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Magdamo CG, Noori A, Liu X, Tyagi T, Li Z, Kondepudi A, Alabsi H, Rudmann E, Wilcox D, Brenner L, Robbins GK, Moura LMV, Hsu J, Zafar SF, Benson N, Serrano‐Pozo A, Dickson J, Hyman BT, Blacker D, Westover MB, Mukerji S, Das S. Development and Evaluation of a Natural Language Processing Annotation Tool (NAT) to Facilitate Phenotyping of Cognitive Status in Electronic Health Records. Alzheimers Dement 2022. [DOI: 10.1002/alz.068929] [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: 12/24/2022]
Affiliation(s)
| | - Ayush Noori
- Massachusetts General Hospital Boston MA USA
| | - Xiao Liu
- Massachusetts General Hospital Boston MA USA
| | | | - Zhaozhi Li
- Massachusetts General Hospital Boston MA USA
| | | | | | | | | | | | | | | | - John Hsu
- Massachusetts General Hospital Boston MA USA
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Rosconi F, Rudmann E, Li J, Surujon D, Anthony J, Frank M, Jones DS, Rock C, Rosch JW, Johnston CD, van Opijnen T. A bacterial pan-genome makes gene essentiality strain-dependent and evolvable. Nat Microbiol 2022; 7:1580-1592. [PMID: 36097170 PMCID: PMC9519441 DOI: 10.1038/s41564-022-01208-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022]
Abstract
Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.
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Affiliation(s)
| | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jien Li
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Jon Anthony
- Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Matthew Frank
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dakota S Jones
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Charles Rock
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Noori A, Magdamo C, Liu X, Tyagi T, Li Z, Kondepudi A, Alabsi H, Rudmann E, Wilcox D, Brenner L, Robbins GK, Moura L, Zafar S, Benson NM, Hsu J, R Dickson J, Serrano-Pozo A, Hyman BT, Blacker D, Westover MB, Mukerji SS, Das S. Development and Evaluation of a Natural Language Processing Annotation Tool to Facilitate Phenotyping of Cognitive Status in Electronic Health Records: Diagnostic Study. J Med Internet Res 2022; 24:e40384. [PMID: 36040790 PMCID: PMC9472045 DOI: 10.2196/40384] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/17/2022] [Revised: 07/29/2022] [Accepted: 07/31/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Electronic health records (EHRs) with large sample sizes and rich information offer great potential for dementia research, but current methods of phenotyping cognitive status are not scalable. OBJECTIVE The aim of this study was to evaluate whether natural language processing (NLP)-powered semiautomated annotation can improve the speed and interrater reliability of chart reviews for phenotyping cognitive status. METHODS In this diagnostic study, we developed and evaluated a semiautomated NLP-powered annotation tool (NAT) to facilitate phenotyping of cognitive status. Clinical experts adjudicated the cognitive status of 627 patients at Mass General Brigham (MGB) health care, using NAT or traditional chart reviews. Patient charts contained EHR data from two data sets: (1) records from January 1, 2017, to December 31, 2018, for 100 Medicare beneficiaries from the MGB Accountable Care Organization and (2) records from 2 years prior to COVID-19 diagnosis to the date of COVID-19 diagnosis for 527 MGB patients. All EHR data from the relevant period were extracted; diagnosis codes, medications, and laboratory test values were processed and summarized; clinical notes were processed through an NLP pipeline; and a web tool was developed to present an integrated view of all data. Cognitive status was rated as cognitively normal, cognitively impaired, or undetermined. Assessment time and interrater agreement of NAT compared to manual chart reviews for cognitive status phenotyping was evaluated. RESULTS NAT adjudication provided higher interrater agreement (Cohen κ=0.89 vs κ=0.80) and significant speed up (time difference mean 1.4, SD 1.3 minutes; P<.001; ratio median 2.2, min-max 0.4-20) over manual chart reviews. There was moderate agreement with manual chart reviews (Cohen κ=0.67). In the cases that exhibited disagreement with manual chart reviews, NAT adjudication was able to produce assessments that had broader clinical consensus due to its integrated view of highlighted relevant information and semiautomated NLP features. CONCLUSIONS NAT adjudication improves the speed and interrater reliability for phenotyping cognitive status compared to manual chart reviews. This study underscores the potential of an NLP-based clinically adjudicated method to build large-scale dementia research cohorts from EHRs.
