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Karampitsakos T, Juan-Guardela BM, Tzouvelekis A, Herazo-Maya JD. Precision medicine advances in idiopathic pulmonary fibrosis. EBioMedicine 2023; 95:104766. [PMID: 37625268 PMCID: PMC10469771 DOI: 10.1016/j.ebiom.2023.104766] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/07/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a highly heterogeneous, unpredictable and ultimately lethal chronic lung disease. Over the last decade, two anti-fibrotic agents have been shown to slow disease progression, however, both drugs are administered uniformly with minimal consideration of disease severity and inter-individual molecular, genetic, and genomic differences. Advances in biological understanding of disease endotyping and the emergence of precision medicine have shown that "a one-size-fits-all approach" to the management of chronic lung diseases is no longer appropriate. While precision medicine approaches have revolutionized the management of other diseases such as lung cancer and asthma, the implementation of precision medicine in IPF clinical practice remains an unmet need despite several reports demonstrating a large number of diagnostic, prognostic and theragnostic biomarker candidates in IPF. This review article aims to summarize our current knowledge of precision medicine in IPF and highlight barriers to translate these research findings into clinical practice.
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Affiliation(s)
- Theodoros Karampitsakos
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Brenda M Juan-Guardela
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | | | - Jose D Herazo-Maya
- Division of Pulmonary, Critical Care and Sleep Medicine, Ubben Center for Pulmonary Fibrosis Research, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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2
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Effendi WI, Nagano T. Epigenetics Approaches toward Precision Medicine for Idiopathic Pulmonary Fibrosis: Focus on DNA Methylation. Biomedicines 2023; 11:biomedicines11041047. [PMID: 37189665 DOI: 10.3390/biomedicines11041047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
Genetic information is not transmitted solely by DNA but by the epigenetics process. Epigenetics describes molecular missing link pathways that could bridge the gap between the genetic background and environmental risk factors that contribute to the pathogenesis of pulmonary fibrosis. Specific epigenetic patterns, especially DNA methylation, histone modifications, long non-coding, and microRNA (miRNAs), affect the endophenotypes underlying the development of idiopathic pulmonary fibrosis (IPF). Among all the epigenetic marks, DNA methylation modifications have been the most widely studied in IPF. This review summarizes the current knowledge concerning DNA methylation changes in pulmonary fibrosis and demonstrates a promising novel epigenetics-based precision medicine.
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3
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Mekhael O, Naiel S, Vierhout M, Hayat AI, Revill SD, Abed S, Inman MD, Kolb MRJ, Ask K. Mouse Models of Lung Fibrosis. Methods Mol Biol 2021; 2299:291-321. [PMID: 34028751 DOI: 10.1007/978-1-0716-1382-5_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
The drug discovery pipeline, from discovery of therapeutic targets through preclinical and clinical development phases, to an approved product by health authorities, is a time-consuming and costly process, where a lead candidates' success at reaching the final stage is rare. Although the time from discovery to final approval has been reduced over the last decade, there is still potential to further optimize and streamline the evaluation process of each candidate as it moves through the different development phases. In this book chapter, we describe our preclinical strategies and overall decision-making process designed to evaluate the tolerability and efficacy of therapeutic candidates suitable for patients diagnosed with fibrotic lung disease. We also describe the benefits of conducting preliminary discovery trials, to aid in the selection of suitable primary and secondary outcomes to be further evaluated and assessed in subsequent internal and external validation studies. We outline all relevant research methodologies and protocols routinely performed by our research group and hope that these strategies and protocols will be a useful guide for biomedical and translational researchers aiming to develop safe and beneficial therapies for patients with fibrotic lung disease.
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Affiliation(s)
- Olivia Mekhael
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Safaa Naiel
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Megan Vierhout
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Aaron I Hayat
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Spencer D Revill
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Soumeya Abed
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Mark D Inman
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Martin R J Kolb
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada
| | - Kjetil Ask
- Department of Medicine, Firestone Institute for Respiratory Health, McMaster University and The Research Institute of St. Joe's Hamilton, Hamilton, ON, Canada.
