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Krohmaly KI, Perez-Losada M, Ramos-Tapia I, Zhu Z, Hasegawa K, Camargo Jr. CA, Harmon B, Espinola JA, Reck Cechinel L, Batabyal R, Freishtat RJ, Hahn A. Bacterial small RNAs may mediate immune response differences seen in respiratory syncytial virus versus rhinovirus bronchiolitis. Front Immunol 2024; 15:1330991. [PMID: 38410509 PMCID: PMC10895043 DOI: 10.3389/fimmu.2024.1330991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Bronchiolitis, a viral lower respiratory infection, is the leading cause of infant hospitalization, which is associated with an increased risk for developing asthma later in life. Bronchiolitis can be caused by several respiratory viruses, such as respiratory syncytial virus (RSV), rhinovirus (RV), and others. It can also be caused by a solo infection (e.g., RSV- or RV-only bronchiolitis) or co-infection with two or more viruses. Studies have shown viral etiology-related differences between RSV- and RV-only bronchiolitis in the immune response, human microRNA (miRNA) profiles, and dominance of certain airway microbiome constituents. Here, we identified bacterial small RNAs (sRNAs), the prokaryotic equivalent to eukaryotic miRNAs, that differ between infants of the 35th Multicenter Airway Research Collaboration (MARC-35) cohort with RSV- versus RV-only bronchiolitis. We first derived reference sRNA datasets from cultures of four bacteria known to be associated with bronchiolitis (i.e., Haemophilus influenzae, Moraxella catarrhalis, Moraxella nonliquefaciens, and Streptococcus pneumoniae). Using these reference sRNA datasets, we found several sRNAs associated with RSV- and RV-only bronchiolitis in our human nasal RNA-Seq MARC-35 data. We also determined potential human transcript targets of the bacterial sRNAs and compared expression of the sRNAs between RSV- and RV-only cases. sRNAs are known to downregulate their mRNA target, we found that, compared to those associated with RV-only bronchiolitis, sRNAs associated with RSV-only bronchiolitis may relatively activate the IL-6 and IL-8 pathways and relatively inhibit the IL-17A pathway. These data support that bacteria may be contributing to inflammation differences seen in RSV- and RV-only bronchiolitis, and for the first time indicate that the potential mechanism in doing so may be through bacterial sRNAs.
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Affiliation(s)
- Kylie I. Krohmaly
- Integrated Biomedical Sciences, The George Washington University, Washington, DC, United States
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Marcos Perez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, The George Washington University, Washington, DC, United States
| | - Ignacio Ramos-Tapia
- Centro de Bioinformática y Biología Integrativa, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Carlos A. Camargo Jr.
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Janice A. Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Laura Reck Cechinel
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
| | - Rachael Batabyal
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Division of Emergency Medicine, Children’s National Hospital, Washington, DC, United States
| | - Robert J. Freishtat
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children’s National Research and Innovation Center, Washington, DC, United States
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, United States
- Division of Infectious Diseases, Children’s National Hospital, Washington, DC, United States
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Fujiogi M, Camargo CA, Bernot JP, Freishtat RJ, Harmon B, Mansbach JM, Castro-Nallar E, Perez-Losada M, Hasegawa K. In infants with severe bronchiolitis: dual-transcriptomic profiling of nasopharyngeal microbiome and host response. Pediatr Res 2020; 88:144-146. [PMID: 31905367 PMCID: PMC7335686 DOI: 10.1038/s41390-019-0742-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/11/2019] [Accepted: 12/15/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Carlos A. Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - James P. Bernot
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC,Division of Emergency Medicine, Children’s National Hospital, Washington, DC,Departments of Pediatrics and Integrative Systems Biology and Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Brennan Harmon
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC
| | - Jonathan M. Mansbach
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Eduardo Castro-Nallar
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Marcos Perez-Losada
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, George Washington University, Washington, DC,Department of Pediatrics, George Washington University School of Medicine and Health Sciences and the Division of Emergency Medicine, Children’s National Hospital, Washington, DC,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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Val S, Poley M, Brown K, Choi R, Jeong S, Colberg-Poley A, Rose MC, Panchapakesan KC, Devaney JC, Perez-Losada M, Preciado D. Proteomic Characterization of Middle Ear Fluid Confirms Neutrophil Extracellular Traps as a Predominant Innate Immune Response in Chronic Otitis Media. PLoS One 2016; 11:e0152865. [PMID: 27078692 PMCID: PMC4831838 DOI: 10.1371/journal.pone.0152865] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/21/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Chronic Otitis Media (COM) is characterized by middle ear effusion (MEE) and conductive hearing loss. MEE reflect mucus hypersecretion, but global proteomic profiling of the mucosal components are limited. OBJECTIVE This study aimed at characterizing the proteome of MEEs from children with COM with the goal of elucidating important innate immune responses. METHOD MEEs were collected from children (n = 49) with COM undergoing myringotomy. Mass spectrometry was employed for proteomic profiling in nine samples. Independent samples were further analyzed by cytokine multiplex assay, immunoblotting, neutrophil elastase activity, next generation DNA sequencing, and/or immunofluorescence analysis. RESULTS 109 unique and common proteins were identified by MS. A majority were innate immune molecules, along with typically intracellular proteins such as histones and actin. 19.5% percent of all mapped peptide counts were from proteins known to be released by neutrophils. Immunofluorescence and immunoblotting demonstrated the presence of neutrophil extracellular traps (NETs) in every MEE, along with MUC5B colocalization. DNA found in effusions revealed unfragmented DNA of human origin. CONCLUSION Proteomic analysis of MEEs revealed a predominantly neutrophilic innate mucosal response in which MUC5B is associated with NET DNA. NETs are a primary macromolecular constituent of human COM middle ear effusions.
