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Xie F, Liu B, Qiao W, He JZ, Cheng J, Wang ZY, Hou YM, Zhang X, Xu BH, Zhang Y, Chen YG, Zhang MX. Smooth muscle NF90 deficiency ameliorates diabetic atherosclerotic calcification in male mice via FBXW7-AGER1-AGEs axis. Nat Commun 2024; 15:4985. [PMID: 38862515 PMCID: PMC11166998 DOI: 10.1038/s41467-024-49315-9] [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: 08/22/2023] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
Hyperglycemia accelerates calcification of atherosclerotic plaques in diabetic patients, and the accumulation of advanced glycation end products (AGEs) is closely related to the atherosclerotic calcification. Here, we show that hyperglycemia-mediated AGEs markedly increase vascular smooth muscle cells (VSMCs) NF90/110 activation in male diabetic patients with atherosclerotic calcified samples. VSMC-specific NF90/110 knockout in male mice decreases obviously AGEs-induced atherosclerotic calcification, along with the inhibitions of VSMC phenotypic changes to osteoblast-like cells, apoptosis, and matrix vesicle release. Mechanistically, AGEs increase the activity of NF90, which then enhances ubiquitination and degradation of AGE receptor 1 (AGER1) by stabilizing the mRNA of E3 ubiquitin ligase FBXW7, thus causing the accumulation of more AGEs and atherosclerotic calcification. Collectively, our study demonstrates the effects of VSMC NF90 in mediating the metabolic imbalance of AGEs to accelerate diabetic atherosclerotic calcification. Therefore, inhibition of VSMC NF90 may be a potential therapeutic target for diabetic atherosclerotic calcification.
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MESH Headings
- Animals
- Male
- Mice
- Glycation End Products, Advanced/metabolism
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Mice, Knockout
- Atherosclerosis/metabolism
- Atherosclerosis/genetics
- Atherosclerosis/pathology
- Humans
- F-Box-WD Repeat-Containing Protein 7/metabolism
- F-Box-WD Repeat-Containing Protein 7/genetics
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Nuclear Factor 90 Proteins/metabolism
- Nuclear Factor 90 Proteins/genetics
- Receptor for Advanced Glycation End Products/metabolism
- Receptor for Advanced Glycation End Products/genetics
- Vascular Calcification/metabolism
- Vascular Calcification/pathology
- Vascular Calcification/genetics
- Mice, Inbred C57BL
- Ubiquitination
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/pathology
- Hyperglycemia/metabolism
- Hyperglycemia/genetics
- Plaque, Atherosclerotic/metabolism
- Plaque, Atherosclerotic/pathology
- Plaque, Atherosclerotic/genetics
- Apoptosis
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Affiliation(s)
- Fei Xie
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
| | - Bin Liu
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China
| | - Wen Qiao
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Zhen He
- Department of Radiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie Cheng
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Zhao-Yang Wang
- Department of Cardiology of Shandong Provincial Hospital, Shandong University, Jinan, China
| | - Ya-Min Hou
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Xu Zhang
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Bo-Han Xu
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Yun Zhang
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.
| | - Yu-Guo Chen
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.
- Department of Emergency and Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China.
| | - Ming-Xiang Zhang
- The Key Laboratory of Cardiovascular Remodelling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.
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2
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Richie TG, Heeren L, Kamke A, Monk K, Pogranichniy S, Summers T, Wiechman H, Ran Q, Sarkar S, Plattner BL, Lee STM. Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model. mSystems 2023; 8:e0070323. [PMID: 37909786 PMCID: PMC10746178 DOI: 10.1128/msystems.00703-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/27/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.
