A Ronai
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Shai Shen-Orr
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
| | - Yuval Shaked
- Faculty of Medicine, Technion Israel Institute of Technology, Haifa, Israel
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22
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Du Y, Wang Y, Xu Q, Zhu J, Lin Y. TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes. BMC Genomics 2021; 22:417. [PMID: 34090334 PMCID: PMC8180059 DOI: 10.1186/s12864-021-07730-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 05/19/2021] [Indexed: 02/15/2023] Open
Abstract
Background Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear. Result In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation. Conclusions By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07730-y.
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Affiliation(s)
- Yu Du
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yong Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Qing Xu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China.,College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China
| | - Jiangjiang Zhu
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China
| | - Yaqiu Lin
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Education Ministry, Southwest Minzu University, Chengdu, China. .,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Exploitation of Sichuan Province, Southwest Minzu University, Chengdu, China. .,College of Animal & Veterinary Science, Southwest Minzu University, Chengdu, China.
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23
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Li HF, Wu YL, Tseng TL, Chao SW, Lin H, Chen HH. Inhibition of miR-155 potentially protects against lipopolysaccharide-induced acute lung injury through the IRF2BP2-NFAT1 pathway. Am J Physiol Cell Physiol 2020; 319:C1070-C1081. [PMID: 33052070 DOI: 10.1152/ajpcell.00116.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Sepsis-induced lung injury is a lethal complication with no effective treatment options, affecting millions of people worldwide. Oroxylin A (OroA) is a natural flavonoid with potent anticancer effects, but its modulating effect on inflammation through microRNAs (miRs) is not apparent. In this report, we investigated the target genes of the miR pathway mediated by OroA and assessed the potential for novel treatments of septic lung injury. An miR array screening and quantitative polymerase chain reaction identified that miR-155-5p could be a candidate regulated by OroA. Bioinformatics analysis indicated that interferon regulatory factor-2-binding protein-2 (IRF2BP2) might be a target of miR-155-5p, and this hypothesis was verified through reporter assays. In addition, an immunoprecipitation assay demonstrated that OroA increased the binding activity of IRF2BP2 to the nuclear factor of activated T-cells 1 (NFAT1), causing inducible nitric oxide synthase to cause an inflammatory reaction. Finally, the direct injection of short hairpin RNA (shRNA)-miR-155-5p into the bone marrow of mice ameliorated LPS-induced acute lung injury and inflammation in mice. Our results provide new mechanistic insights into the role of the OroA-induced miR-155-5p-IRF2BP2-NFAT1 axis in sepsis, demonstrating that direct bone marrow injection of lentivirus containing shRNA-155-5p could prove to be a potential future clinical application in alleviating sepsis-induced acute lung injury.
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Affiliation(s)
- Hsiao-Fen Li
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,PhD Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yueh-Lin Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Tzu-Ling Tseng
- Department of Medical Research, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Shih-Wei Chao
- Drug Development Center, China Medical University, Taichung, Taiwan
| | - Heng Lin
- Department of Physiology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,PhD Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Hsi-Hsien Chen
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.,Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
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24
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Alotaibi AS, Abdulrazzaq M, Patel KP, Ravandi F, Konoplev S, Bueso-Ramos C, Yin CC, Muzzafar T, Tang G, Futreal A, Jain N, Konopleva MY, Pemmaraju N. Acute promyelocytic leukemia (APL) with an IRF2BP2-RARA fusion transcript: an aggressive APL variant. Leuk Lymphoma 2020; 61:3018-3020. [DOI: 10.1080/10428194.2020.1791853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ahmad S. Alotaibi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mustafa Abdulrazzaq
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Keyur P. Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Farhad Ravandi
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergej Konoplev
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carlos Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C. Cameron Yin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tariq Muzzafar
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nitin Jain
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marina Y. Konopleva
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naveen Pemmaraju
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Identification of Functional Interactome of Gastric Cancer Cells with Helicobacter pylori Outer Membrane Protein HpaA by HPLC-MS/MS. BIOMED RESEARCH INTERNATIONAL 2020; 2020:1052926. [PMID: 32566649 PMCID: PMC7293730 DOI: 10.1155/2020/1052926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/02/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022]
Abstract
HpaA as an outer membrane protein of Helicobacter pylori (H. pylori) plays a significant role in the adhesion to the human stomach, but the functional relation between HpaA and gastric epithelial cells is still not clear. To screen the interaction between HpaA and cellular proteins in gastric epithelial cells, the HpaA protein from H. pylori 26695 fused with a tag (6× His) was expressed and purified successfully, the secondary structure was estimated by the Circular Dichroism (CD) spectrum, and the purified recombinant protein was used to perform the pull-down assays with gastric cancer cell lines (AGS and SGC-7901) lysates, respectively. The pull-down proteins were identified by high-performance liquid chromatography tandem mass spectrometry system (HPLC-MS/MS). A total of 9 and 13 proteins related were analyzed from AGS and SGC-7901 cell lysates, respectively. ANXA2 was considered as putative HpaA functional partner discovered from lysates of both cell lines with high score and coverage. It is hypothesized that HpaA may be involved in the biological process of regulation of transcription and nucleic acid metabolism during the adhesion of H. pylori to human gastric epithelial cells, and HpaA-binding proteins also be used as targets for the development of antiadhesion drugs against H. pylori.
