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Flynn J, Ahmadi MM, McFarland CT, Kubal MD, Taylor MA, Cheng Z, Torchia EC, Edwards MG. Crowdsourcing temporal transcriptomic coronavirus host infection data: Resources, guide, and novel insights. Biol Methods Protoc 2023; 8:bpad033. [PMID: 38107402 PMCID: PMC10723038 DOI: 10.1093/biomethods/bpad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
The emergence of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) reawakened the need to rapidly understand the molecular etiologies, pandemic potential, and prospective treatments of infectious agents. The lack of existing data on SARS-CoV-2 hampered early attempts to treat severe forms of coronavirus disease-2019 (COVID-19) during the pandemic. This study coupled existing transcriptomic data from severe acute respiratory syndrome-related coronavirus 1 (SARS-CoV-1) lung infection animal studies with crowdsourcing statistical approaches to derive temporal meta-signatures of host responses during early viral accumulation and subsequent clearance stages. Unsupervised and supervised machine learning approaches identified top dysregulated genes and potential biomarkers (e.g. CXCL10, BEX2, and ADM). Temporal meta-signatures revealed distinct gene expression programs with biological implications to a series of host responses underlying sustained Cxcl10 expression and Stat signaling. Cell cycle switched from G1/G0 phase genes, early in infection, to a G2/M gene signature during late infection that correlated with the enrichment of DNA damage response and repair genes. The SARS-CoV-1 meta-signatures were shown to closely emulate human SARS-CoV-2 host responses from emerging RNAseq, single cell, and proteomics data with early monocyte-macrophage activation followed by lymphocyte proliferation. The circulatory hormone adrenomedullin was observed as maximally elevated in elderly patients who died from COVID-19. Stage-specific correlations to compounds with potential to treat COVID-19 and future coronavirus infections were in part validated by a subset of twenty-four that are in clinical trials to treat COVID-19. This study represents a roadmap to leverage existing data in the public domain to derive novel molecular and biological insights and potential treatments to emerging human pathogens.
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Affiliation(s)
- James Flynn
- Illumina Corporation, San Diego, CA 92122, United States
| | - Mehdi M Ahmadi
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
| | | | | | - Mark A Taylor
- Bioinfo Solutions LLC, Parker, CO 80134, United States
| | - Zhang Cheng
- Illumina Corporation, San Diego, CA 92122, United States
| | - Enrique C Torchia
- Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States
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2
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Xu K, Saaoud F, Shao Y, Lu Y, Wu S, Zhao H, Chen K, Vazquez-Padron R, Jiang X, Wang H, Yang X. Early hyperlipidemia triggers metabolomic reprogramming with increased SAH, increased acetyl-CoA-cholesterol synthesis, and decreased glycolysis. Redox Biol 2023; 64:102771. [PMID: 37364513 PMCID: PMC10310484 DOI: 10.1016/j.redox.2023.102771] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
To identify metabolomic reprogramming in early hyperlipidemia, unbiased metabolome was screened in four tissues from ApoE-/- mice fed with high fat diet (HFD) for 3 weeks. 30, 122, 67, and 97 metabolites in the aorta, heart, liver, and plasma, respectively, were upregulated. 9 upregulated metabolites were uremic toxins, and 13 metabolites, including palmitate, promoted a trained immunity with increased syntheses of acetyl-CoA and cholesterol, increased S-adenosylhomocysteine (SAH) and hypomethylation and decreased glycolysis. The cross-omics analysis found upregulation of 11 metabolite synthetases in ApoE‾/‾ aorta, which promote ROS, cholesterol biosynthesis, and inflammation. Statistical correlation of 12 upregulated metabolites with 37 gene upregulations in ApoE‾/‾ aorta indicated 9 upregulated new metabolites to be proatherogenic. Antioxidant transcription factor NRF2-/- transcriptome analysis indicated that NRF2 suppresses trained immunity-metabolomic reprogramming. Our results have provided novel insights on metabolomic reprogramming in multiple tissues in early hyperlipidemia oriented toward three co-existed new types of trained immunity.