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Affiliation(s)
- Tanner G. Richie
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Leah Heeren
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Abigail Kamke
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kourtney Monk
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | | | - Trey Summers
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Hallie Wiechman
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Qinghong Ran
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Soumyadev Sarkar
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Brandon L. Plattner
- Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, Kansas, USA
| | - Sonny T. M. Lee
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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3
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Mimatsu H, Onoda A, Kazama T, Nishijima K, Shimoyama Y, Go S, Ueda K, Takahashi Y, Matsumoto T, Hayakawa M, Sato Y. Dedifferentiated fat cells administration ameliorates abnormal expressions of fatty acids metabolism-related protein expressions and intestinal tissue damage in experimental necrotizing enterocolitis. Sci Rep 2023; 13:8266. [PMID: 37217485 DOI: 10.1038/s41598-023-34156-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
Neonatal necrotizing enterocolitis (NEC) is a serious disease of premature infants that necessitates intensive care and frequently results in life-threatening complications and high mortality. Dedifferentiated fat cells (DFATs) are mesenchymal stem cell-like cells derived from mature adipocytes. DFATs were intraperitoneally administrated to a rat NEC model, and the treatment effect and its mechanism were evaluated. The NEC model was created using rat pups hand fed with artificial milk, exposed to asphyxia and cold stress, and given oral lipopolysaccharides after cesarean section. The pups were sacrificed 96 h after birth for macroscopic histological examination and proteomics analysis. DFATs administration significantly improved the survival rate from 25.0 (vehicle group) to 60.6% (DFAT group) and revealed a significant reduction in macroscopical, histological, and apoptosis evaluation compared with the vehicle group. Additionally, the expression of C-C motif ligand 2 was significantly decreased, and that of interleukin-6 decreased in the DFAT group. DFAT administration ameliorated 93 proteins mainly related to proteins of fatty acid metabolism of the 436 proteins up-/down-regulated by NEC. DFATs improved mortality and restored damaged intestinal tissues in NEC, possibly by improving the abnormal expression of fatty acid-related proteins and reducing inflammation.
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Affiliation(s)
- Haruka Mimatsu
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Atsuto Onoda
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan
- Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda, Yamaguchi, Japan
| | - Tomohiko Kazama
- Department of Functional Morphology, Division of Cell Regeneration and Transplantation, Nihon University School of Medicine, Tokyo, Japan
| | - Koji Nishijima
- Center for Perinatal, Maternal and Neonatal Medicine, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Yoshie Shimoyama
- Department of Pathology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Shoji Go
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuto Ueda
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Takahashi
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Taro Matsumoto
- Department of Functional Morphology, Division of Cell Regeneration and Transplantation, Nihon University School of Medicine, Tokyo, Japan
| | - Masahiro Hayakawa
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshiaki Sato
- Division of Neonatology, Center for Maternal-Neonatal Care, Nagoya University Hospital, 65 Tsurumai-Cho Showa-Ku, Nagoya, 466-8550, Japan.
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4
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Girardi E, Messmer M, Lopez P, Fender A, Chicher J, Chane-Woon-Ming B, Hammann P, Pfeffer S. Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection. RNA (NEW YORK, N.Y.) 2023; 29:361-375. [PMID: 36617674 PMCID: PMC9945444 DOI: 10.1261/rna.079270.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Viruses are obligate intracellular parasites, which depend on the host cellular machineries to replicate their genome and complete their infectious cycle. Long double-stranded (ds)RNA is a common viral by-product originating during RNA virus replication and is universally sensed as a danger signal to trigger the antiviral response. As a result, viruses hide dsRNA intermediates into viral replication factories and have evolved strategies to hijack cellular proteins for their benefit. The characterization of the host factors associated with viral dsRNA and involved in viral replication remains a major challenge to develop new antiviral drugs against RNA viruses. Here, we performed anti-dsRNA immunoprecipitation followed by mass spectrometry analysis to fully characterize the dsRNA interactome in Sindbis virus (SINV) infected human cells. Among the identified proteins, we characterized SFPQ (splicing factor, proline-glutamine rich) as a new dsRNA-associated proviral factor upon SINV infection. We showed that SFPQ depletion reduces SINV infection in human HCT116 and SK-N-BE(2) cells, suggesting that SFPQ enhances viral production. We demonstrated that the cytoplasmic fraction of SFPQ partially colocalizes with dsRNA upon SINV infection. In agreement, we proved by RNA-IP that SFPQ can bind dsRNA and viral RNA. Furthermore, we showed that overexpression of a wild-type, but not an RNA binding mutant SFPQ, increased viral infection, suggesting that RNA binding is essential for its positive effect on the virus. Overall, this study provides the community with a compendium of dsRNA-associated factors during viral infection and identifies SFPQ as a new proviral dsRNA binding protein.
