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Chawla DG, Cappuccio A, Tamminga A, Sealfon SC, Zaslavsky E, Kleinstein SH. Benchmarking transcriptional host response signatures for infection diagnosis. Cell Syst 2022; 13:974-988.e7. [PMID: 36549274 PMCID: PMC9768893 DOI: 10.1016/j.cels.2022.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/04/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
Identification of host transcriptional response signatures has emerged as a new paradigm for infection diagnosis. For clinical applications, signatures must robustly detect the pathogen of interest without cross-reacting with unintended conditions. To evaluate the performance of infectious disease signatures, we developed a framework that includes a compendium of 17,105 transcriptional profiles capturing infectious and non-infectious conditions and a standardized methodology to assess robustness and cross-reactivity. Applied to 30 published signatures of infection, the analysis showed that signatures were generally robust in detecting viral and bacterial infections in independent data. Asymptomatic and chronic infections were also detectable, albeit with decreased performance. However, many signatures were cross-reactive with unintended infections and aging. In general, we found robustness and cross-reactivity to be conflicting objectives, and we identified signature properties associated with this trade-off. The data compendium and evaluation framework developed here provide a foundation for the development of signatures for clinical application. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Daniel G Chawla
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Antonio Cappuccio
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Tamminga
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elena Zaslavsky
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Steven H Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA; Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA.
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2
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Zhang H, He F, Li P, Hardwidge PR, Li N, Peng Y. The Role of Innate Immunity in Pulmonary Infections. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6646071. [PMID: 33553427 PMCID: PMC7847335 DOI: 10.1155/2021/6646071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/26/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023]
Abstract
Innate immunity forms a protective line of defense in the early stages of pulmonary infection. The primary cellular players of the innate immunity against respiratory infections are alveolar macrophages (AMs), dendritic cells (DCs), neutrophils, natural killer (NK) cells, and innate lymphoid cells (ILCs). They recognize conserved structures of microorganisms through membrane-bound and intracellular receptors to initiate appropriate responses. In this review, we focus on the prominent roles of innate immune cells and summarize transmembrane and cytosolic pattern recognition receptor (PRR) signaling recognition mechanisms during pulmonary microbial infections. Understanding the mechanisms of PRR signal recognition during pulmonary pathogen infections will help us to understand pulmonary immunopathology and lay a foundation for the development of effective therapies to treat and/or prevent pulmonary infections.
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Affiliation(s)
- Huihui Zhang
- College of Animal Medicine, Southwest University, Chongqing, China
| | - Fang He
- College of Animal Medicine, Southwest University, Chongqing, China
| | - Pan Li
- College of Animal Medicine, Southwest University, Chongqing, China
| | | | - Nengzhang Li
- College of Animal Medicine, Southwest University, Chongqing, China
| | - Yuanyi Peng
- College of Animal Medicine, Southwest University, Chongqing, China
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3
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Costa Sa AC, Madsen H, Brown JR. Shared Molecular Signatures Across Neurodegenerative Diseases and Herpes Virus Infections Highlights Potential Mechanisms for Maladaptive Innate Immune Responses. Sci Rep 2019; 9:8795. [PMID: 31217489 PMCID: PMC6584587 DOI: 10.1038/s41598-019-45129-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
Growing evidence suggests that peripheral factors to the brain driving neuro-inflammation could affect Alzheimer’s Disease (AD) and Parkinson’s Disease (PD) severity. Herpes simplex virus type 1 (HSV1) infection has been associated with AD while other related viruses, including cytomegalovirus (CMV), Epstein-Bar virus and human herpesvirus 6 (HHV6), are known to infect neurons. Here we compare gene expression profiles between AD or PD patients to those afflicted with herpes viral infections as to discover novel potential neuro-inflammation pathways. We found multiple significant differentially expressed genes (DEGs) shared between AD/PD and viral infections including SESN3 which has a genetic association for increased AD risk. Pathway enrichment analysis revealed viruses shared Oxidative Stress Defense System and LRRK2 pathways with AD and PD, respectively. We further processed our data to identify novel target and drug-repurposing opportunities including anti-inflammatory therapy, immune-modulators and cholinesterase inhibitors which could lead to new therapeutics paradigms for these neurodegenerative diseases.
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Affiliation(s)
- Ana Caroline Costa Sa
- Computational Biology, Human Genetics, Research and Development (R&D), GlaxoSmithKline (GSK), Collegeville, PA, 19426, USA
| | - Heather Madsen
- HIV Discovery, ViiV Healthcare, Research, Triangle Park, NC, 27713, USA
| | - James R Brown
- Computational Biology, Human Genetics, Research and Development (R&D), GlaxoSmithKline (GSK), Collegeville, PA, 19426, USA.