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Affiliation(s)
- Keman Xu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Fatma Saaoud
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Ying Shao
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Yifan Lu
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Sheng Wu
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Huaqing Zhao
- Medical Education and Data Science, Temple University Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Kaifu Chen
- Computational Biology Program, Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Roberto Vazquez-Padron
- DeWitt Daughtry Family Department of Surgery, Leonard M. Miller School of Medicine, University of Miami, Miami, FL, 33125, USA
| | - Xiaohua Jiang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Hong Wang
- Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA
| | - Xiaofeng Yang
- Centers of Cardiovascular Research, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA; Metabolic Disease Research, Thrombosis Research, Departments of Cardiovascular Sciences, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, USA.
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Zhang X, Hu C, Huang C, Wei Y, Li X, Hu M, Li H, Wu J, Czajkowsky DM, Guo Y, Shao Z. Robust Acquisition of Spatial Transcriptional Programs in Tissues With Immunofluorescence-Guided Laser Capture Microdissection. Front Cell Dev Biol 2022; 10:853188. [PMID: 35399504 PMCID: PMC8990165 DOI: 10.3389/fcell.2022.853188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue, as local interactions precipitate intra-cellular events that often lead to changes in expression. However, our understanding of these processes in tissues, whether healthy or diseased, is limited at present owing to the difficulty in acquiring comprehensive transcriptional programs of spatially- and phenotypically-defined cells in situ. Here we present a robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to acquire finely resolved transcriptional programs with as few as tens of cells from snap-frozen or RNAlater-treated clinical tissues sufficient to resolve even isoforms. The protocol is optimized to protect the RNA with a small molecule inhibitor, the ribonucleoside vanadyl complex (RVC), which thereby enables the typical time-consuming immunostaining and laser capture steps of this procedure during which RNA is usually severely degraded in existing approaches. The efficacy of this approach is exemplified by the characterization of differentially expressed genes between the mouse small intestine lacteal cells at the tip versus the main capillary body, including those that function in sensing and responding to local environmental cues to stimulate intra-cellular signalling. With the extensive repertoire of specific antibodies that are presently available, our method provides an unprecedented capability for the analysis of transcriptional networks and signalling pathways during development, pathogenesis, and aging of specific cell types within native tissues.
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Affiliation(s)
- Xiaodan Zhang
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chuansheng Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Huang
- Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Wei
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowei Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Miaomiao Hu
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Hua Li
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Wu
- Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel M. Czajkowsky
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Yan Guo
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
| | - Zhifeng Shao
- State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Daniel M. Czajkowsky, ; Yan Guo, ; Zhifeng Shao,
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Schlafens Can Put Viruses to Sleep. Viruses 2022; 14:v14020442. [PMID: 35216035 PMCID: PMC8875196 DOI: 10.3390/v14020442] [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: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 12/21/2022] Open
Abstract
The Schlafen gene family encodes for proteins involved in various biological tasks, including cell proliferation, differentiation, and T cell development. Schlafens were initially discovered in mice, and have been studied in the context of cancer biology, as well as their role in protecting cells during viral infection. This protein family provides antiviral barriers via direct and indirect effects on virus infection. Schlafens can inhibit the replication of viruses with both RNA and DNA genomes. In this review, we summarize the cellular functions and the emerging relationship between Schlafens and innate immunity. We also discuss the functions and distinctions of this emerging family of proteins as host restriction factors against viral infection. Further research into Schlafen protein function will provide insight into their mechanisms that contribute to intrinsic and innate host immunity.
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Metzner FJ, Huber E, Hopfner KP, Lammens K. Structural and biochemical characterization of human Schlafen 5. Nucleic Acids Res 2022; 50:1147-1161. [PMID: 35037067 PMCID: PMC8789055 DOI: 10.1093/nar/gkab1278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 11/15/2022] Open
Abstract
The Schlafen family belongs to the interferon-stimulated genes and its members are involved in cell cycle regulation, T cell quiescence, inhibition of viral replication, DNA-repair and tRNA processing. Here, we present the cryo-EM structure of full-length human Schlafen 5 (SLFN5) and the high-resolution crystal structure of the highly conserved N-terminal core domain. We show that the core domain does not resemble an ATPase-like fold and neither binds nor hydrolyzes ATP. SLFN5 binds tRNA as well as single- and double-stranded DNA, suggesting a potential role in transcriptional regulation. Unlike rat Slfn13 or human SLFN11, human SLFN5 did not cleave tRNA. Based on the structure, we identified two residues in proximity to the zinc finger motif that decreased DNA binding when mutated. These results indicate that Schlafen proteins have divergent enzymatic functions and provide a structural platform for future biochemical and genetic studies.