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Affiliation(s)
- Erika Girardi
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Mélanie Messmer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Paula Lopez
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Aurélie Fender
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Johana Chicher
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg-Esplanade, 67084 Strasbourg France
| | - Béatrice Chane-Woon-Ming
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
| | - Philippe Hammann
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Plateforme Protéomique Strasbourg-Esplanade, 67084 Strasbourg France
| | - Sébastien Pfeffer
- Université de Strasbourg, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 67084 Strasbourg France
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5
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Labeau A, Fery-Simonian L, Lefevre-Utile A, Pourcelot M, Bonnet-Madin L, Soumelis V, Lotteau V, Vidalain PO, Amara A, Meertens L. Characterization and functional interrogation of the SARS-CoV-2 RNA interactome. Cell Rep 2022; 39:110744. [PMID: 35477000 PMCID: PMC9040432 DOI: 10.1016/j.celrep.2022.110744] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/28/2021] [Accepted: 04/07/2022] [Indexed: 12/12/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic, which has led to a devastating global health crisis. The emergence of variants that escape neutralizing responses emphasizes the urgent need to deepen our understanding of SARS-CoV-2 biology. Using a comprehensive identification of RNA-binding proteins (RBPs) by mass spectrometry (ChIRP-MS) approach, we identify 107 high-confidence cellular factors that interact with the SARS-CoV-2 genome during infection. By systematically knocking down their expression in human lung epithelial cells, we find that the majority of the identified RBPs are SARS-CoV-2 proviral factors. In particular, we show that HNRNPA2B1, ILF3, QKI, and SFPQ interact with the SARS-CoV-2 genome and promote viral RNA amplification. Our study provides valuable resources for future investigations into the mechanisms of SARS-CoV-2 replication and the identification of host-centered antiviral therapies.
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Affiliation(s)
- Athéna Labeau
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Luc Fery-Simonian
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Alain Lefevre-Utile
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Marie Pourcelot
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Lucie Bonnet-Madin
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vassili Soumelis
- Université Paris Cité, INSERM U976, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Pierre-Olivier Vidalain
- Centre International de Recherche en Infectiologie (CIRI), Univ Lyon, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, 69007 Lyon, France
| | - Ali Amara
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
| | - Laurent Meertens
- Université Paris Cité, INSERM U944 CNRS 7212, Institut de Recherche Saint-Louis, Hôpital Saint-Louis, 75010 Paris, France.
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Lodde V, Floris M, Munk R, Martindale JL, Piredda D, Napodano CMP, Cucca F, Uzzau S, Abdelmohsen K, Gorospe M, Noh JH, Idda ML. Systematic identification of NF90 target RNAs by iCLIP analysis. Sci Rep 2022; 12:364. [PMID: 35013429 PMCID: PMC8748789 DOI: 10.1038/s41598-021-04101-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNAs directing numerous essential roles in cellular physiology. Nuclear Factor 90 (NF90) is an RBP encoded by the interleukin enhancer-binding factor 3 (ILF3) gene that has been found to influence RNA metabolism at several levels, including pre-RNA splicing, mRNA turnover, and translation. To systematically identify the RNAs that interact with NF90, we carried out iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) analysis in the human embryonic fibroblast cell line HEK-293. Interestingly, many of the identified RNAs encoded proteins involved in the response to viral infection and RNA metabolism. We validated a subset of targets and investigated the impact of NF90 on their expression levels. Two of the top targets, IRF3 and IRF9 mRNAs, encode the proteins IRF3 and IRF9, crucial regulators of the interferon pathway involved in the SARS-CoV-2 immune response. Our results support a role for NF90 in modulating key genes implicated in the immune response and offer insight into the immunological response to the SARS-CoV-2 infection.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Davide Piredda
- Intensive Care Unit, Emergency Department, AOU Sassari, Sassari, Italy
| | | | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Microbiology and Virology Unit, Diagnostic Department, AOU Sassari, Sassari, Italy
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA.
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy.
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Comprehensive Genomic and Transcriptomic Analysis of Three Synchronous Primary Tumours and a Recurrence from a Head and Neck Cancer Patient. Int J Mol Sci 2021; 22:ijms22147583. [PMID: 34299215 PMCID: PMC8305204 DOI: 10.3390/ijms22147583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 11/17/2022] Open
Abstract
Synchronous primary malignancies occur in a small proportion of head and neck squamous cell carcinoma (HNSCC) patients. Here, we analysed three synchronous primaries and a recurrence from one patient by comparing the genomic and transcriptomic profiles among the tumour samples and determining the recurrence origin. We found remarkable levels of heterogeneity among the primary tumours, and through the patterns of shared mutations, we traced the origin of the recurrence. Interestingly, the patient carried germline variants that might have predisposed him to carcinogenesis, together with a history of alcohol and tobacco consumption. The mutational signature analysis confirmed the impact of alcohol exposure, with Signature 16 present in all tumour samples. Characterisation of immune cell infiltration highlighted an immunosuppressive environment in all samples, which exceeded the potential activity of T cells. Studies such as the one described here have important clinical value and contribute to personalised treatment decisions for patients with synchronous primaries and matched recurrences.
