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Dartois V, Bonfield TL, Boyce JP, Daley CL, Dick T, Gonzalez-Juarrero M, Gupta S, Kramnik I, Lamichhane G, Laughon BE, Lorè NI, Malcolm KC, Olivier KN, Tuggle KL, Jackson M. Preclinical murine models for the testing of antimicrobials against Mycobacterium abscessus pulmonary infections: Current practices and recommendations. Tuberculosis (Edinb) 2024; 147:102503. [PMID: 38729070 PMCID: PMC11168888 DOI: 10.1016/j.tube.2024.102503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Accepted: 03/17/2024] [Indexed: 05/12/2024]
Abstract
Mycobacterium abscessus, a rapidly growing nontuberculous mycobacterium, is increasingly recognized as an important pathogen of the human lung, disproportionally affecting people with cystic fibrosis (CF) and other susceptible individuals with non-CF bronchiectasis and compromised immune functions. M. abscessus infections are extremely difficult to treat due to intrinsic resistance to many antibiotics, including most anti-tuberculous drugs. Current standard-of-care chemotherapy is long, includes multiple oral and parenteral repurposed drugs, and is associated with significant toxicity. The development of more effective oral antibiotics to treat M. abscessus infections has thus emerged as a high priority. While murine models have proven instrumental in predicting the efficacy of therapeutic treatments for M. tuberculosis infections, the preclinical evaluation of drugs against M. abscessus infections has proven more challenging due to the difficulty of establishing a progressive, sustained, pulmonary infection with this pathogen in mice. To address this issue, a series of three workshops were hosted in 2023 by the Cystic Fibrosis Foundation (CFF) and the National Institute of Allergy and Infectious Diseases (NIAID) to review the current murine models of M. abscessus infections, discuss current challenges and identify priorities toward establishing validated and globally harmonized preclinical models. This paper summarizes the key points from these workshops. The hope is that the recommendations that emerged from this exercise will facilitate the implementation of informative murine models of therapeutic efficacy testing across laboratories, improve reproducibility from lab-to-lab and accelerate preclinical-to-clinical translation.
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Affiliation(s)
- Véronique Dartois
- Center for Discovery and Innovation & Department of Medical Sciences, Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA.
| | - Tracey L Bonfield
- Genetics and Genome Sciences and National Center for Regenerative Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jim P Boyce
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Charles L Daley
- Department of Medicine, National Jewish Health, Denver, CO, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Thomas Dick
- Center for Discovery and Innovation & Department of Medical Sciences, Hackensack Meridian School of Medicine, Hackensack Meridian Health, Nutley, NJ, USA; Department of Microbiology and Immunology, Georgetown University, Washington, DC, USA
| | - Mercedes Gonzalez-Juarrero
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA
| | - Shashank Gupta
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, USA; Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Igor Kramnik
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, 02215, USA; Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Gyanu Lamichhane
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Barbara E Laughon
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicola I Lorè
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Kenneth C Malcolm
- Department of Medicine, National Jewish Health, Denver, CO, USA; Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kenneth N Olivier
- Department of Medicine, Division of Pulmonary Diseases and Critical Care Medicine, University of North Carolina, USA; Marsico Lung Institute, Chapel Hill, 27599-7248, NC, USA
| | | | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80523-1682, USA.
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Turco G, Chang C, Wang RY, Kim G, Stoops EH, Richardson B, Sochat V, Rust J, Oughtred R, Thayer N, Kang F, Livstone MS, Heinicke S, Schroeder M, Dolinski KJ, Botstein D, Baryshnikova A. Global analysis of the yeast knockout phenome. SCIENCE ADVANCES 2023; 9:eadg5702. [PMID: 37235661 PMCID: PMC11326039 DOI: 10.1126/sciadv.adg5702] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/20/2023] [Indexed: 05/28/2023]
Abstract
Genome-wide phenotypic screens in the budding yeast Saccharomyces cerevisiae, enabled by its knockout collection, have produced the largest, richest, and most systematic phenotypic description of any organism. However, integrative analyses of this rich data source have been virtually impossible because of the lack of a central data repository and consistent metadata annotations. Here, we describe the aggregation, harmonization, and analysis of ~14,500 yeast knockout screens, which we call Yeast Phenome. Using this unique dataset, we characterized two unknown genes (YHR045W and YGL117W) and showed that tryptophan starvation is a by-product of many chemical treatments. Furthermore, we uncovered an exponential relationship between phenotypic similarity and intergenic distance, which suggests that gene positions in both yeast and human genomes are optimized for function.