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Abstract
Bacterial infections have been traditionally controlled by antibiotics and vaccines, and these approaches have greatly improved health and longevity. However, multiple stakeholders are declaring that the lack of new interventions is putting our ability to prevent and treat bacterial infections at risk. Vaccine and antibiotic approaches still have the potential to address this threat. Innovative vaccine technologies, such as reverse vaccinology, novel adjuvants, and rationally designed bacterial outer membrane vesicles, together with progress in polysaccharide conjugation and antigen design, have the potential to boost the development of vaccines targeting several classes of multidrug-resistant bacteria. Furthermore, new approaches to deliver small-molecule antibacterials into bacteria, such as hijacking active uptake pathways and potentiator approaches, along with a focus on alternative modalities, such as targeting host factors, blocking bacterial virulence factors, monoclonal antibodies, and microbiome interventions, all have potential. Both vaccines and antibacterial approaches are needed to tackle the global challenge of antimicrobial resistance (AMR), and both areas have the underpinning science to address this need. However, a concerted research agenda and rethinking of the value society puts on interventions that save lives, by preventing or treating life-threatening bacterial infections, are needed to bring these ideas to fruition.
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Wang Z, Arat S, Magid-Slav M, Brown JR. Meta-analysis of human gene expression in response to Mycobacterium tuberculosis infection reveals potential therapeutic targets. BMC SYSTEMS BIOLOGY 2018; 12:3. [PMID: 29321020 PMCID: PMC5763539 DOI: 10.1186/s12918-017-0524-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/22/2017] [Indexed: 01/24/2023]
Abstract
Background With the global emergence of multi-drug resistant strains of Mycobacterium tuberculosis, new strategies to treat tuberculosis are urgently needed such as therapeutics targeting potential human host factors. Results Here we performed a statistical meta-analysis of human gene expression in response to both latent and active pulmonary tuberculosis infections from nine published datasets. We found 1655 genes that were significantly differentially expressed during active tuberculosis infection. In contrast, no gene was significant for latent tuberculosis. Pathway enrichment analysis identified 90 significant canonical human pathways, including several pathways more commonly related to non-infectious diseases such as the LRRK2 pathway in Parkinson’s disease, and PD-1/PD-L1 signaling pathway important for new immuno-oncology therapies. The analysis of human genome-wide association studies datasets revealed tuberculosis-associated genetic variants proximal to several genes in major histocompatibility complex for antigen presentation. We propose several new targets and drug-repurposing opportunities including intravenous immunoglobulin, ion-channel blockers and cancer immuno-therapeutics for development as combination therapeutics with anti-mycobacterial agents. Conclusions Our meta-analysis provides novel insights into host genes and pathways important for tuberculosis and brings forth potential drug repurposing opportunities for host-directed therapies. Electronic supplementary material The online version of this article (doi: 10.1186/s12918-017-0524-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhang Wang
- Computational Biology, Target Sciences, GlaxoSmithKline (GSK) R & D, Collegeville, PA, 19426, USA
| | - Seda Arat
- Computational Biology, Target Sciences, GlaxoSmithKline (GSK) R & D, Collegeville, PA, 19426, USA.,Current address: The Jackson Laboratory, Farmington, CT, 06032, USA
| | - Michal Magid-Slav
- Computational Biology, Target Sciences, GlaxoSmithKline (GSK) R & D, Collegeville, PA, 19426, USA.
| | - James R Brown
- Computational Biology, Target Sciences, GlaxoSmithKline (GSK) R & D, Collegeville, PA, 19426, USA.
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Martínez I, Oliveros JC, Cuesta I, de la Barrera J, Ausina V, Casals C, de Lorenzo A, García E, García-Fojeda B, Garmendia J, González-Nicolau M, Lacoma A, Menéndez M, Moranta D, Nieto A, Ortín J, Pérez-González A, Prat C, Ramos-Sevillano E, Regueiro V, Rodriguez-Frandsen A, Solís D, Yuste J, Bengoechea JA, Melero JA. Apoptosis, Toll-like, RIG-I-like and NOD-like Receptors Are Pathways Jointly Induced by Diverse Respiratory Bacterial and Viral Pathogens. Front Microbiol 2017; 8:276. [PMID: 28298903 PMCID: PMC5331050 DOI: 10.3389/fmicb.2017.00276] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/09/2017] [Indexed: 12/18/2022] Open
Abstract
Lower respiratory tract infections are among the top five leading causes of human death. Fighting these infections is therefore a world health priority. Searching for induced alterations in host gene expression shared by several relevant respiratory pathogens represents an alternative to identify new targets for wide-range host-oriented therapeutics. With this aim, alveolar macrophages were independently infected with three unrelated bacterial (Streptococcus pneumoniae, Klebsiella pneumoniae, and Staphylococcus aureus) and two dissimilar viral (respiratory syncytial virus and influenza A virus) respiratory pathogens, all of them highly relevant for human health. Cells were also activated with bacterial lipopolysaccharide (LPS) as a prototypical pathogen-associated molecular pattern. Patterns of differentially expressed cellular genes shared by the indicated pathogens were searched by microarray analysis. Most of the commonly up-regulated host genes were related to the innate immune response and/or apoptosis, with Toll-like, RIG-I-like and NOD-like receptors among the top 10 signaling pathways with over-expressed genes. These results identify new potential broad-spectrum targets to fight the important human infections caused by the bacteria and viruses studied here.