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Chen Y, Hu J, Liu S, Chen B, Xiao M, Li Y, Liao Y, Rai KR, Zhao Z, Ouyang J, Pan Q, Zhang L, Huang S, Chen JL. RDUR, a lncRNA, Promotes Innate Antiviral Responses and Provides Feedback Control of NF-κB Activation. Front Immunol 2021; 12:672165. [PMID: 34054851 PMCID: PMC8160526 DOI: 10.3389/fimmu.2021.672165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Influenza A virus (IAV), a highly infectious respiratory pathogen, remains a major threat to global public health. Numerous long non-coding RNAs (lncRNAs) have been shown to be implicated in various cellular processes. Here, we identified a new lncRNA termed RIG-I-dependent IAV-upregulated noncoding RNA (RDUR), which was induced by infections with IAV and several other viruses. Both in vitro and in vivo studies revealed that robust expression of host RDUR induced by IAV was dependent on the RIG-I/NF-κB pathway. Overexpression of RDUR suppressed IAV replication and downregulation of RDUR promoted the virus replication. Deficiency of mouse RDUR increased virus production in lungs, body weight loss, acute organ damage and consequently reduced survival rates of mice, in response to IAV infection. RDUR impaired the viral replication by upregulating the expression of several vital antiviral molecules including interferons (IFNs) and interferon-stimulated genes (ISGs). Further study showed that RDUR interacted with ILF2 and ILF3 that were required for the efficient expression of some ISGs such as IFITM3 and MX1. On the other hand, we found that while NF-κB positively regulated the expression of RDUR, increased expression of RDUR, in turn, inactivated NF-κB through a negative feedback mechanism to suppress excessive inflammatory response to viral infection. Together, the results demonstrate that RDUR is an important lncRNA acting as a critical regulator of innate immunity against the viral infection.
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Affiliation(s)
- Yuhai Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayue Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shasha Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Biao Chen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Meng Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yingying Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Yuan Liao
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kul Raj Rai
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Zhonghui Zhao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, China
| | - Jing Ouyang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Qidong Pan
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Zhang
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Beijing, China
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Ji-Long Chen
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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9
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Qi F, Zhang W, Huang J, Fu L, Zhao J. Single-Cell RNA Sequencing Analysis of the Immunometabolic Rewiring and Immunopathogenesis of Coronavirus Disease 2019. Front Immunol 2021; 12:651656. [PMID: 33936072 PMCID: PMC8079812 DOI: 10.3389/fimmu.2021.651656] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/29/2021] [Indexed: 12/16/2022] Open
Abstract
Although immune dysfunction is a key feature of coronavirus disease 2019 (COVID-19), the metabolism-related mechanisms remain elusive. Here, by reanalyzing single-cell RNA sequencing data, we delineated metabolic remodeling in peripheral blood mononuclear cells (PBMCs) to elucidate the metabolic mechanisms that may lead to the progression of severe COVID-19. After scoring the metabolism-related biological processes and signaling pathways, we found that mono-CD14+ cells expressed higher levels of glycolysis-related genes (PKM, LDHA and PKM) and PPP-related genes (PGD and TKT) in severe patients than in mild patients. These genes may contribute to the hyperinflammation in mono-CD14+ cells of patients with severe COVID-19. The mono-CD16+ cell population in COVID-19 patients showed reduced transcription levels of genes related to lysine degradation (NSD1, KMT2E, and SETD2) and elevated transcription levels of genes involved in OXPHOS (ATP6V1B2, ATP5A1, ATP5E, and ATP5B), which may inhibit M2-like polarization. Plasma cells also expressed higher levels of the OXPHOS gene ATP13A3 in COVID-19 patients, which was positively associated with antibody secretion and survival of PCs. Moreover, enhanced glycolysis or OXPHOS was positively associated with the differentiation of memory B cells into plasmablasts or plasma cells. This study comprehensively investigated the metabolic features of peripheral immune cells and revealed that metabolic changes exacerbated inflammation in monocytes and promoted antibody secretion and cell survival in PCs in COVID-19 patients, especially those with severe disease.