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Affiliation(s)
- Gina Turco
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Christie Chang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Griffin Kim
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Brianna Richardson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Vanessa Sochat
- Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Rust
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Rose Oughtred
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | | | - Fan Kang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Michael S Livstone
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sven Heinicke
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mark Schroeder
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kara J Dolinski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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Leli NM, Koumenis C. A Novel Ubiquitin Complex Regulates Aneuploid Epithelial Tumors by Moderating an Integrated Stress Response. Cancer Discov 2023; 13:535-537. [PMID: 36855916 DOI: 10.1158/2159-8290.cd-22-1440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
SUMMARY Tumor fitness coessentiality gene analysis that aims to expand the repertoire of druggable targets reveals a novel ubiquitin ligase complex, the BICR6 module. Along with the other complex members (UBA6, KCMF1, and UBR4), BIRC6 selectively contributes to the survival of a subset of epithelial tumors with a high degree of aneuploidy by ubiquitinating and suppressing HRI, a component of the integrated stress response adaptive pathway. See related article by Cervia et al., p. 766 (2).
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Affiliation(s)
- Nektaria Maria Leli
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Constantinos Koumenis
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Espin-Garcia O, Baghel M, Brar N, Whittaker JL, Ali SA. Can genetics guide exercise prescriptions in osteoarthritis? FRONTIERS IN REHABILITATION SCIENCES 2022; 3:930421. [PMID: 36188938 PMCID: PMC9397982 DOI: 10.3389/fresc.2022.930421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022]
Abstract
Osteoarthritis (OA) is the most common form of arthritis and has a multifactorial etiology. Current management for OA focuses on minimizing pain and functional loss, typically involving pharmacological, physical, psychosocial, and mind-body interventions. However, there remain challenges in determining which patients will benefit most from which interventions. Although exercise-based interventions are recommended as first-line treatments and are known to be beneficial for managing both the disease and illness of OA, the optimal exercise “prescription” is unknown, due in part to our limited understanding of the precise mechanisms underlying its action. Here we present our perspective on the potential role of genetics in guiding exercise prescription for persons with OA. We describe key publications in the areas of exercise and OA, genetics and OA, and exercise and genetics, and point to a paucity of knowledge at the intersection of exercise, genetics, and OA. We suggest there is emerging evidence to support the use of genetics and epigenetics to explain the beneficial effects of exercise for OA. We identify missing links in the existing research relating to exercise, genetics, and OA, and highlight epigenetics as a promising mechanism through which environmental exposures such as exercise may impact OA outcomes. We anticipate future studies will improve our understanding of how genetic and epigenetic factors mediate exercise-based interventions to support implementation and ultimately improve OA patient care.