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4
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Adegunsoye A, Ryerson CJ. Diagnostic Classification of Interstitial Lung Disease in Clinical Practice. Clin Chest Med 2021; 42:251-261. [PMID: 34024401 DOI: 10.1016/j.ccm.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Interstitial lung diseases (ILDs) are challenging to diagnose, requiring integration of multiple complex features that are often difficult to interpret. This article reviews a pragmatic approach to ILD diagnosis and classification, focusing on diagnostic tools and strategies that are used to separate different subtypes and identify the most appropriate management. We discuss the evolution of ILD classification and the contemporary approach that integrates routinely used diagnostic tools in a multidisciplinary discussion. We highlight the increasing importance of taking a multipronged approach to ILD classification that reflects the recent emphasis on disease behavior while also considering etiopathogenesis and morphologic features.
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Affiliation(s)
- Ayodeji Adegunsoye
- Section of Pulmonary & Critical Care, The University of Chicago Medicine, 5841 South Maryland Avenue - MC6076
- M662, Chicago, IL 60637, USA
| | - Christopher J Ryerson
- Department of Medicine, University of British Columbia, Centre for Heart Lung Innovation, St. Paul's Hospital, Ward 8B, 1081 Burrard Street, Vancouver, British Columbia V6Z 1Y6, Canada.
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5
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Precision medicine: integration of genetics and functional genomics in prediction of bronchiolitis obliterans after lung transplantation. Curr Opin Pulm Med 2019; 25:308-316. [PMID: 30883449 DOI: 10.1097/mcp.0000000000000579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Lung transplantation (LTx) can be a life saving treatment in end-stage pulmonary diseases, but survival after transplantation is still limited. Posttransplant development of chronic lung allograft dysfunction with bronchiolits obliterans syndrome (BOS) as the major subphenotype, is the main cause of morbidity and mortality. Early identification of high-risk patients for BOS is a large unmet clinical need. In this review, we discuss gene polymorphisms and gene expression related to the development of BOS. RECENT FINDINGS Candidate gene studies showed that donor and recipient gene polymorphisms affect transplant outcome and BOS-free survival after LTx. Both selective and nonselective gene expression studies revealed differentially expressed fibrosis and apoptosis-related genes in BOS compared with non-BOS patients. Significantly, recent microarray expression analysis of blood and broncho-alveolar lavage suggest a role for B-cell and T-cell responses prior to the development of BOS. Furthermore, 6 months prior to the development of BOS differentially expressed genes were identified in peripheral blood cells. SUMMARY Genetic polymorphisms and gene expression changes are associated with the development of BOS. Future genome wide studies are needed to identify easily accessible biomarkers for prediction of BOS toward precision medicine.
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6
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Evolving Genomics of Pulmonary Fibrosis. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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7
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Proteome Investigation of Rat Lungs subjected to Ex Vivo Perfusion (EVLP). Molecules 2018; 23:molecules23123061. [PMID: 30467300 PMCID: PMC6321151 DOI: 10.3390/molecules23123061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/14/2018] [Accepted: 11/21/2018] [Indexed: 11/23/2022] Open
Abstract
Ex vivo lung perfusion (EVLP) is an emerging procedure that allows organ preservation, assessment and reconditioning, increasing the number of marginal donor lungs for transplantation. However, physiological and airflow measurements are unable to unveil the molecular mechanisms responsible of EVLP beneficial effects on lung graft and monitor the proper course of the treatment. Thus, it is urgent to find specific biomarkers that possess these requirements but also accurate and reliable techniques that identify them. The purpose of this study is to give an overview on the potentiality of shotgun proteomic platforms in characterizing the status and the evolution of metabolic pathways during EVLP in order to find new potential EVLP-related biomarkers. A nanoLC-MS/MS system was applied to the proteome analysis of lung tissues from an optimized rat model in three experimental groups: native, pre- and post-EVLP. Technical and biological repeatability were evaluated and, together with clustering analysis, underlined the good quality of data produced. In-house software and bioinformatics tools allowed the label-free extraction of differentially expressed proteins among the three examined conditions and the network visualization of the pathways mainly involved. These promising findings encourage further proteomic investigations of the molecular mechanisms behind EVLP procedure.