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Affiliation(s)
- Furong Qi
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, China.,Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, China
| | - Wenbo Zhang
- Trinity School of Durham and Chapel Hill, Durham, NC, United States
| | - Jialu Huang
- Electronic and Computer Engineering, China North Vehicle Research Institute, Beijing, China
| | - Lili Fu
- Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jinfang Zhao
- Center for Life Sciences, Tsinghua University, Beijing, China
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10
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Pham T, Liao R, Labaer J, Guo J. Multiplexed In Situ Protein Profiling with High-Performance Cleavable Fluorescent Tyramide. Molecules 2021; 26:molecules26082206. [PMID: 33921211 PMCID: PMC8070642 DOI: 10.3390/molecules26082206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022] Open
Abstract
Understanding the composition, function and regulation of complex cellular systems requires tools that quantify the expression of multiple proteins at their native cellular context. Here, we report a highly sensitive and accurate protein in situ profiling approach using off-the-shelf antibodies and cleavable fluorescent tyramide (CFT). In each cycle of this method, protein targets are stained with horseradish peroxidase (HRP) conjugated antibodies and CFT. Subsequently, the fluorophores are efficiently cleaved by mild chemical reagents, which simultaneously deactivate HRP. Through reiterative cycles of protein staining, fluorescence imaging, fluorophore cleavage, and HRP deactivation, multiplexed protein quantification in single cells in situ can be achieved. We designed and synthesized the high-performance CFT, and demonstrated that over 95% of the staining signals can be erased by mild chemical reagents while preserving the integrity of the epitopes on protein targets. Applying this method, we explored the protein expression heterogeneity and correlation in a group of genetically identical cells. With the high signal removal efficiency, this approach also enables us to accurately profile proteins in formalin-fixed paraffin-embedded (FFPE) tissues in the order of low to high and also high to low expression levels.
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Affiliation(s)
| | | | | | - Jia Guo
- Correspondence: ; Tel.: +1-480-727-2096
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11
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Liao R, Mondal M, Nazaroff CD, Mastroeni D, Coleman PD, Labaer J, Guo J. Highly Sensitive and Multiplexed Protein Imaging With Cleavable Fluorescent Tyramide Reveals Human Neuronal Heterogeneity. Front Cell Dev Biol 2021; 8:614624. [PMID: 33585449 PMCID: PMC7874177 DOI: 10.3389/fcell.2020.614624] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/09/2020] [Indexed: 12/18/2022] Open
Abstract
The ability to comprehensively profile proteins in intact tissues in situ is crucial for our understanding of health and disease. However, the existing methods suffer from low sensitivity and limited sample throughput. To address these issues, here we present a highly sensitive and multiplexed in situ protein analysis approach using cleavable fluorescent tyramide and off-the-shelf antibodies. Compared with the current methods, this approach enhances the detection sensitivity and reduces the imaging time by 1-2 orders of magnitude, and can potentially detect hundreds of proteins in intact tissues at the optical resolution. Applying this approach, we studied protein expression heterogeneity in a population of genetically identical cells, and performed protein expression correlation analysis to identify co-regulated proteins. We also profiled >6,000 neurons in a human formalin-fixed paraffin-embedded (FFPE) hippocampus tissue. By partitioning these neurons into varied cell clusters based on their multiplexed protein expression profiles, we observed different sub-regions of the hippocampus consist of neurons from distinct clusters.
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Affiliation(s)
- Renjie Liao
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Manas Mondal
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Christopher D. Nazaroff
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
- Division of Pulmonary Medicine, Department of Biochemistry and Molecular Biology, Mayo Clinic Arizona, Scottsdale, AZ, United States
| | - Diego Mastroeni
- Arizona State University-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, United States
- L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Paul D. Coleman
- Arizona State University-Banner Neurodegenerative Disease Research Center, Biodesign Institute and School of Life Sciences, Arizona State University, Tempe, AZ, United States
- L.J. Roberts Center for Alzheimer's Research, Banner Sun Health Research Institute, Sun City, AZ, United States
| | - Joshua Labaer
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
| | - Jia Guo
- Biodesign Institute & School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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