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Affiliation(s)
- Stephanie Val
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Marian Poley
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Kristy Brown
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Rachel Choi
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Stephanie Jeong
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
| | - Annie Colberg-Poley
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Mary C. Rose
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Karuna C. Panchapakesan
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Joe C. Devaney
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Marcos Perez-Losada
- Center for Genetic Medicine Research, Children’s National Health System, Washington, DC, United States of America
| | - Diego Preciado
- Sheikh Zayed Center for Pediatric Surgical Innovation, Children’s National Health System, Washington, DC, United States of America
- Division of Pediatric Otolaryngology, Children’s National Health System, Washington, DC, United States of America
- * E-mail:
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Perez-Losada M, Goldstein A, Alamri L, Crandall KA, Freishtat RJ. 20: NASOPHARYNX MICROBIOME COMPOSITION VARIES OVER TIME IN PEDIATRIC ASTHMA. J Investig Med 2016. [DOI: 10.1136/jim-2016-000080.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Purpose of StudyThe application of next-generation sequencing (NGS) technology has shown that microbial communities in the respiratory airways (i.e., the microbiome) play a significant role in the onset, development and severity of asthma. However, little is known about their temporal dynamics (i.e., microbial succession), which poses a significant obstacle to identifying pulmotypes of disease and assessing inter-patient variation. Here, we couple NGS and 16S rRNA data to characterize the nasopharynx microbiome of children with asthma and determine its stability over time.Methods UsedWe collected nasal washes from 40 children with asthma enrolled in the AsthMaP-2 Project from two consecutive visits, six months apart. Total DNA was extracted and sequenced for the 16S-V4 rRNA gene region (∼250 bp) using the MySeq Illumina platform. Reads were analyzed in Mothur using the SILVAv119 reference database. Alpha diversity metrics and phylogenetic and count-base distance community indexes of beta diversity were compared across samples and time points. PCoA and NJ clustering analysis were used to assess community relatedness. Differences in alpha diversity and OTU abundance between sample pairs across time points were also compared.Summary of ResultsA mean of 27,479 clean 16S sequences corresponding to an average of 173 OTUs were sequenced and detected per sample, respectively. Representatives of Moraxella, Corynebacterium, Prevotella, Staphylococcus, Alloiococcus, Streptococcus, Peptoniphilus, Fusobacterium, and Haemophilus accounted for 36 to 99% of the reads across samples. These genera have been previously found in the nasopharynx of asthmatic and healthy children. A total of 61 OTUs from these genera were present in at least 50% of the samples (i.e., the nasal core microbiome). Significant differences in core microbiome composition were detected between sample pairs, but no directional trend (increase or decrease) was observed across sample pairs. Samples were randomly ordinated and did not cluster together.ConclusionsOur analysis of nasal microbiomes in 40 asthmatic children revealed significant differences in composition within individuals over six months. Future cross-sectional microbiome studies need to be aware of short span temporal dynamics in nasal microbiota.
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Groah S, Perez-Losada M, Caldovic L, Ljungberg I, Sprague B, Castro-Nallar E, Shah N, Hsieh M, Pohl H. MP20-07 ALL ASYMPTOMATIC BACTERIURIA, ALL THE TIME. J Urol 2015. [DOI: 10.1016/j.juro.2015.02.979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Perez-Losada M, Hoeg JT, Crandall KA. Deep Phylogeny and Character Evolution in Thecostraca (Crustacea: Maxillopoda). Integr Comp Biol 2012; 52:430-42. [DOI: 10.1093/icb/ics051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Weaver KF, Perez-Losada M, Guralnick RP, Nelson A, Blatt S, Crandall KA. Assessing the conservation status of the land snail Oreohelix peripherica wasatchensis (Family Oreohelicidae). CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9415-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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