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Affiliation(s)
- Ayush Noori
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Colin Magdamo
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Xiao Liu
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Tanish Tyagi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Zhaozhi Li
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Akhil Kondepudi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
| | - Haitham Alabsi
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Emily Rudmann
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Vaccine and Immunotherapy Center, Division of Infectious Disease, Boston, MA, United States
| | - Douglas Wilcox
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Laura Brenner
- Harvard Medical School, Boston, MA, United States
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Gregory K Robbins
- Harvard Medical School, Boston, MA, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Lidia Moura
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Sahar Zafar
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Nicole M Benson
- Harvard Medical School, Boston, MA, United States
- Mongan Institute, Massachusetts General Hospital, Boston, MA, United States
- McLean Hospital, Belmont, MA, United States
| | - John Hsu
- Harvard Medical School, Boston, MA, United States
- Mongan Institute, Massachusetts General Hospital, Boston, MA, United States
| | - John R Dickson
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Alberto Serrano-Pozo
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Deborah Blacker
- Harvard Medical School, Boston, MA, United States
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, United States
| | - M Brandon Westover
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Shibani S Mukerji
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, United States
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
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Leshchiner D, Rosconi F, Sundaresh B, Rudmann E, Ramirez LMN, Nishimoto AT, Wood SJ, Jana B, Buján N, Li K, Gao J, Frank M, Reeve SM, Lee RE, Rock CO, Rosch JW, van Opijnen T. A genome-wide atlas of antibiotic susceptibility targets and pathways to tolerance. Nat Commun 2022; 13:3165. [PMID: 35672367 PMCID: PMC9174251 DOI: 10.1038/s41467-022-30967-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/26/2022] [Indexed: 11/10/2022] Open
Abstract
Detailed knowledge on how bacteria evade antibiotics and eventually develop resistance could open avenues for novel therapeutics and diagnostics. It is thereby key to develop a comprehensive genome-wide understanding of how bacteria process antibiotic stress, and how modulation of the involved processes affects their ability to overcome said stress. Here we undertake a comprehensive genetic analysis of how the human pathogen Streptococcus pneumoniae responds to 20 antibiotics. We build a genome-wide atlas of drug susceptibility determinants and generated a genetic interaction network that connects cellular processes and genes of unknown function, which we show can be used as therapeutic targets. Pathway analysis reveals a genome-wide atlas of cellular processes that can make a bacterium less susceptible, and often tolerant, in an antibiotic specific manner. Importantly, modulation of these processes confers fitness benefits during active infections under antibiotic selection. Moreover, screening of sequenced clinical isolates demonstrates that mutations in genes that decrease antibiotic sensitivity and increase tolerance readily evolve and are frequently associated with resistant strains, indicating such mutations could be harbingers for the emergence of antibiotic resistance.
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Affiliation(s)
| | - Federico Rosconi
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Emily Rudmann
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Andrew T Nishimoto
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephen J Wood
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Bimal Jana
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Noemí Buján
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Kaicheng Li
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Jianmin Gao
- Chemistry Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Matthew Frank
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stephanie M Reeve
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Charles O Rock
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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Valizadeh N, Rudmann E, Solomon IH, Mukerji SS. Mechanisms of Entry Into the Central Nervous System by Neuroinvasive Pathogens. J Neuroophthalmol 2022; 42:163-172. [PMID: 35195546 PMCID: PMC9124664 DOI: 10.1097/wno.0000000000001455] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The literature on neurological manifestations, cerebrospinal fluid analyses, and autopsies in patients with COVID-19 continues to grow. The proposed mechanisms for neurological disease in patients with COVID-19 include indirect processes such as inflammation, microvascular injury, and hypoxic-ischemic damage. An alternate hypothesis suggests direct viral entry of SARS-CoV-2 into the brain and cerebrospinal fluid, given varying reports regarding isolation of viral components from these anatomical sites. EVIDENCE ACQUISITION PubMed, Google Scholar databases, and neuroanatomical textbooks were manually searched and reviewed. RESULTS We provide clinical concepts regarding the mechanisms of viral pathogen invasion in the central nervous system (CNS); advances in our mechanistic understanding of CNS invasion in well-known neurotropic pathogens can aid in understanding how viruses evolve strategies to enter brain parenchyma. We also present the structural components of CNS compartments that influence viral entry, focusing on hematogenous and transneuronal spread, and discuss this evidence as it relates to our understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). CONCLUSIONS Although there is a paucity of data supporting direct viral entry of SARS-CoV-2 in humans, increasing our knowledge of the structural components of CNS compartments that block viral entry and pathways exploited by pathogens is fundamental to preparing clinicians and researchers for what to expect when a novel emerging virus with neurological symptoms establishes infection in the CNS, and how to design therapeutics to mitigate such an infection.
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Affiliation(s)
- Navid Valizadeh
- Division of Neuroimmunology and Neuro-infectious Disease, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- John C Lincoln Hospital, Phoenix, Arizona, USA
| | - Emily Rudmann
- Division of Neuroimmunology and Neuro-infectious Disease, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Isaac H. Solomon
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | - Shibani S. Mukerji
- Division of Neuroimmunology and Neuro-infectious Disease, Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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