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Lousada MB, Edelkamp J, Lachnit T, Fehrholz M, Jimenez F, Paus R. Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile. BMC Res Notes 2023; 16:29. [PMID: 36879274 PMCID: PMC9987047 DOI: 10.1186/s13104-023-06302-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
OBJECTIVE Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations. RESULTS HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.
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Affiliation(s)
- Marta B Lousada
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany. .,Zoological Institute, Christian-Albrechts University Kiel, Kiel, Germany.
| | - J Edelkamp
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany
| | - T Lachnit
- Zoological Institute, Christian-Albrechts University Kiel, Kiel, Germany
| | - M Fehrholz
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany
| | - F Jimenez
- Mediteknia Skin & Hair Lab, Las Palmas de Gran Canaria, Spain.,Medical Pathology Group, IUIBS, Universidad de Las Palmas de Gran Canaria, Las Palmas, Spain
| | - R Paus
- Monasterium Laboratory, Skin&Hair Research, Muenster, Germany.,Dr Phillip Frost Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, USA.,CUTANEON Skin & Hair Innovations, Hamburg, Germany
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Maughan EF, Hynds RE, Pennycuick A, Nigro E, Gowers KH, Denais C, Gómez-López S, Lazarus KA, Orr JC, Pearce DR, Clarke SE, Lee DDH, Woodall MN, Masonou T, Case KM, Teixeira VH, Hartley BE, Hewitt RJ, Al Yaghchi C, Sandhu GS, Birchall MA, O’Callaghan C, Smith CM, De Coppi P, Butler CR, Janes SM. Cell-intrinsic differences between human airway epithelial cells from children and adults. iScience 2022; 25:105409. [PMID: 36388965 PMCID: PMC9664344 DOI: 10.1016/j.isci.2022.105409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 09/30/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The airway epithelium is a protective barrier that is maintained by the self-renewal and differentiation of basal stem cells. Increasing age is a principle risk factor for chronic lung diseases, but few studies have explored age-related molecular or functional changes in the airway epithelium. We retrieved epithelial biopsies from histologically normal tracheobronchial sites from pediatric and adult donors and compared their cellular composition and gene expression profile (in laser capture-microdissected whole epithelium, fluorescence-activated cell-sorted basal cells, and basal cells in cell culture). Histologically, pediatric and adult tracheobronchial epithelium was similar in composition. We observed age-associated changes in RNA sequencing studies, including higher interferon-associated gene expression in pediatric epithelium. In cell culture, pediatric cells had higher colony formation ability, sustained in vitro growth, and outcompeted adult cells in a direct competitive proliferation assay. Our results demonstrate cell-intrinsic differences between airway epithelial cells from children and adults in both homeostatic and proliferative states.
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Affiliation(s)
- Elizabeth F. Maughan
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Robert E. Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Adam Pennycuick
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Ersilia Nigro
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Kate H.C. Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Celine Denais
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Sandra Gómez-López
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Kyren A. Lazarus
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Jessica C. Orr
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - David R. Pearce
- University College London Cancer Institute, University College London, London WC1E 6DD, UK
| | - Sarah E. Clarke
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | - Dani Do Hyang Lee
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Maximillian N.J. Woodall
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Tereza Masonou
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Katie-Marie Case
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
| | | | | | - Chadwan Al Yaghchi
- The National Centre for Airway Reconstruction, Department of Otolaryngology, Charing Cross Hospital, London W6 8RF, UK
| | - Gurpreet S. Sandhu
- The National Centre for Airway Reconstruction, Department of Otolaryngology, Charing Cross Hospital, London W6 8RF, UK
| | - Martin A. Birchall
- University College London Ear Institute, University College London, London WC1X 8EE, UK
| | - Christopher O’Callaghan
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Claire M. Smith
- Infection, Immunity and Inflammation Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1E 1EH, UK
| | - Paolo De Coppi
- Stem Cell and Regenerative Medicine Section, University College London Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
| | - Colin R. Butler
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1DZ, UK
- Tracheal Service, Great Ormond Street Hospital, London WC1N 3JH, UK
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London WC1E 6JF, UK
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Resolving Clinical Phenotypes into Endotypes in Allergy: Molecular and Omics Approaches. Clin Rev Allergy Immunol 2020; 60:200-219. [PMID: 32378146 DOI: 10.1007/s12016-020-08787-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Allergic diseases are highly complex with respect to pathogenesis, inflammation, and response to treatment. Current efforts for allergic disease diagnosis have focused on clinical evidence as a binary outcome. Although outcome status based on clinical phenotypes (observable characteristics) is convenient and inexpensive to measure in large studies, it does not adequately provide insight into the complex molecular determinants of allergic disease. Individuals with similar clinical diagnoses do not necessarily have similar disease etiologies, natural histories, or responses to treatment. This heterogeneity contributes to the ineffective response to treatment leading to an annual estimated cost of $350 billion in the USA alone. There has been a recent focus to deconvolute the clinical heterogeneity of allergic diseases into specific endotypes using molecular and omics approaches. Endotypes are a means to classify patients based on the underlying pathophysiological mechanisms involving distinct functions or treatment response. The advent of high-throughput molecular omics, immunophenotyping, and bioinformatics methods including machine learning algorithms is facilitating the development of endotype-based diagnosis. As we move to the next decade, we should truly start treating clinical endotypes not clinical phenotype. This review highlights current efforts taking place to improve allergic disease endotyping via molecular omics profiling, immunophenotyping, and machine learning approaches in the context of precision diagnostics in allergic diseases. Graphical Abstract.
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