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Affiliation(s)
- Isidoro Martínez
- Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | | | - Isabel Cuesta
- Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Jorge de la Barrera
- Centro Nacional de Microbiología, Instituto de Salud Carlos III Madrid, Spain
| | - Vicente Ausina
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Badalona, Institut d' Investigació Germans Trias i Pujol, Universitat Autònoma de BarcelonaBarcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Cristina Casals
- Departmento de Bioquímica y Biología Molecular I, Universidad ComplutenseMadrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Alba de Lorenzo
- Departmento de Bioquímica y Biología Molecular I, Universidad ComplutenseMadrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Belén García-Fojeda
- Departmento de Bioquímica y Biología Molecular I, Universidad ComplutenseMadrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Universidad Pública de Navarra-GobNavarra, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Mar González-Nicolau
- Fundación de Investigación Sanitaria de las Islas Baleares, Instituto de Investigación Sanitaria de PalmaPalma, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Alicia Lacoma
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Badalona, Institut d' Investigació Germans Trias i Pujol, Universitat Autònoma de BarcelonaBarcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Margarita Menéndez
- Instituto de Química Física Rocasolano (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - David Moranta
- Fundación de Investigación Sanitaria de las Islas Baleares, Instituto de Investigación Sanitaria de PalmaPalma, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Amelia Nieto
- Centro Nacional de Biotecnología (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Juan Ortín
- Centro Nacional de Biotecnología (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Alicia Pérez-González
- Centro Nacional de Biotecnología (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Cristina Prat
- Servei de Microbiologia, Hospital Universitari Germans Trias i Pujol, Badalona, Institut d' Investigació Germans Trias i Pujol, Universitat Autònoma de BarcelonaBarcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Elisa Ramos-Sevillano
- Centro de Investigaciones Biológicas (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Verónica Regueiro
- Fundación de Investigación Sanitaria de las Islas Baleares, Instituto de Investigación Sanitaria de PalmaPalma, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Ariel Rodriguez-Frandsen
- Centro Nacional de Biotecnología (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - Dolores Solís
- Instituto de Química Física Rocasolano (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - José Yuste
- Centro de Investigaciones Biológicas (CSIC)Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - José A Bengoechea
- Fundación de Investigación Sanitaria de las Islas Baleares, Instituto de Investigación Sanitaria de PalmaPalma, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
| | - José A Melero
- Centro Nacional de Microbiología, Instituto de Salud Carlos IIIMadrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos IIIMadrid, Spain
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Payne DJ, Miller LF, Findlay D, Anderson J, Marks L. Time for a change: addressing R&D and commercialization challenges for antibacterials. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140086. [PMID: 25918443 DOI: 10.1098/rstb.2014.0086] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The antibacterial therapeutic area has been described as the perfect storm. Resistance is increasing to the point that our hospitals encounter patients infected with untreatable pathogens, the overall industry pipeline is described as dry and most multinational pharmaceutical companies have withdrawn from the area. Major contributing factors to the declining antibacterial industry pipeline include scientific challenges, clinical/regulatory hurdles and low return on investment. This paper examines these challenges and proposes approaches to address them. There is a need for a broader scientific agenda to explore new approaches to discover and develop antibacterial agents. Additionally, ideas of how industry and academia could be better integrated will be presented. While promising progress in the regulatory environment has been made, more streamlined regulatory paths are still required and the solutions will lie in global harmonization and clearly defined guidance. Creating the right incentives for antibacterial research and development is critical and a new commercial model for antibacterial agents will be proposed. One key solution to help resolve both the problem of antimicrobial resistance (AMR) and lack of new drug development are rapid, cost-effective, accurate point of care diagnostics that will transform antibacterial prescribing and enable more cost-effective and efficient antibacterial clinical trials. The challenges of AMR are too great for any one group to resolve and success will require leadership and partnerships among academia, industry and governments globally.
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Affiliation(s)
- David J Payne
- Infectious Diseases Therapeutic Area Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Linda Federici Miller
- Infectious Diseases Therapeutic Area Unit, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - David Findlay
- Immuno-inflammation and Infectious Diseases Franchise, GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
| | - James Anderson
- Government Affairs, Public Policy and Patient Advocacy, Communications and Government Affairs, GlaxoSmithKline, 980 Great West Road, Brentford, Middlesex TW8 9GS, UK
| | - Lynn Marks
- Projects, Clinical Platforms and Sciences, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, PA 19406, USA
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