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26
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Vissers JHA, Dent LG, House CM, Kondo S, Harvey KF. Pits and CtBP Control Tissue Growth in Drosophila melanogaster with the Hippo Pathway Transcription Repressor Tgi. Genetics 2020; 215:117-128. [PMID: 32122936 PMCID: PMC7198276 DOI: 10.1534/genetics.120.303147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/01/2020] [Indexed: 12/11/2022] Open
Abstract
The Hippo pathway is an evolutionarily conserved signaling network that regulates organ size, cell fate, and tumorigenesis. In the context of organ size control, the pathway incorporates a large variety of cellular cues, such as cell polarity and adhesion, into an integrated transcriptional response. The central Hippo signaling effector is the transcriptional coactivator Yorkie, which controls gene expression in partnership with different transcription factors, most notably Scalloped. When it is not activated by Yorkie, Scalloped can act as a repressor of transcription, at least in part due to its interaction with the corepressor protein Tgi. The mechanism by which Tgi represses transcription is incompletely understood, and therefore we sought to identify proteins that potentially operate together with Tgi. Using an affinity purification and mass-spectrometry approach we identified Pits and CtBP as Tgi-interacting proteins, both of which have been linked to transcriptional repression. Both Pits and CtBP were required for Tgi to suppress the growth of the Drosophila melanogaster eye and CtBP loss suppressed the undergrowth of yorkie mutant eye tissue. Furthermore, as reported previously for Tgi, overexpression of Pits repressed transcription of Hippo pathway target genes. These findings suggest that Tgi might operate together with Pits and CtBP to repress transcription of genes that normally promote tissue growth. The human orthologs of Tgi, CtBP, and Pits (VGLL4, CTBP2, and IRF2BP2) have previously been shown to physically and functionally interact to control transcription, implying that the mechanism by which these proteins control transcriptional repression is conserved throughout evolution.
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Affiliation(s)
- Joseph H A Vissers
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia 3000
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia 3010
| | - Lucas G Dent
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia 3000
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia 3010
| | - Colin M House
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia 3000
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia 3010
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Kieran F Harvey
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia 3000
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia 3010
- Department of Anatomy and Developmental Biology, and Biomedicine Discovery Institute, Monash University, Clayton, Australia 3800
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27
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Geoffroy MC, de Thé H. Classic and Variants APLs, as Viewed from a Therapy Response. Cancers (Basel) 2020; 12:E967. [PMID: 32295268 PMCID: PMC7226009 DOI: 10.3390/cancers12040967] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/09/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
Most acute promyelocytic leukemia (APL) are caused by PML-RARA, a translocation-driven fusion oncoprotein discovered three decades ago. Over the years, several other types of rare X-RARA fusions have been described, while recently, oncogenic fusion proteins involving other retinoic acid receptors (RARB or RARG) have been associated to very rare cases of acute promyelocytic leukemia. PML-RARA driven pathogenesis and the molecular basis for therapy response have been the focus of many studies, which have now converged into an integrated physio-pathological model. The latter is well supported by clinical and molecular studies on patients, making APL one of the rare hematological disorder cured by targeted therapies. Here we review recent data on APL-like diseases not driven by the PML-RARA fusion and discuss these in view of current understanding of "classic" APL pathogenesis and therapy response.