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Gibbons MA, Scotton CJ. Delving Deep into the Proteome of Lung Fibrosis Brings Plasma Cells to the Surface. Am J Respir Crit Care Med 2017; 196:1238-1240. [PMID: 28696776 DOI: 10.1164/rccm.201706-1186ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Michael A Gibbons
- 1 Institute of Biomedical and Clinical Science University of Exeter Medical School Exeter, United Kingdom and.,2 Respiratory Department Royal Devon and Exeter NHS Foundation Trust Exeter, United Kingdom
| | - Chris J Scotton
- 1 Institute of Biomedical and Clinical Science University of Exeter Medical School Exeter, United Kingdom and
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Greiffo FR, Eickelberg O, Fernandez IE. Systems medicine advances in interstitial lung disease. Eur Respir Rev 2017; 26:26/145/170021. [PMID: 28954764 DOI: 10.1183/16000617.0021-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 01/17/2023] Open
Abstract
Fibrotic lung diseases involve subject-environment interactions, together with dysregulated homeostatic processes, impaired DNA repair and distorted immune functions. Systems medicine-based approaches are used to analyse diseases in a holistic manner, by integrating systems biology platforms along with clinical parameters, for the purpose of understanding disease origin, progression, exacerbation and remission.Interstitial lung diseases (ILDs) refer to a heterogeneous group of complex fibrotic diseases. The increase of systems medicine-based approaches in the understanding of ILDs provides exceptional advantages by improving diagnostics, unravelling phenotypical differences, and stratifying patient populations by predictable outcomes and personalised treatments. This review discusses the state-of-the-art contributions of systems medicine-based approaches in ILDs over the past 5 years.
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Affiliation(s)
- Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany.,Division of Respiratory Sciences and Critical Care Medicine, Dept of Medicine, University of Colorado, Denver, CO, USA
| | - Isis E Fernandez
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
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10
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Vukmirovic M, Herazo-Maya JD, Blackmon J, Skodric-Trifunovic V, Jovanovic D, Pavlovic S, Stojsic J, Zeljkovic V, Yan X, Homer R, Stefanovic B, Kaminski N. Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis. BMC Pulm Med 2017; 17:15. [PMID: 28081703 PMCID: PMC5228096 DOI: 10.1186/s12890-016-0356-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 12/20/2016] [Indexed: 12/21/2022] Open
Abstract
Background Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A major limitation in transcriptomic profiling of lung tissue in IPF has been a dependence on snap-frozen fresh tissues (FF). In this project we sought to determine whether genome scale transcript profiling using RNA Sequencing (RNA-Seq) could be applied to archived Formalin-Fixed Paraffin-Embedded (FFPE) IPF tissues. Results We isolated total RNA from 7 IPF and 5 control FFPE lung tissues and performed 50 base pair paired-end sequencing on Illumina 2000 HiSeq. TopHat2 was used to map sequencing reads to the human genome. On average ~62 million reads (53.4% of ~116 million reads) were mapped per sample. 4,131 genes were differentially expressed between IPF and controls (1,920 increased and 2,211 decreased (FDR < 0.05). We compared our results to differentially expressed genes calculated from a previously published dataset generated from FF tissues analyzed on Agilent microarrays (GSE47460). The overlap of differentially expressed genes was very high (760 increased and 1,413 decreased, FDR < 0.05). Only 92 differentially expressed genes changed in opposite directions. Pathway enrichment analysis performed using MetaCore confirmed numerous IPF relevant genes and pathways including extracellular remodeling, TGF-beta, and WNT. Gene network analysis of MMP7, a highly differentially expressed gene in both datasets, revealed the same canonical pathways and gene network candidates in RNA-Seq and microarray data. For validation by NanoString nCounter® we selected 35 genes that had a fold change of 2 in at least one dataset (10 discordant, 10 significantly differentially expressed in one dataset only and 15 concordant genes). High concordance of fold change and FDR was observed for each type of the samples (FF vs FFPE) with both microarrays (r = 0.92) and RNA-Seq (r = 0.90) and the number of discordant genes was reduced to four. Conclusions Our results demonstrate that RNA sequencing of RNA obtained from archived FFPE lung tissues is feasible. The results obtained from FFPE tissue are highly comparable to FF tissues. The ability to perform RNA-Seq on archived FFPE IPF tissues should greatly enhance the availability of tissue biopsies for research in IPF. Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0356-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Jose D Herazo-Maya
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - John Blackmon
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Vesna Skodric-Trifunovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Pulmonology, Clinical Center of Serbia, Belgrade, Serbia
| | - Dragana Jovanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia.,Clinic for Pulmonology, Clinical Center of Serbia, Belgrade, Serbia
| | - Sonja Pavlovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Jelena Stojsic
- Departement of Thoracopulmonary Pathology, Service of Pathology, Clinical Centre of Serbia, Belgrade, Serbia
| | - Vesna Zeljkovic
- Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Robert Homer
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.,Pathology and Laboratory Medicine Service, VA CT Healthcare System, West Haven, CT, USA
| | - Branko Stefanovic
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
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11
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Nathan N, Corvol H, Amselem S, Clement A. Biomarkers in Interstitial lung diseases. Paediatr Respir Rev 2015; 16:219-24. [PMID: 26027849 DOI: 10.1016/j.prrv.2015.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 01/11/2023]
Abstract
Interstitial lung diseases (ILD)s represent a heterogeneous group of rare respiratory disorders, mostly chronic and associated with high morbidity and mortality. They are complex diseases that remain, in children, largely underdiagnosed and difficult to manage. Therefore, identification of biomarkers, which could be used for ILD diagnosis, measurements of disease severity and progression, and responsiveness to treatments, is a major challenge for clinical practice and for translational research. The present review focuses on blood biomarkers and provides an overview on the current information on molecular parameters of interest for ILD patient management.
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Affiliation(s)
- Nadia Nathan
- Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Service de pneumologie pédiatrique; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 933; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06
| | - Harriet Corvol
- Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Service de pneumologie pédiatrique; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 938; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06
| | - Serge Amselem
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 933; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06; Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Unité de génétique moléculaire; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06
| | - Annick Clement
- Assistance Publique-Hopitaux de Paris (AP-HP), Hôpital Trousseau, Service de pneumologie pédiatrique; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06; Institut National de la Santé et de la Recherche Médicale (INSERM), UMR_S 933; Sorbonne Universités, Université Pierre et Marie Curie (UPMC) Paris06.
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12
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Personalized Management of Pulmonary Disorders. TEXTBOOK OF PERSONALIZED MEDICINE 2015. [PMCID: PMC7121715 DOI: 10.1007/978-1-4939-2553-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
There are a large number of pulmonary disorders some of which present challenges in management. Role of genetic ancestry in lung function is under investigation. There is still limited information on pharmacogenomics and pharmacogenetics of pulmonary therapeutics. Personalized approaches to some pulmonary diseases will be described briefly as examples in this chapter.