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Affiliation(s)
- Felix J Metzner
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Elisabeth Huber
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
| | - Katja Lammens
- Department of Biochemistry, Gene Center, Feodor-Lynen-Straße 25, 81377 München, Germany
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6
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Schlafens: Emerging Proteins in Cancer Cell Biology. Cells 2021; 10:cells10092238. [PMID: 34571887 PMCID: PMC8465726 DOI: 10.3390/cells10092238] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/29/2022] Open
Abstract
Schlafens (SLFN) are a family of genes widely expressed in mammals, including humans and rodents. These intriguing proteins play different roles in regulating cell proliferation, cell differentiation, immune cell growth and maturation, and inhibiting viral replication. The emerging evidence is implicating Schlafens in cancer biology and chemosensitivity. Although Schlafens share common domains and a high degree of homology, different Schlafens act differently. In particular, they show specific and occasionally opposing effects in some cancer types. This review will briefly summarize the history, structure, and non-malignant biological functions of Schlafens. The roles of human and mouse Schlafens in different cancer types will then be outlined. Finally, we will discuss the implication of Schlafens in the anti-tumor effect of interferons and the use of Schlafens as predictors of chemosensitivity.
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Adlat S, Sah RK, Hayel F, Chen Y, Bah FB, Al-Azab M, Bahadar N, Myint M, Oo ZM, Nasser MI, Zhang L, Feng X, Zheng Y. Global transcriptome study of Dip2B-deficient mouse embryonic lung fibroblast reveals its important roles in cell proliferation and development. Comput Struct Biotechnol J 2020; 18:2381-2390. [PMID: 33005301 PMCID: PMC7502710 DOI: 10.1016/j.csbj.2020.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/20/2020] [Accepted: 08/29/2020] [Indexed: 12/20/2022] Open
Abstract
Disco-interacting protein 2 homolog B (Dip2B) is a member of Dip2 family encoded by Dip2b gene. Dip2B has been reported to regulate murine epithelial KIT+ progenitor cell expansion and differentiation epigenetically via exosomal miRNA targeting during salivary gland organogenesis. However, its molecular functions, cellular activities and biological process remain unstudied. Here, we investigated the transcriptome of Dip2B-deficient mouse embryonic lung fibroblasts (MELFs) isolated from E14.5 embryos by RNA-Seq. Expression profiling identified 1369 and 1104 differentially expressed genes (DEGs) from Dip2b−/− and Dip2b+/− MELFs in comparisons to wild-type (Dip2b+/+). Functional clustering of DEGs revealed that many gene ontology terms belong to membrane activities such as ‘integral component of plasma membrane’, and ‘ion channel activity’, suggesting possible roles of Dip2B in membrane integrity and membrane function. KEGG pathway analysis revealed that multiple metabolic pathways are affected in Dip2b−/− and Dip2b+/− when compared to Dip2b+/+ MELFs. These include ‘protein digestion and absorption’, ‘pancreatic secretion’ and ‘steroid hormone synthesis pathway’. These results suggest that Dip2B may play important roles in metabolism. Molecular function analysis shows transcription factors including Hox-genes, bHLH-genes, and Forkhead-genes are significantly down-regulated in Dip2b−/− MELFs. These genes are critical in embryo development and cell differentiation. In addition, Dip2B-deficient MELFs demonstrated a reduction in cell proliferation and migration, and an increase in apoptosis. All results indicate that Dip2B plays multiple roles in cell proliferation, migration and apoptosis during embryogenesis and may participate in control of metabolism. This study provides valuable information for further understanding of the function and regulatory mechanisms of Dip2B.