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Affiliation(s)
- Marie-Claude Geoffroy
- Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Equipe Labellisée par la Ligue Nationale contre le Cancer, 75010 Paris, France;
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 7212, Institut Universitaire d'Hématologie (IUH), 75010 Paris, France
- Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
| | - Hugues de Thé
- Institut National de la Santé et de la Recherche Médicale (INSERM) U944, Equipe Labellisée par la Ligue Nationale contre le Cancer, 75010 Paris, France;
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 7212, Institut Universitaire d'Hématologie (IUH), 75010 Paris, France
- Institut de Recherche Saint-Louis, Université de Paris, 75010 Paris, France
- Assistance Publique-Hôpitaux de Paris, Service de Biochimie, Hôpital St-Louis, 75010 Paris, France
- Collège de France, PSL Research University, INSERM U1050, CNRS UMR 7241, 75005 Paris, France
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28
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Genomic analyses of PMBL reveal new drivers and mechanisms of sensitivity to PD-1 blockade. Blood 2020; 134:2369-2382. [PMID: 31697821 DOI: 10.1182/blood.2019002067] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/14/2019] [Indexed: 12/15/2022] Open
Abstract
Primary mediastinal large B-cell lymphomas (PMBLs) are aggressive tumors that typically present as large mediastinal masses in young women. PMBLs share clinical, transcriptional, and molecular features with classical Hodgkin lymphoma (cHL), including constitutive activation of nuclear factor κB (NF-κB), JAK/STAT signaling, and programmed cell death protein 1 (PD-1)-mediated immune evasion. The demonstrated efficacy of PD-1 blockade in relapsed/refractory PMBLs led to recent approval by the US Food and Drug Administration and underscored the importance of characterizing targetable genetic vulnerabilities in this disease. Here, we report a comprehensive analysis of recurrent genetic alterations -somatic mutations, somatic copy number alterations, and structural variants-in a cohort of 37 newly diagnosed PMBLs. We identified a median of 9 genetic drivers per PMBL, including known and newly identified components of the JAK/STAT and NF-κB signaling pathways and frequent B2M alterations that limit major histocompatibility complex class I expression, as in cHL. PMBL also exhibited frequent, newly identified driver mutations in ZNF217 and an additional epigenetic modifier, EZH2. The majority of these alterations were clonal, which supports their role as early drivers. In PMBL, we identified several previously uncharacterized molecular features that may increase sensitivity to PD-1 blockade, including high tumor mutational burden, microsatellite instability, and an apolipoprotein B mRNA editing catalytic polypeptide-like (APOBEC) mutational signature. The shared genetic features between PMBL and cHL provide a framework for analyzing the mechanism of action of PD-1 blockade in these related lymphoid malignancies.
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29
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Philipp J, Sievert W, Azimzadeh O, von Toerne C, Metzger F, Posch A, Hladik D, Subedi P, Multhoff G, Atkinson MJ, Tapio S. Data independent acquisition mass spectrometry of irradiated mouse lung endothelial cells reveals a STAT-associated inflammatory response. Int J Radiat Biol 2020; 96:642-650. [PMID: 31914348 DOI: 10.1080/09553002.2020.1712492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Purpose: Pulmonary inflammation is an adverse consequence of radiation therapy in breast cancer. The aim of this study was to elucidate biological pathways leading to this pathology.Materials and methods: Lung endothelial cells were isolated 24 h after thorax-irradiation (sham or 10 Gy X-ray) from female C57Bl/6 mice and cultivated for 6 days.Results: Quantitative proteomic analysis of lung endothelial cells was done using data independent acquisition (DIA) mass spectrometry. The data were analyzed using Ingenuity Pathway Analysis and STRINGdb. In total, 4220 proteins were identified using DIA of which 60 were dysregulated in the irradiated samples (fold change ≥2.00 or ≤0.50; q-value <0.05). Several (12/40) upregulated proteins formed a cluster of inflammatory proteins with STAT1 and IRF3 as predicted upstream regulators. The several-fold increased expression of STAT1 and STAT-associated ISG15 was confirmed by immunoblotting. The expression of antioxidant proteins SOD1 and PRXD5 was downregulated suggesting radiation-induced oxidative stress. Similarly, the phosphorylated (active) forms of STING and IRF3, both members of the cGAS/STING pathway, were downregulated.Conclusions: These data suggest the involvement of JAK/STAT and cGas/STING pathways in the genesis of radiation-induced lung inflammation. These pathways may be used as novel targets for the prevention of radiation-induced lung damage.
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Affiliation(s)
- Jos Philipp
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Wolfgang Sievert
- Radiation Immuno Oncology Group, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Omid Azimzadeh
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Christine von Toerne
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Research Unit Protein Science, Munich, Germany
| | - Fabian Metzger
- Helmholtz Zentrum München, German Research Centre for Environmental Health GmbH, Research Unit Protein Science, Munich, Germany
| | - Anton Posch
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Daniela Hladik
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Prabal Subedi
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Gabriele Multhoff
- Radiation Immuno Oncology Group, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Michael J Atkinson
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, Neuherberg, Germany
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