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13
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Kumar A, Dougherty M, Findlay GM, Geisheker M, Klein J, Lazar J, Machkovech H, Resnick J, Resnick R, Salter AI, Talebi-Liasi F, Arakawa C, Baudin J, Bogaard A, Salesky R, Zhou Q, Smith K, Clark JI, Shendure J, Horwitz MS. Genome sequencing of idiopathic pulmonary fibrosis in conjunction with a medical school human anatomy course. PLoS One 2014; 9:e106744. [PMID: 25192356 PMCID: PMC4156421 DOI: 10.1371/journal.pone.0106744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/02/2014] [Indexed: 12/21/2022] Open
Abstract
Even in cases where there is no obvious family history of disease, genome sequencing may contribute to clinical diagnosis and management. Clinical application of the genome has not yet become routine, however, in part because physicians are still learning how best to utilize such information. As an educational research exercise performed in conjunction with our medical school human anatomy course, we explored the potential utility of determining the whole genome sequence of a patient who had died following a clinical diagnosis of idiopathic pulmonary fibrosis (IPF). Medical students performed dissection and whole genome sequencing of the cadaver. Gross and microscopic findings were more consistent with the fibrosing variant of nonspecific interstitial pneumonia (NSIP), as opposed to IPF per se. Variants in genes causing Mendelian disorders predisposing to IPF were not detected. However, whole genome sequencing identified several common variants associated with IPF, including a single nucleotide polymorphism (SNP), rs35705950, located in the promoter region of the gene encoding mucin glycoprotein MUC5B. The MUC5B promoter polymorphism was recently found to markedly elevate risk for IPF, though a particular association with NSIP has not been previously reported, nor has its contribution to disease risk previously been evaluated in the genome-wide context of all genetic variants. We did not identify additional predicted functional variants in a region of linkage disequilibrium (LD) adjacent to MUC5B, nor did we discover other likely risk-contributing variants elsewhere in the genome. Whole genome sequencing thus corroborates the association of rs35705950 with MUC5B dysregulation and interstitial lung disease. This novel exercise additionally served a unique mission in bridging clinical and basic science education.
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Affiliation(s)
- Akash Kumar
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Max Dougherty
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gregory M. Findlay
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Madeleine Geisheker
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Jason Klein
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - John Lazar
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Heather Machkovech
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Jesse Resnick
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Rebecca Resnick
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Alexander I. Salter
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Faezeh Talebi-Liasi
- University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Christopher Arakawa
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Jacob Baudin
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Andrew Bogaard
- University of Washington School of Medicine, Seattle, Washington, United States of America
- Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington, United States of America
| | - Rebecca Salesky
- University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Qian Zhou
- University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kelly Smith
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - John I. Clark
- Department of Biological Structure, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Marshall S. Horwitz
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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14
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Huang LS, Mathew B, Li H, Zhao Y, Ma SF, Noth I, Reddy SP, Harijith A, Usatyuk PV, Berdyshev EV, Kaminski N, Zhou T, Zhang W, Zhang Y, Rehman J, Kotha SR, Gurney TO, Parinandi NL, Lussier YA, Garcia JGN, Natarajan V. The mitochondrial cardiolipin remodeling enzyme lysocardiolipin acyltransferase is a novel target in pulmonary fibrosis. Am J Respir Crit Care Med 2014; 189:1402-15. [PMID: 24779708 DOI: 10.1164/rccm.201310-1917oc] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Lysocardiolipin acyltransferase (LYCAT), a cardiolipin-remodeling enzyme regulating the 18:2 linoleic acid pattern of mammalian mitochondrial cardiolipin, is necessary for maintaining normal mitochondrial function and vascular development. We hypothesized that modulation of LYCAT expression in lung epithelium regulates development of pulmonary fibrosis. OBJECTIVES To define a role for LYCAT in human and murine models of pulmonary fibrosis. METHODS We analyzed the correlation of LYCAT expression in peripheral blood mononuclear cells (PBMCs) with the outcomes of pulmonary functions and overall survival, and used the murine models to establish the role of LYCAT in fibrogenesis. We studied the LYCAT action on cardiolipin remodeling, mitochondrial reactive oxygen species generation, and apoptosis of alveolar epithelial cells under bleomycin challenge. MEASUREMENTS AND MAIN RESULTS LYCAT expression was significantly altered in PBMCs and lung tissues from patients with idiopathic pulmonary fibrosis (IPF), which was confirmed in two preclinical murine models of IPF, bleomycin- and radiation-induced pulmonary fibrosis. LYCAT mRNA expression in PBMCs directly and significantly correlated with carbon monoxide diffusion capacity, pulmonary function outcomes, and overall survival. In both bleomycin- and radiation-induced pulmonary fibrosis murine models, hLYCAT overexpression reduced several indices of lung fibrosis, whereas down-regulation of native LYCAT expression by siRNA accentuated fibrogenesis. In vitro studies demonstrated that LYCAT modulated bleomycin-induced cardiolipin remodeling, mitochondrial membrane potential, reactive oxygen species generation, and apoptosis of alveolar epithelial cells, potential mechanisms of LYCAT-mediated lung protection. CONCLUSIONS This study is the first to identify modulation of LYCAT expression in fibrotic lungs and offers a novel therapeutic approach for ameliorating lung inflammation and pulmonary fibrosis.