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Affiliation(s)
- Salah Adlat
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Rajiv Kumar Sah
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Farooq Hayel
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Yang Chen
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Fatoumata Binta Bah
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Mahmoud Al-Azab
- Department of Immunology, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou 510623, China
| | - Noor Bahadar
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - May Myint
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Zin Mar Oo
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - M I Nasser
- Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Luqing Zhang
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Xuechao Feng
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.,Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
| | - Yaowu Zheng
- Transgenic Research Center, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China.,Key Laboratory of Molecular Epigenetics of Ministry of Education, School of Life Sciences, Northeast Normal University, Changchun, Jilin 130024, China
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8
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Komici K, Faris P, Negri S, Rosti V, García-Carrasco M, Mendoza-Pinto C, Berra-Romani R, Cervera R, Guerra G, Moccia F. Systemic lupus erythematosus, endothelial progenitor cells and intracellular Ca2+ signaling: A novel approach for an old disease. J Autoimmun 2020; 112:102486. [DOI: 10.1016/j.jaut.2020.102486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 02/07/2023]
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9
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Nakagawa K, Matsuki T, Zhao L, Kuniyoshi K, Tanaka H, Ebina I, Yoshida KJ, Nabeshima H, Fukushima K, Kanemaru H, Yamane F, Kawasaki T, Machida T, Naito H, Takakura N, Satoh T, Akira S. Schlafen-8 is essential for lymphatic endothelial cell activation in experimental autoimmune encephalomyelitis. Int Immunol 2019. [PMID: 29528433 DOI: 10.1093/intimm/dxx079] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Schlafen-8 (Slfn8) is a member of the Schlafen family of proteins, which harbor helicase domains and are induced by LPS and interferons. It has been reported that the Schlafen family are involved in various cellular functions, including proliferation, differentiation and regulation of virus replication. Slfn8 has been implicated in T-cell differentiation in the thymus. However, the roles of Slfn8 in the immune system remains unclear. In this study, we generated Slfn8 knockout mice (Slfn8-/-) and investigated the immunological role of Slfn8 using the T-cell-mediated autoimmune model experimental autoimmune encephalomyelitis (EAE). We found that the clinical score was reduced in Slfn8-/- mice. IL-6 and IL-17A cytokine production, which are associated with EAE onset and progression, were decreased in the lymph nodes of Slfn8-/- mice. Immune cell populations in Slfn8-/- mice, including macrophages, neutrophils, T cells and B cells, did not reveal significant differences compared with wild-type mice. In vitro activation of Slfn8-/- T cells in response to TCR stimulation also did not reveal significant differences. To confirm the involvement of non-hematopoietic cells, we isolated CD45- CD31+ endothelial cells and CD45-CD31- gp38+ fibroblastic reticular cells by FACS sorting. We showed that the levels of IL-6 and Slfn8 mRNA in CD45- CD31+ endothelial cells were increased after EAE induction. In contrast, the level of IL-6 mRNA after EAE induction was markedly decreased in CD31+ endothelial cells from Slfn8-/- mice. These results indicate that Slfn8 may play a role in EAE by regulating inflammation in endothelial cells.
