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Susanto TT, Hung V, Levine AG, Kerr CH, Yoo Y, Chen Y, Oses-Prieto JA, Fromm L, Fujii K, Wernig M, Burlingame AL, Ruggero D, Barna M. RAPIDASH: A tag-free enrichment of ribosome-associated proteins reveals compositional dynamics in embryonic tissues and stimulated macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570613. [PMID: 38106052 PMCID: PMC10723405 DOI: 10.1101/2023.12.07.570613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Ribosomes are emerging as direct regulators of gene expression, with ribosome-associated proteins (RAPs) allowing ribosomes to modulate translational control. However, a lack of technologies to enrich RAPs across many sample types has prevented systematic analysis of RAP number, dynamics, and functions. Here, we have developed a label-free methodology called RAPIDASH to enrich ribosomes and RAPs from any sample. We applied RAPIDASH to mouse embryonic tissues and identified hundreds of potential RAPs, including DHX30 and LLPH, two forebrain RAPs important for neurodevelopment. We identified a critical role of LLPH in neural development that is linked to the translation of genes with long coding sequences. Finally, we characterized ribosome composition remodeling during immune activation and observed extensive changes post-stimulation. RAPIDASH has therefore enabled the discovery of RAPs ranging from those with neuroregulatory functions to those activated by immune stimuli, thereby providing critical insights into how ribosomes are remodeled.
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Affiliation(s)
- Teodorus Theo Susanto
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Victoria Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Craig H Kerr
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yongjin Yoo
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yuxiang Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lisa Fromm
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Kotaro Fujii
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marius Wernig
- Institute for Stem Cell Biology and Regenerative Medicine and Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Maria Barna
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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Liu Y, Shao YH, Zhang JM, Wang Y, Zhou M, Li HQ, Zhang CC, Yu PJ, Gao SJ, Wang XR, Jia LX, Piao CM, Du J, Li YL. Macrophage CARD9 mediates cardiac injury following myocardial infarction through regulation of lipocalin 2 expression. Signal Transduct Target Ther 2023; 8:394. [PMID: 37828006 PMCID: PMC10570328 DOI: 10.1038/s41392-023-01635-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/15/2023] [Accepted: 08/31/2023] [Indexed: 10/14/2023] Open
Abstract
Immune cell infiltration in response to myocyte death regulates extracellular matrix remodeling and scar formation after myocardial infarction (MI). Caspase-recruitment domain family member 9 (CARD9) acts as an adapter that mediates the transduction of pro-inflammatory signaling cascades in innate immunity; however, its role in cardiac injury and repair post-MI remains unclear. We found that Card9 was one of the most upregulated Card genes in the ischemic myocardium of mice. CARD9 expression increased considerably 1 day post-MI and declined by day 7 post-MI. Moreover, CARD9 was mainly expressed in F4/80-positive macrophages. Card9 knockout (KO) led to left ventricular function improvement and infarct scar size reduction in mice 28 days post-MI. Additionally, Card9 KO suppressed cardiomyocyte apoptosis in the border region and attenuated matrix metalloproteinase (MMP) expression. RNA sequencing revealed that Card9 KO significantly suppressed lipocalin 2 (Lcn2) expression post-MI. Both LCN2 and the receptor solute carrier family 22 member 17 (SL22A17) were detected in macrophages. Subsequently, we demonstrated that Card9 overexpression increased LCN2 expression, while Card9 KO inhibited necrotic cell-induced LCN2 upregulation in macrophages, likely through NF-κB. Lcn2 KO showed beneficial effects post-MI, and recombinant LCN2 diminished the protective effects of Card9 KO in vivo. Lcn2 KO reduced MMP9 post-MI, and Lcn2 overexpression increased Mmp9 expression in macrophages. Slc22a17 knockdown in macrophages reduced MMP9 release with recombinant LCN2 treatment. In conclusion, our results demonstrate that macrophage CARD9 mediates the deterioration of cardiac function and adverse remodeling post-MI via LCN2.