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Affiliation(s)
- Osvaldo Espin-Garcia
- Department of Biostatistics, Princess Margaret Cancer Centre and Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Division of Biostatistics, Dalla Lana School of Public Health and Department of Statistical Sciences, University of Toronto, Toronto, ON, Canada
- *Correspondence: Osvaldo Espin-Garcia
| | - Madhu Baghel
- Bone and Joint Center, Department of Orthopaedic Surgery, Henry Ford Health, Detroit, MI, United States
| | - Navraj Brar
- Faculty of Kinesiology and Physical Education, University of Toronto, Toronto, ON, Canada
| | - Jackie L. Whittaker
- Department of Physical Therapy, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Arthritis Research Canada, Vancouver, BC, Canada
| | - Shabana Amanda Ali
- Bone and Joint Center, Department of Orthopaedic Surgery, Henry Ford Health, Detroit, MI, United States
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, United States
- Department of Physiology, College of Human Medicine, Michigan State University, East Lansing, MI, United States
- Shabana Amanda Ali
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Scullen T, Mathkour M, Dumont AS. Commentary: Formation, Growth, or Rupture of De Novo Intracranial Aneurysms: Long-Term Follow-up Study of Subarachnoid Hemorrhage Survivors. Neurosurgery 2022; 90:e67-e69. [PMID: 34995253 DOI: 10.1227/neu.0000000000001789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 09/18/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
- Tyler Scullen
- Department of Neurological Surgery, Tulane Medical Center, Tulane University School of Medicine, New Orleans, Louisiana, USA
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Hennessy EJ, FitzGerald GA. Battle for supremacy: nucleic acid interactions between viruses and cells. J Clin Invest 2021; 131:144227. [PMID: 33290272 PMCID: PMC7843224 DOI: 10.1172/jci144227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since the COVID-19 pandemic swept across the globe, researchers have been trying to understand its origin, life cycle, and pathogenesis. There is a striking variability in the phenotypic response to infection with SARS-CoV-2 that may reflect differences in host genetics and/or immune response. It is known that the human epigenome is influenced by ethnicity, age, lifestyle, and environmental factors, including previous viral infections. This Review examines the influence of viruses on the host epigenome. We describe general lessons and methodologies that can be used to understand how the virus evades the host immune response. We consider how variation in the epigenome may contribute to heterogeneity in the response to SARS-CoV-2 and may identify a precision medicine approach to treatment.
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Academia Europaea Position Paper on Translational Medicine: The Cycle Model for Translating Scientific Results into Community Benefits. J Clin Med 2020; 9:jcm9051532. [PMID: 32438747 PMCID: PMC7290380 DOI: 10.3390/jcm9051532] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 01/07/2023] Open
Abstract
Introduction: Translational science has gained prominence in medicine, but there is still much work to be done before scientific results are used optimally and incorporated into everyday health practice. As the main focus is still on generating new scientific data with financial resources primarily available for that purpose, other activities that are necessary in the transition from research to community benefit are considered less needy. The European Statistical Office of the European Commission has recently reported that 1.7 million people under 75 years of age died in Europe in 2016, with around 1.2 million of those deaths being avoidable through effective primary prevention and public health intervention. Therefore, Academia Europaea, one of the five Pan-European networks that form SAPEA (Science Advice for Policy by European Academies), a key element of the European Commission’s Scientific Advice Mechanism (SAM), has launched a project to develop a model to facilitate and accelerate the utilisation of scientific knowledge for public and community benefit. Methods: During the process, leaders in the field, including prominent basic and clinical researchers, editors-in-chief of high-impact journals publishing translational research articles, translational medicine (TM) centre leaders, media representatives, academics and university leaders, developed the TM cycle, a new model that we believe could significantly advance the development of TM. Results: This model focuses equally on the acquisition of new scientific results healthcare, understandable and digestible summation of results, and their communication to all participants. We have also renewed the definition in TM, identified challenges and recommended solutions. Conclusion: The authors, including senior officers of Academia Europaea, produced this document to serve as a basis for revising thinking on TM with the end result of enabling more efficient and cost-effective healthcare.
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Scullen T, Amenta PS, Nerva JD, Dumont AS. Commentary: Predicting Long-Term Outcomes After Poor-Grade Aneurysmal Subarachnoid Hemorrhage Using Decision Tree Modeling. Neurosurgery 2020; 87:E293-E295. [DOI: 10.1093/neuros/nyaa074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 02/03/2020] [Indexed: 12/16/2022] Open
Affiliation(s)
- Tyler Scullen
- Department of Neurological Surgery, Tulane Medical Center, New Orleans, Louisiana
| | - Peter S Amenta
- Department of Neurological Surgery, Tulane Medical Center, New Orleans, Louisiana
| | - John D Nerva
- Department of Neurological Surgery, Tulane Medical Center, New Orleans, Louisiana
| | - Aaron S Dumont
- Department of Neurological Surgery, Tulane Medical Center, New Orleans, Louisiana
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