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Affiliation(s)
- Katsuhiro Nakagawa
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takanori Matsuki
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Liang Zhao
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Kanako Kuniyoshi
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Hiroki Tanaka
- Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Isao Ebina
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Kenta J Yoshida
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Hiroshi Nabeshima
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Hisashi Kanemaru
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Fumihiro Yamane
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takahiro Kawasaki
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Tomohisa Machida
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Hisamichi Naito
- Department of Signal Transduction, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Nobuyuki Takakura
- Department of Signal Transduction, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Takashi Satoh
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Shizuo Akira
- Department of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan.,Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
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Rodrigues PG, Miranda-Silva D, Costa SM, Barros C, Hamdani N, Moura C, Mendes MJ, Sousa-Mendes C, Trindade F, Fontoura D, Vitorino R, Linke WA, Leite-Moreira AF, Falcão-Pires I. Early myocardial changes induced by doxorubicin in the nonfailing dilated ventricle. Am J Physiol Heart Circ Physiol 2019; 316:H459-H475. [DOI: 10.1152/ajpheart.00401.2018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several studies have demonstrated that administration of doxorubicin (DOXO) results in cardiotoxicity, which eventually progresses to dilated cardiomyopathy. The present work aimed to evaluate the early myocardial changes of DOXO-induced cardiotoxicity. Male New Zealand White rabbits were injected intravenously with DOXO twice weekly for 8 wk [DOXO-induced heart failure (DOXO-HF)] or with an equivolumetric dose of saline (control). Echocardiographic evaluation was performed, and myocardial samples were collected to evaluate myocardial cellular and molecular modifications. The DOXO-HF group presented cardiac hypertrophy and higher left ventricular cavity diameters, showing a dilated phenotype but preserved ejection fraction. Concerning cardiomyocyte function, the DOXO-HF group presented a trend toward increased active tension without significant differences in passive tension. The myocardial GSSG-to-GSH ratio and interstitial fibrosis were increased and Bax-to- Bcl-2 ratio presented a trend toward an increase, suggesting the activation of apoptosis signaling pathways. The macromolecule titin shifted toward the more compliant isoform (N2BA), whereas the stiffer one (N2B) was shown to be hypophosphorylated. Differential protein analysis from the aggregate-enriched fraction through gel liquid chromatography-tandem mass spectrometry revealed an increase in the histidine-rich glycoprotein fragment in DOXO-HF animals. This work describes novel and early myocardial effects of DOXO-induced cardiotoxicity. Thus, tracking these changes appears to be of extreme relevance for the early detection of cardiac damage (as soon as ventricular dilation becomes evident) before irreversible cardiac function deterioration occurs (reduced ejection fraction). Moreover, it allows for the adjustment of the therapeutic approach and thus the prevention of cardiomyopathy progression. NEW & NOTEWORTHY Identification of early myocardial effects of doxorubicin in the heart is essential to hinder the development of cardiac complications and adjust the therapeutic approach. This study describes doxorubicin-induced cellular and molecular modifications before the onset of dilated cardiomyopathy. Myocardial samples from doxorubicin-treated rabbits showed a tendency for higher cardiomyocyte active tension, titin isoform shift from N2B to N2BA, hypophosphorylation of N2B, increased apoptotic genes, left ventricular interstitial fibrosis, and increased aggregation of histidine-rich glycoprotein.
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Affiliation(s)
- Patricia G. Rodrigues
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Daniela Miranda-Silva
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Sofia M. Costa
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Carla Barros
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Nazha Hamdani
- Department of Systems Physiology, Ruhr University, Bochum, Germany
| | - Cláudia Moura
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Maria J. Mendes
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Cláudia Sousa-Mendes
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Fábio Trindade
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Dulce Fontoura
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
| | - Rui Vitorino
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Wolfgang A. Linke
- Institute of Physiology II, University of Muenster, Muenster, Germany
| | - Adelino F. Leite-Moreira
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
- Department of Cardiothoracic Surgery, São João Hospital Centre, Porto, Portugal
| | - Inês Falcão-Pires
- Department of Surgery and Physiology, Faculty of Medicine, Unidade de Investigação Cardiovascular, Universidade do Porto, Porto, Portugal
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Coppin E, Florentin J, Vasamsetti SB, Arunkumar A, Sembrat J, Rojas M, Dutta P. Splenic hematopoietic stem cells display a pre-activated phenotype. Immunol Cell Biol 2018; 96:10.1111/imcb.12035. [PMID: 29526053 PMCID: PMC6379147 DOI: 10.1111/imcb.12035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 02/16/2018] [Accepted: 03/05/2018] [Indexed: 12/12/2022]
Abstract
Splenic hematopoiesis is crucial to the pathogenesis of diseases including myocardial infarction and atherosclerosis. The spleen acts as a reservoir of myeloid cells, which are quickly expelled out in response to acute inflammation. In contrast to the well-defined bone marrow hematopoiesis, the cellular and molecular components sustaining splenic hematopoiesis are poorly understood. Surprisingly, we found that, unlike quiescent bone marrow hematopoietic stem cells (HSC), most of splenic HSC are in the G1 phase in C57BL/6 mice. Moreover, splenic HSC were enriched for genes involved in G0-G1 transition and expressed lower levels of genes responsible for G1-S transition. These data indicate that, at steady state, splenic HSC are pre-activated, which may expedite their cell cycle entry in emergency conditions. Consistently, in the acute phase of septic shock induced by LPS injection, splenic HSC entered the S-G2-M phase, whereas bone marrow HSC did not. Mobilization and transplantation experiments displayed that bone marrow HSC, once in the spleen, acquired cell cycle status similar to splenic HSC, strongly suggesting that the splenic microenvironment plays an important role in HSC pre-activation. In addition, we found that myeloid translocation gene 16 (Mtg16) deficiency in C57BL/6 mice resulted in significantly increased S-G2-M entry of splenic but not bone marrow HSC, suggesting that Mtg16 is an intrinsic negative regulator of G1-S transition in splenic HSC. Altogether, this study demonstrates that compared to bone marrow, splenic HSC are in a pre-activated state, which is driven by extracellular signals provided by splenic microenvironment and HSC intrinsic factor Mtg16.