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Affiliation(s)
- Yan Liu
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Yi-Hui Shao
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Jun-Meng Zhang
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Ying Wang
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Mei Zhou
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Hui-Qin Li
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Cong-Cong Zhang
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Pei-Jie Yu
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Shi-Juan Gao
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Xue-Rui Wang
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Li-Xin Jia
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Chun-Mei Piao
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Yu-Lin Li
- Beijing Anzhen Hospital, Capital Medical University; The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education; Beijing Collaborative Innovative Research Center for Cardiovascular Diseases; Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China.
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Fallahi M, Mahdaviani SA, Shafiei M, Ghadimi S, Rezaei N, Klein C, Strobel S, Jamee M. CARD9 deficiency with allergic bronchopulmonary aspergillosis (ABPA)-like presentation: a case report. Oxf Med Case Reports 2023; 2023:omad103. [PMID: 37881270 PMCID: PMC10597618 DOI: 10.1093/omcr/omad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/10/2023] [Accepted: 08/02/2023] [Indexed: 10/27/2023] Open
Abstract
PURPOSE We present a patient with CARD9 deficiency and allergic bronchopulmonary aspergillosis (ABPA)-like presentation. METHODS Following medical history taking and routine laboratory investigations, an inborn error of immunity was suspected, and the responsible variant was identified using Whole Exome Sequencing and confirmed by Sanger sequencing. RESULTS A 14-year-old Iranian female presented with a history of chest pain, productive cough, dyspnea, malaise, and recurrent fever. Imaging by computed tomography (CT scan), chest X-ray (CXR), bronchoscopy, transbronchial lung biopsy (TBLB), and histopathology findings led to a diagnosis of ABPA-like presentation. The genetic study showed an autosomal recessive homozygous mutation in the CARD9 gene. Clinical remission was achieved following the administration of voriconazole, which was continued as prophylaxis. CONCLUSIONS This is the first-time report of a patient with inherited CARD9 deficiency and ABPA-like presentation due to Aspergillus Terrus. This study paves the way to elucidate immunological mechanisms underlying CARD9 deficiency and aspergillosis.
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Affiliation(s)
- Mazdak Fallahi
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Shafiei
- Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Soodeh Ghadimi
- Immunology and Allergy Department, Mofid Children’s Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Ludwig Maximilians, University Munich, Munich, Germany
| | - Sophie Strobel
- Institute of Nutritional Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Mahnaz Jamee
- Laboratory for Pediatric Immunology, Department of Pediatrics, Willem-Alexander Children’s Hospital, Leiden University Medical Center, Leiden, Netherlands
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Deng R, Meng X, Li R, Wang A, Song Y. Asymptomatic Candida glabrata urinary tract infection in an immunocompetent young female: A case report. Medicine (Baltimore) 2023; 102:e33798. [PMID: 37335701 DOI: 10.1097/md.0000000000033798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
INTRODUCTION Fungal urinary tract infections (UTIs) are becoming increasingly common in hospitalized patients and Candida species are the most prevalent organisms. However, recurrent candiduria in young healthy outpatients is rare thus require further examination to find the etiologic factors. CASE PRESENTATION We described a case of recurrent asymptomatic c caused by azole-resistant C. glabrata in a healthy young female who only had previous use of antibiotics without other risk factors. However, after removal of the predisposing factor and the use of sensitive antifungal agents, the patient's urine cultures remained positive. This phenomenon indicated to us that the patient might have an immune-related genetic deficiency. We found a novel caspase-associated recruitment domain-containing protein 9 (CARD9) gene mutation (c.808-11G > T) which might be the cause of recurrent asymptomatic candiduria in this immune-competent young female without any underlying diseases. CONCLUSIONS We report a case of recurrent asymptomatic candiduria caused by azole-resistant Candida glabrata in a young healthy female with a novel CARD9 mutation. A functional study of this mutation should be performed in the future to determine its effect on asymptomatic fungal UTIs.
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Affiliation(s)
- Ruixin Deng
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Xingye Meng
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Ruoyu Li
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Aiping Wang
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
| | - Yinggai Song
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing, China
- National Clinical Research Center for Skin and Immune Diseases, Beijing, China
- Research Center for Medical Mycology, Peking University, Beijing, China
- Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Beijing, China
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