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Herazo-Maya JD, Noth I, Duncan SR, Kim S, Ma SF, Tseng GC, Feingold E, Juan-Guardela BM, Richards TJ, Lussier Y, Huang Y, Vij R, Lindell KO, Xue J, Gibson KF, Shapiro SD, Garcia JGN, Kaminski N. Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. Sci Transl Med 2014; 5:205ra136. [PMID: 24089408 DOI: 10.1126/scitranslmed.3005964] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF) by performing microarray experiments of PBMCs in discovery and replication cohorts of IPF patients. Microarray analyses identified 52 genes associated with transplant-free survival (TFS) in the discovery cohort. Clustering the microarray samples of the replication cohort using the 52-gene outcome-predictive signature distinguished two patient groups with significant differences in TFS. We studied the pathways associated with TFS in each independent microarray cohort and identified decreased expression of "The costimulatory signal during T cell activation" Biocarta pathway and, in particular, the genes CD28, ICOS, LCK, and ITK, results confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). A proportional hazards model, including the qRT-PCR expression of CD28, ICOS, LCK, and ITK along with patient's age, gender, and percent predicted forced vital capacity (FVC%), demonstrated an area under the receiver operating characteristic curve of 78.5% at 2.4 months for death and lung transplant prediction in the replication cohort. To evaluate the potential cellular source of CD28, ICOS, LCK, and ITK expression, we analyzed and found significant correlation of these genes with the PBMC percentage of CD4(+)CD28(+) T cells in the replication cohort. Our results suggest that CD28, ICOS, LCK, and ITK are potential outcome biomarkers in IPF and should be further evaluated for patient prioritization for lung transplantation and stratification in drug studies.
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Affiliation(s)
- Jose D Herazo-Maya
- Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
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Spagnolo P, Rossi G, Cavazza A. Pathogenesis of idiopathic pulmonary fibrosis and its clinical implications. Expert Rev Clin Immunol 2014; 10:1005-17. [PMID: 24953006 DOI: 10.1586/1744666x.2014.917050] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common and lethal form of idiopathic interstitial pneumonia. The disease is thought to arise following an aberrant reparative response to recurrent alveolar epithelial cell injury leading to progressive loss of function. The median survival time is 3-5 years from diagnosis. Cigarette smoking, exposure to organic and inorganic dust and genetic factors have been shown to increase the risk of disease, although the cause of IPF remains elusive and its pathogenesis incompletely understood. In the last decade, several clinical trials evaluating novel therapies for IPF have been conducted but the results have been mostly disappointing. Conversely, compounds that target anti-fibrotic and growth factor pathways have been proven effective in slowing functional decline and disease progression. These promising results notwithstanding, truly effective therapeutic strategies will likely require combinations of drugs in order to target the multitude of pathways involved in disease pathogenesis.
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Affiliation(s)
- Paolo Spagnolo
- Center for Rare Lung Diseases, Respiratory Disease Unit, University Hospital of Modena, Via del Pozzo 71, 41124 Modena, Italy
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