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Affiliation(s)
- Emilie Coppin
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Jonathan Florentin
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Sathish Babu Vasamsetti
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Anagha Arunkumar
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
| | - John Sembrat
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, PA 15261, USA
| | - Mauricio Rojas
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh, PA 15261, USA
| | - Partha Dutta
- Division of Cardiology, Department of Medicine, Vascular Medicine Institute, University of Pittsburgh Medical Center, BST 1720.1, 200 Lothrop Street, Pittsburgh, PA 15213, USA
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12
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Haberzettl P, Conklin DJ, Abplanalp WT, Bhatnagar A, O'Toole TE. Inhalation of Fine Particulate Matter Impairs Endothelial Progenitor Cell Function Via Pulmonary Oxidative Stress. Arterioscler Thromb Vasc Biol 2017; 38:131-142. [PMID: 29191925 DOI: 10.1161/atvbaha.117.309971] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 11/20/2017] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Exposure to fine particulate matter (PM2.5) air pollution is associated with the depletion of circulating endothelial progenitor cells (EPCs), as well as vascular injury and dysfunction. Nevertheless, it remains unclear whether PM2.5 exposure leads to significant impairments in EPC function. Hence, we studied the effects of PM2.5 on EPC-mediated recovery of vascular perfusion after hindlimb ischemia and examined the mechanisms whereby PM2.5 exposure affects EPC abundance and function. APPROACH AND RESULTS In comparison with EPCs isolated from mice breathing filtered air, EPCs from mice exposed for 9 consecutive days (6 hours per day) to concentrated ambient PM2.5 (CAP) had defects in both proliferation and tube formation. However, CAP exposure of mice overexpressing extracellular superoxide dismutase (ecSOD-Tg) in the lungs did not affect EPC tube formation. Exposure to CAP also suppressed circulating EPC levels, VEGF (vascular endothelial growth factor)-stimulated aortic Akt phosphorylation, and plasma NO levels in wild-type but not in ecSOD-Tg mice. EPCs from CAP-exposed wild-type mice failed to augment basal recovery of hindlimb perfusion when injected into unexposed mice subjected to hindlimb ischemia; however, these deficits in recovery of hindlimb perfusion were absent when using EPCs derived from CAP-exposed ecSOD-Tg mice. The improved reparative function of EPCs from CAP-exposed ecSOD-Tg mice was also reflected by greater expression of Mmp-9 and Nos3 when compared with EPCs from CAP-exposed wild-type mice. CONCLUSIONS Exposure to PM2.5 impairs EPC abundance and function and prevents EPC-mediated vascular recovery after hindlimb ischemia. This defect is attributed, in part, to pulmonary oxidative stress and was associated with vascular VEGF resistance and a decrement in NO bioavailability.
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Affiliation(s)
- Petra Haberzettl
- From the Department of Medicine, Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville, KY
| | - Daniel J Conklin
- From the Department of Medicine, Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville, KY
| | - Wesley T Abplanalp
- From the Department of Medicine, Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville, KY
| | - Aruni Bhatnagar
- From the Department of Medicine, Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville, KY
| | - Timothy E O'Toole
- From the Department of Medicine, Diabetes and Obesity Center, Institute of Molecular Cardiology, University of Louisville, KY.
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13
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Zhao B, Zhao Z, Sun X, Zhang Y, Guo Y, Tian P, Ma J, Ma X. Effect of micro strain stress on proliferation of endothelial progenitor cells in vitro by the MAPK-ERK1/2 signaling pathway. Biochem Biophys Res Commun 2017; 492:206-211. [DOI: 10.1016/j.bbrc.2017.08.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/13/2017] [Indexed: 10/19/2022]
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14
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Liu F, Zhou P, Wang Q, Zhang M, Li D. The Schlafen family: complex roles in different cell types and virus replication. Cell Biol Int 2017; 42:2-8. [PMID: 28460425 DOI: 10.1002/cbin.10778] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/23/2017] [Indexed: 12/28/2022]
Abstract
The Schlafen (slfn) gene family members express broadly, but the research has mainly focused on human slfn (h-slfn) and mouse slfn (m-slfn). The slfn members can be divided into three groups, and each group has its own characteristics and functions. Although the effects of slfns are still poorly understood, it has been confirmed that slfns are involved in the defense of immune system and regulate immune cells' proliferation and differentiation. In some malignant tumors, the slfn proteins can inhibit the growth and invasion of cancer cells, promote cancer cells sensibility to chemotherapeutics, and can be a promising new therapeutic target. In addition, the slfn proteins also disturb replication and virulence of viruses. In this review, we summarize the characteristics of the Schlafen family's structures and functions with the aim to achieve a more comprehensive understanding of slfns.
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Affiliation(s)
- Furao Liu
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Pingting Zhou
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qian Wang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Meichao Zhang
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Dong Li
- Department of Oncology, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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15
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Ding L, Hayes MM, Photenhauer A, Eaton KA, Li Q, Ocadiz-Ruiz R, Merchant JL. Schlafen 4-expressing myeloid-derived suppressor cells are induced during murine gastric metaplasia. J Clin Invest 2016; 126:2867-80. [PMID: 27427984 DOI: 10.1172/jci82529] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 05/19/2016] [Indexed: 12/29/2022] Open
Abstract
Chronic Helicobacter pylori infection triggers neoplastic transformation of the gastric mucosa in a small subset of patients, but the risk factors that induce progression to gastric metaplasia have not been identified. Prior to cancer development, the oxyntic gastric glands atrophy and are replaced by metaplastic cells in response to chronic gastritis. Previously, we identified schlafen 4 (Slfn4) as a GLI1 target gene and myeloid differentiation factor that correlates with spasmolytic polypeptide-expressing metaplasia (SPEM) in mice. Here, we tested the hypothesis that migration of SLFN4-expressing cells from the bone marrow to peripheral organs predicts preneoplastic changes in the gastric microenvironment. Lineage tracing in Helicobacter-infected Slfn4 reporter mice revealed that SLFN4+ cells migrated to the stomach, where they exhibited myeloid-derived suppressor cell (MDSC) markers and acquired the ability to inhibit T cell proliferation. SLFN4+ MDSCs were not observed in infected GLI1-deficient mice. Overexpression of sonic hedgehog ligand (SHH) in infected WT mice accelerated the appearance of SLFN4+ MDSCs in the gastric corpus. Similarly, in the stomachs of H. pylori-infected patients, the human SLFN4 ortholog SLFN12L colocalized to cells that expressed MDSC surface markers CD15+CD33+HLA-DRlo. Together, these results indicate that SLFN4 marks a GLI1-dependent population of MDSCs that predict a shift in the gastric mucosa to a metaplastic phenotype.
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16
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Clarke RL, Robitaille AM, Moon RT, Keller G. A Quantitative Proteomic Analysis of Hemogenic Endothelium Reveals Differential Regulation of Hematopoiesis by SOX17. Stem Cell Reports 2016; 5:291-304. [PMID: 26267830 PMCID: PMC4618836 DOI: 10.1016/j.stemcr.2015.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/14/2015] [Accepted: 07/22/2015] [Indexed: 10/27/2022] Open
Abstract
The in vitro derivation of hematopoietic stem cells (HSCs) from pluripotent stem cells (PSCs) is complicated by the existence of multiple overlapping embryonic blood cell programs called primitive, erythromyeloid progenitor (EMP), and definitive. As HSCs are only generated during the definitive stage of hematopoiesis, deciphering the regulatory pathways that control the emergence of this program and identifying markers that distinguish it from the other programs are essential. To identify definitive specific pathways and marker sets, we used label-free proteomics to determine the proteome of embryo-derived and mouse embryonic stem cell-derived VE-CADHERIN(+)CD45(-) definitive hematopoietic progenitors. With this approach, we identified Stat1 as a marker that distinguishes the definitive erythroid lineage from the primitive- and EMP-derived lineages. Additionally, we provide evidence that the generation of the Stat1(+) definitive lineage is dependent on Sox17. These findings establish an approach for monitoring the emergence of definitive hematopoiesis in the PSC differentiation cultures.
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Affiliation(s)
- Raedun L Clarke
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Aaron M Robitaille
- Institute for Stem Cell and Regenerative Medicine and Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Randall T Moon
- Institute for Stem Cell and Regenerative Medicine and Department of Pharmacology, University of Washington School of Medicine, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Gordon Keller
- McEwen Centre for Regenerative Medicine, University Health Network, Toronto, ON M5G 1L7, Canada.
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17
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Marconi C, Di Buduo CA, Barozzi S, Palombo F, Pardini S, Zaninetti C, Pippucci T, Noris P, Balduini A, Seri M, Pecci A. SLFN14-related thrombocytopenia: identification within a large series of patients with inherited thrombocytopenia. Thromb Haemost 2016; 115:1076-9. [PMID: 26769223 DOI: 10.1160/th15-11-0884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/13/2015] [Indexed: 01/05/2023]
Abstract
Supplementary Material to this article is available online at www.thrombosis-online.com.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Alessandro Pecci
- Alessandro Pecci, Department of Internal Medicine, IRCCS Policlinico San Matteo Foundation and University of Pavia, Piazzale Golgi, 27100 Pavia, Italy, Tel.: +39 0382 501358, Fax: +39 0382 526223, E-mail:
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18
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Fletcher SJ, Johnson B, Lowe GC, Bem D, Drake S, Lordkipanidzé M, Guiú IS, Dawood B, Rivera J, Simpson MA, Daly ME, Motwani J, Collins PW, Watson SP, Morgan NV. SLFN14 mutations underlie thrombocytopenia with excessive bleeding and platelet secretion defects. J Clin Invest 2015; 125:3600-5. [PMID: 26280575 DOI: 10.1172/jci80347] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/08/2015] [Indexed: 01/08/2023] Open
Abstract
Inherited thrombocytopenias are a group of disorders that are characterized by a low platelet count and are sometimes associated with excessive bleeding that ranges from mild to severe. We evaluated 36 unrelated patients and 17 family members displaying thrombocytopenia that were recruited to the UK Genotyping and Phenotyping of Platelets (GAPP) study. All patients had a history of excessive bleeding of unknown etiology. We performed platelet phenotyping and whole-exome sequencing (WES) on all patients and identified mutations in schlafen 14 (SLFN14) in 12 patients from 3 unrelated families. Patients harboring SLFN14 mutations displayed an analogous phenotype that consisted of moderate thrombocytopenia, enlarged platelets, decreased ATP secretion, and a dominant inheritance pattern. Three heterozygous missense mutations were identified in affected family members and predicted to encode substitutions (K218E, K219N, and V220D) within an ATPase-AAA-4, GTP/ATP-binding region of SLFN14. Endogenous SLFN14 expression was reduced in platelets from all patients, and mutant SLFN14 expression was markedly decreased compared with that of WT SLFN14 when overexpressed in transfected cells. Electron microscopy revealed a reduced number of dense granules in affected patients platelets, correlating with a decreased ATP secretion observed in lumiaggregometry studies. These results identify SLFN14 mutations as cause for an inherited thrombocytopenia with excessive bleeding, outlining a fundamental role for SLFN14 in platelet formation and function.
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